Quinolone resistance in salmonella: clinical experience

EnvR is a potent repressor of acrAB transcription in Salmonella

BACKGROUND

Resistance nodulation division (RND) family efflux pumps, including the major pump AcrAB-TolC, are important mediators of intrinsic and evolved antibiotic resistance. Expression of these pumps is carefully controlled by a network of regulators that respond to different environmental cues. EnvR is a TetR family transcriptional regulator encoded upstream of the RND efflux pump acrEF.

METHODS

Binding of EnvR protein upstream of acrAB was determined by electrophoretic mobility shift assays and the phenotypic consequence of envR overexpression on antimicrobial susceptibility, biofilm motility and invasion of eukaryotic cells in vitro was measured. Additionally, the global transcriptome of clinical Salmonella isolates overexpressing envR was determined by RNA-Seq.

RESULTS

EnvR bound to the promoter region upstream of the genes coding for the major efflux pump AcrAB in Salmonella, inhibiting transcription and preventing production of AcrAB protein. The phenotype conferred by overexpression of envR mimicked deletion of acrB as it conferred multidrug susceptibility, decreased motility and decreased invasion into intestinal cells in vitro. Importantly, we demonstrate the clinical relevance of this regulatory mechanism because RNA-Seq revealed that a drug-susceptible clinical isolate of Salmonella had low acrB expression even though expression of its major regulator RamA was very high; this was caused by very high EnvR expression.

CONCLUSIONS

In summary, we show that EnvR is a potent repressor of acrAB transcription in Salmonella, and can override binding by RamA so preventing MDR to clinically useful drugs. Finding novel tools to increase EnvR expression may form the basis of a new way to prevent or treat MDR infections.

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.

Evolution of Salmonella within Hosts

Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections.

Salmonella is a bacterial pathogen with remarkable diversity in its host range and pathogenicity due to past within-host evolution in vertebrate species that modified ancestral mechanisms of pathogenesis.

Variation arising during infection includes point mutations, new genes acquired through horizontal gene transfer (HGT), deletions, and genomic rearrangements.

Beneficial mutations increase in frequency within the host and, if they retain the ability to be transmitted to subsequent hosts, may become fixed in the population.

Whole-genome sequencing of sequential isolates from clinical infections reveals within-host HGT and point mutations that impact therapy and clinical management.

HGT is the primary mechanism for evolution in prokaryotes and is synergised by complex networks of transfer involving the microbiome.

Within-host evolution of Salmonella, resulting in new pathovars, can proceed in the absence of HGT.

Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium

AcrAB-TolC is the paradigm resistance-nodulation-division (RND) multidrug resistance efflux system in Gram-negative bacteria, with AcrB being the pump protein in this complex. We constructed a nonfunctional AcrB mutant by replacing D408, a highly conserved residue essential for proton translocation. Western blotting confirmed that the AcrB D408A mutant had the same native level of expression of AcrB as the parental strain. The mutant had no growth deficiencies in rich or minimal medium. However, compared with wild-type SL1344, the mutant had increased accumulation of Hoechst 33342 dye and decreased efflux of ethidium bromide and was multidrug hypersusceptible. The D408A mutant was attenuated in vivo in mouse and Galleria mellonella models and showed significantly reduced invasion into intestinal epithelial cells and macrophages in vitro A dose-dependent inhibition of invasion was also observed when two different efflux pump inhibitors were added to the wild-type strain during infection of epithelial cells. RNA sequencing (RNA-seq) revealed downregulation of bacterial factors necessary for infection, including those in the Salmonella pathogenicity islands 1, 2, and 4; quorum sensing genes; and phoPQ Several general stress response genes were upregulated, probably due to retention of noxious molecules inside the bacterium. Unlike loss of AcrB protein, loss of efflux function did not induce overexpression of other RND efflux pumps. Our data suggest that gene deletion mutants are unsuitable for studying membrane transporters and, importantly, that inhibitors of AcrB efflux function will not induce expression of other RND pumps.IMPORTANCE Antibiotic resistance is a major public health concern. In Gram-negative bacteria, overexpression of the AcrAB-TolC multidrug efflux system confers resistance to clinically useful drugs. Here, we show that loss of AcrB efflux function causes loss of virulence in Salmonella enterica serovar Typhimurium. This is due to the reduction of bacterial factors necessary for infection, which is likely to be caused by the retention of noxious molecules inside the bacterium. We also show that, in contrast to loss of AcrB protein, loss of efflux does not induce overexpression of other efflux pumps from the same family. This indicates that there are differences between loss of efflux protein and loss of efflux that make gene deletion mutants unsuitable for studying the biological function of membrane transporters. Understanding the biological role of AcrB will help to assess the risks of targeting efflux pumps as a strategy to combat antibiotic resistance.

Risks Involved in the Use of Enrofloxacin for Salmonella Enteritidis or Salmonella Heidelberg in Commercial Poultry

The objectives of the present study were to evaluate the risks involved in the use of Enrofloxacin for Salmonella Enteritidis (SE) or Salmonella Heidelberg (SH) in commercial poultry and determine the effects of a probiotic as an antibiotic alternative. Two experiments were conducted to evaluate the risks involved in the use of Enrofloxacin for SE or SH in commercial poultry. Experiment 1 consisted of two trials. In each trial, chickens were assigned to one of three groups; control + SE challenged; Enrofloxacin 25 mg/kg + SE; and Enrofloxacin 50 mg/kg + SE. Chickens received Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, all groups received fresh water without any treatment. All chickens were orally gavaged with 10⁷ cfu/chick of SE at 7 days of age and euthanized on 8 days of age. In Experiment 2, turkey poults were assigned to one of the three groups; control + SH; probiotic + SH; and Enrofloxacin 50 mg/kg + SH. Poults received probiotic or Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, poults received fresh water without any treatment. Poults were orally gavaged with 10⁷ cfu/poult of SH at 7 days of age. Poults were weighed and humanely killed 24 h post-SH challenge to evaluate serum concentration of fluorescein isothiocyanate-dextran to evaluate intestinal permeability, metagenomics, and SH infection. In both trials of Experiment 1, chickens treated with Enrofloxacin were more susceptible to SE organ invasion and intestinal colonization when compared with control non-treated chickens (P < 0.05). In Experiment 2, poults treated with 50 mg/kg of Enrofloxacin showed an increase in body weight, however, this group also showed an increase in SH susceptibility, intestinal permeability, and lower proportion of Firmicutes and Bacteroidetes, but with control group had the highest proportion of Proteobacteria. By contrast, poults that received the probiotic had the highest proportion of Firmicutes and Bacteroidetes, but lowest Proteobacteria. The results of the present study suggest that prophylactic utilization of Enrofloxacin at five times the recommended dose in poultry increases the susceptibility to salmonellae infections, and confirms that probiotics may be an effective tool in salmonellae infections.

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity

The incidence of multidrug-resistant bacterial infections is increasing globally and the need to understand the underlying mechanisms is paramount to discover new therapeutics. The efflux pumps of Gram-negative bacteria have a broad substrate range and transport antibiotics out of the bacterium, conferring intrinsic multidrug resistance (MDR). The genomes of pre- and posttherapy MDR clinical isolates of Salmonella Typhimurium from a patient that failed antibacterial therapy and died were sequenced. In the posttherapy isolate we identified a novel G288D substitution in AcrB, the resistance-nodulation division transporter in the AcrAB-TolC tripartite MDR efflux pump system. Computational structural analysis suggested that G288D in AcrB heavily affects the structure, dynamics, and hydration properties of the distal binding pocket altering specificity for antibacterial drugs. Consistent with this hypothesis, recreation of the mutation in standard Escherichia coli and Salmonella strains showed that G288D AcrB altered substrate specificity, conferring decreased susceptibility to the fluoroquinolone antibiotic ciprofloxacin by increased efflux. At the same time, the substitution increased susceptibility to other drugs by decreased efflux. Information about drug transport is vital for the discovery of new antibacterials; the finding that one amino acid change can cause resistance to some drugs, while conferring increased susceptibility to others, could provide a basis for new drug development and treatment strategies.

Expression of homologous RND efflux pump genes is dependent upon AcrB expression: implications for efflux and virulence inhibitor design

Objectives

Enterobacteriaceae have multiple efflux pumps that confer intrinsic resistance to antibiotics. AcrB mediates clinically relevant multidrug resistance and is required for virulence and biofilm formation, making it an attractive target for the design of inhibitors. The aim of this study was to assess the viability of single transporters as a target for efflux inhibition using Salmonella Typhimurium as the model pathogen.

Methods

The expression of resistance–nodulation–division (RND) efflux pump genes in response to the inactivation of single or multiple homologues was measured using real-time RT–PCR. Phenotypes of mutants were characterized by measuring antimicrobial susceptibility, dye accumulation and the ability to cause infection in vitro.

Results

The expression of all RND efflux pump genes was increased when single or multiple acr genes were inactivated, suggesting a feedback mechanism that activates the transcription of homologous efflux pump genes. When two or three acr genes were inactivated, the mutants had further reduced efflux, altered susceptibility to antimicrobials (including increased susceptibility to some, but conversely and counterintuitively, decreased susceptibility to some others) and were more attenuated in the tissue culture model than mutants lacking single pumps were.

Conclusions

These data indicate that it is critical to understand which pumps an inhibitor is active against and the effect of this on the expression of homologous systems. For some antimicrobials, an inhibitor with activity against multiple pumps will have a greater impact on susceptibility, but an unintended consequence of this may be decreased susceptibility to other drugs, such as aminoglycosides.

Understanding the basis of antibiotic resistance: a platform for drug discovery

There are numerous genes in Salmonella enterica serovar Typhimurium that can confer resistance to fluoroquinolone antibiotics, including those that encode topoisomerase proteins, the primary targets of this class of drugs. However, resistance is often multifactorial in clinical isolates and it is not uncommon to also detect mutations in genes that affect the expression of proteins involved in permeability and multi-drug efflux. The latter mechanism, mediated by tripartite efflux systems, such as that formed by the AcrAB-TolC system, confers inherent resistance to many antibiotics, detergents and biocides. Genetic inactivation of efflux genes gives multi-drug hyper-susceptibility, and in the absence of an intact AcrAB-TolC system some chromosomal and transmissible antibiotic resistance genes no longer confer clinically relevant levels of resistance. Furthermore, a functional multi-drug resistance efflux pump, such as AcrAB-TolC, is required for virulence and the ability to form a biofilm. In part, this is due to altered expression of virulence and biofilm genes being sensitive to efflux status. Efflux pump expression can be increased, usually due to mutations in regulatory genes, and this confers resistance to clinically useful drugs such as fluoroquinolones and β-lactams. Here, I discuss some of the work my team has carried out characterizing the mechanisms of antibiotic resistance in Salmonella enterica serovar Typhimurium from the late 1980s to 2014. A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2014, can be viewed via this link: https://www.youtube.com/watch?v=MCRumMV99Yw.

In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards

Fluoroquinolone (FQ) resistance in Salmonella enterica is a significant clinical concern. Recognition of resistance by the clinical laboratory is complicated by the multiple FQ resistance mechanisms found in Salmonella. The Clinical Laboratory Standards Institute (CLSI) recently addressed this issue by revising the ciprofloxacin break points for Salmonella species. It is critical for clinicians and laboratory workers to be aware of the multiple technical issues surrounding these revised break points. In this article, we review FQ resistance mechanisms in Salmonella, their clinical significance, and data supporting the revised ciprofloxacin break points. We encourage clinical laboratories to adopt the revised CLSI ciprofloxacin break points for all Salmonella isolates in which susceptibility testing is indicated and discuss the technical issues for laboratories using commercial antimicrobial susceptibility systems.

Molecular characterization of antimicrobial resistance in non-typhoidal salmonellae associated with systemic manifestations from India

Extended-spectrum cephalosporins and fluoroquinolones are essential antimicrobials for treating invasive salmonellosis, although emerging resistance to these antimicrobials is of growing concern, especially in India. Therefore, a study was conducted to characterize the antimicrobial susceptibility phenotypes, types of extended-spectrum β-lactamase (ESBL) gene plasmids and serological relationships of 21 non-typhoidal Salmonella isolates from patients who attended three different hospitals in India from 2006 to 2008. The isolates were cultured from stool, blood and cerebrospinal fluid samples obtained from patients presenting with diarrhoea and accompanying systemic manifestations such as fever, vomiting and meningism. Non-typhoidal Salmonella isolates were investigated using serotyping and antimicrobial susceptibility testing. PCR screening was also performed to detect the β-lactamase, qnr and aac(6′)-Ib-cr genes and class 1 integrons. Sequencing for quinolone resistance mutations and plasmid replicon typing were also performed. An antimicrobial resistance microarray was used for preliminary screening and identification of bla TEM and bla SHV genes, and phenotypic testing for the presence of efflux pumps was also performed. Ten out of 21 isolates (48 %) possessed the extended-spectrum cephalosporin resistance phenotype, with PCR amplification and sequencing revealing that isolates possessed TEM-1, SHV-12, DHA-1, OXA-1-like and CTX-M-15 ESBL genes. FIIs plasmid replicons were detected in seven isolates (33 %). The involvement of efflux pumps was detected in four isolates (19 %) resistant to ciprofloxacin. It was concluded that SHV-12-carrying Salmonella serotype Agona may play an important role in ESBL-mediated resistance in non-typhoidal salmonellae in India. The very high percentage (48 %) of ESBL-producing non-typhoidal salmonellae isolated from these patients represents a real and immediate challenge to the effective antimicrobial therapy of Salmonella infections associated with systemic manifestations. Continued surveillance for the presence of ESBL-producing (non-typhoidal) salmonellae in India is essential.

An imported enteric fever caused by a quinolone-resistant Salmonella Typhi

Recent reports indicate that nalidixic acid susceptibility correlates well with the clinical outcome of patients with Salmonella Typhi infection treated with quinolones. We report a case of enteric fever caused by S Typhi in which the isolate was resistant to nalidixic acid, but showed in vitro susceptibility to ciprofloxacin. Following treatment with ciprofloxacin, the clinical outcome was not satisfactory and the patient had a relapse. However, after using a higher dose of ciprofloxacin, the patient was cured. We recommend that all Salmonella systemic infections resistant to nalidixic acid with in vitro but decreased susceptibility to fluoroquinolones be treated with other antibiotics like third-generation cephalosporins or azithromycin. These patients should be closely followed up and observed for further relapse.

Ciprofloxacin selects for multidrug resistance in Salmonella enterica serovar Typhimurium mediated by at least two different pathways

OBJECTIVES

The aim of this study was to understand the role of ramA in conferring multidrug resistance (MDR) in Salmonella enterica serovar Typhimurium.

METHODS

Two phenotypically distinct isogenic MDR laboratory mutants derived from Salmonella Typhimurium SL1344 and three human clinical isolates from a patient that failed antibiotic therapy, including with ciprofloxacin, were investigated for the cause of MDR. MICs were determined by agar dilution and efflux activity assessed by monitoring the accumulation of Hoechst 33342. The combination of specific genes and MDR was assessed by inactivation, and complementation RT-PCR was used to assess gene expression and DNA sequencing to identify mutations within genes of interest.

RESULTS

Mutation in ramR and the consequent over-production of ramA and acrB were revealed in one laboratory mutant selected with ciprofloxacin and this was associated with cyclohexane tolerance. Complementation of SL1344 ramR::aph with pUC19 ramR(mutant) conferred MDR and cyclohexane tolerance. However, analysis of a second ciprofloxacin-selected MDR mutant, which was susceptible to cyclohexane, revealed no mutation in ramR or altered expression of marA, soxS or rob. There was a mutation in ramR in both the pre- and post-therapy clinical isolates and no difference between the isolates in the level of expression of ramA.

CONCLUSIONS

These data show that ciprofloxacin exposure can select for mutations within ramR and consequently mediate MDR. These data also indicate that there is at least one further unidentified gene in addition to marA, soxS, rob and ramA that confers MDR in S. enterica.

Cefotaxime-ciprofloxacin combination therapy for nontyphoid Salmonella bacteremia and paravertebral abscess after failure of monotherapy

Therapeutic failure of monotherapy with either a third-generation cephalosporin or a fluoroquinolone against nontyphoid salmonellae has been observed in clinical practice. Combination therapy with both agents is recommended in the literature for treating life-threatening infections. However, we know of no published case reports that indicate a therapeutic advantage of this combination therapy for nontyphoid salmonellae infections. We describe a 60-year-old man who had breakthrough bacteremia with vertebral osteomyelitis and paravertebral abscess caused by Salmonella enterica serotype Choleraesuis. This was not controlled with sequential monotherapy but was eventually cured with cefotaxime-ciprofloxacin combination therapy. The Etest showed that the strain was susceptible to cefotaxime and ciprofloxacin, but resistant to nalidixic acid. Cefotaxime and ciprofloxacin in combination may be considered as an option for difficult-to-treat salmonellosis.

Available options in the management of non-typhi Salmonella

Gastroenteritis, caused by Salmonella spp. is usually a self-limiting infection and does not require treatment. However, in some immunosuppressed patients (such as the newborn, the elderly, those with AIDS or neoplasms), there is a greater risk of developing a severe systemic infection, and in these cases, antibiotic treatment is recommended. Third-generation cephalosporins and fluoroquinolones are the most useful antibiotics in the treatment of these infections, although resistant strains are sometimes isolated. Therapeutic failures have been reported with fluoroquinolones in extra-intestinal infections caused by nalidixic acid resistant strains.

Increasing prevalence of quinolone resistance in human nontyphoid Salmonella enterica isolates obtained in Spain from 1981 to 2003

From January 1981 to December 2003, susceptibility to nalidixic acid was tested in 10,504 nontyphoid Salmonella enterica isolates from patients with acute enteric disease in Gipuzkoa, Spain. The prevalence of nalidixic acid resistance steadily increased from less than 0.5% before 1991 to 38.5% in 2003, mainly due to the increase in resistance among isolates of the most prevalent serovar, S. enterica serovar Enteritidis. For nalidixic acid-resistant isolates, the ciprofloxacin MIC was eightfold higher than that for susceptible isolates, and the nalidixic acid-resistant isolates contained a single point mutation in the gyrA gene (at codons for Ser83 or Asp87). The same mutations were found in a sample of nalidixic acid-resistant nontyphoid Salmonella strains isolated between 1999 and 2003 from retail food for human consumption. In 2003, we identified five S. enterica serovar Typhimurium clinical isolates with high-level fluoroquinolone resistance (ciprofloxacin MIC, 16 microg/ml) with two point mutations in the gyrA gene (coding for Ser83-->Phe and Asp87-->Asn) and one point mutation in the parC gene (coding for Ser80-->Arg). Strict sanitary controls are needed to avoid the spread of ciprofloxacin-resistant serovar Typhimurium isolates, and a more efficient veterinary policy must be adopted to decrease the large burden of Salmonella serovar Enteritidis infections in humans in our region.

Mutations in the gyrA gene in Salmonella enterica clinical isolates with decreased ciprofloxacin susceptibility

The incidence of resistance to nalidixic acid has increased in the University General Hospital of Elche, Spain, and this paper describes the investigation of this phenomenon. This increase was mainly due to an increase of nalidixic-resistant Salmonella enterica serotype Enteritidis. Resistance to nalidixic acid is an indicator of decreased ciprofloxacin susceptibility (sensitivity 100%, specificity 96.7%). Strains that were resistant to nalidixic acid and exhibited decreased susceptibility to ciprofloxacin had a single mutation in QRDR of gyrA: Asp87-Asn, Asp87-Tyr or Ser83-Phe. The sensitivity of S. enterica strains to nalidixic acid should be tested and the breakpoint of ciprofloxacin established by MENSURA applied, instead of that of the NCCLS for these strains.

Mutations in topoisomerase genes of fluoroquinolone-resistant salmonellae in Hong Kong

A total of 88 salmonella isolates (72 clinical isolates for which the ciprofloxacin MIC was >0.06 microg/ml, 15 isolates for which the ciprofloxacin MIC was < or =0.06 microg/ml, and Salmonella enterica serotype Typhimurium ATCC 13311) were studied for the presence of genetic alterations in four quinolone resistance genes, gyrA, gyrB, parC, and parE, by multiplex PCR amplimer conformation analysis. The genetic alterations were confirmed by direct nucleotide sequencing. A considerable number of strains had a mutation in parC, the first to be reported in salmonellae. Seven of the isolates sensitive to 0.06 micro g of ciprofloxacin per ml had a novel mutation at codon 57 of parC (Tyr57-->Ser) which was also found in 29 isolates for which ciprofloxacin MICs were >0.06 micro g/ml. Thirty-two isolates had a single gyrA mutation (Ser83-->Phe, Ser83-->Tyr, Asp87-->Asn, Asp87-->Tyr, or Asp87-->Gly), 34 had both a gyrA mutation and a parC mutation (29 isolates with a parC mutation of Tyr57-->Ser and 5 isolates with a parC mutation of Ser80-->Arg). Six isolates which were isolated recently (from 1998 to 2001) were resistant to 4 micro g of ciprofloxacin per ml. Two of these isolates had double gyrA mutations (Ser83-->Phe and Asp87-->Asn) and a parC mutation (Ser80-->Arg) (MICs, 8 to 32 microg/ml), and four of these isolates had double gyrA mutations (Ser83-->Phe and Asp87-->Gly), one parC mutation (Ser80-->Arg), and one parE mutation (Ser458-->Pro) (MICs, 16 to 64 micro g/ml). All six of these isolates and those with a Ser80-->Arg parC mutation were S. enterica serotype Typhimurium. One S. enterica serotype Typhi isolate harbored a single gyrA mutation (Ser83-->Phe), and an S. enterica serotype Paratyphi A isolate harbored a gyrA mutation (Ser83-->Tyr) and a parC mutation (Tyr57-->Ser); both of these isolates had decreased susceptibilities to the fluoroquinolones. The MICs of ciprofloxacin, levofloxacin, and sparfloxacin were in general the lowest of those of the six fluoroquinolones tested. Isolates with a single gyrA mutation were less resistant to fluoroquinolones than those with an additional parC mutation (Tyr57-->Ser or Ser80-->Arg), while those with double gyrA mutations were more resistant.

Reevaluating fluoroquinolone breakpoints for Salmonella enterica serotype Typhi and for non-Typhi salmonellae

Salmonella enterica infections cause considerable morbidity and mortality worldwide. Antimicrobial therapy may be life-saving for patients with extraintestinal infections with S. enterica serotype Typhi or non-Typhi salmonellae. Because antimicrobial resistance to several classes of traditional first-line drugs has emerged in the past several decades, the quinolone antimicrobial agents, particularly the fluoroquinolones, have become the drugs of choice. Recently, resistance to nalidixic acid has emerged among both Typhi and non-Typhi Salmonella serotypes. Such Salmonella isolates typically also have decreased susceptibility to fluoroquinolones, although minimum inhibitory concentrations of the fluoroquinolones usually are within the susceptible range of the interpretive criteria of the NCCLS. A growing body of clinical and microbiological evidence indicates that such nalidixic acid-resistant S. enterica infections also exhibit a decreased clinical response to fluoroquinolones. In this article, we recommend that laboratories test extraintestinal Salmonella isolates for nalidixic acid resistance, we recommend that short-course fluoroquinolone therapy be avoided for infection with nalidixic acid-resistant extraintestinal salmonellae, and we summarize existing data and data needs that would contribute to reevaluation of the current NCCLS fluoroquinolone breakpoints for salmonellae.

Fluoroquinolone resistance in Salmonella serovars isolated from humans and food animals

Quinolone-resistant Salmonella enterica usually contain a mutation in gyrA within the region encoding the quinolone resistance determining region of the A subunit of DNA gyrase. These mutations confer substitutions analogous to Escherichia coli Ser83-->Phe and Asp87-->Gly or Tyr, or a novel mutation resulting in Ala119-->Glu or Val. Mutations in gyrB are rare, and no mutations in parC or parE have been described. Quinolone-resistant Salmonella can also be cross-resistant to other agents including chloramphenicol and tetracycline. Increased efflux has been demonstrated and for some strains this has been associated with increased expression of acrB. Mutation in soxR has also been shown for one isolate. Detection of low level resistance (minimum inhibitory concentrations <0.5 microg ml(-1)) to fluoroquinolones is proving an increasing problem in the treatment of invasive Salmonella infections.

Prevalence and antibiotic susceptibility of Salmonella isolated from beef animal hides and carcasses

This study determined the prevalence of Salmonella on beef animal hides and carcasses and antimicrobial susceptibility profiles against a panel of 13 antibiotics. In each of the eight commercial packing facilities, of which five processed primarily heifers and steers and the remaining three processed primarily cows and bulls, hide and carcass sponge swab samples were obtained immediately before hide removal and before carcass chilling, respectively. Overall, prevalence of Salmonella on external surfaces (hides) of cattle was 15.4% (49 of 319), whereas prevalence after dehiding and other slaughtering/dressing processes, including the application of decontamination treatments, was, as expected, reduced (P < 0.05) to 1.3% (4 of 320) on carcass surfaces. From 53 total Salmonella-positive hide and carcass samples, 526 biochemically confirmed isolates were obtained to determine antimicrobial susceptibility profiles. Of 53 Salmonella-positive samples, individually, 24 (45.3%), 17 (32.1%), 17 (32.1%), 11 (20.8%), 8 (15.1%), 8 (15.1%), 8 (15.1%), 4 (7.5%), and 2 (3.8%) samples yielded at least one isolate resistant to amoxicillin/clavulanic acid, tetracycline, streptomycin, sulfonamides, ampicillin, ampicillin/sulbactam, chloramphenicol, gentamicin, and trimethoprim/sulfamethoxazole, respectively. None of the Salmonella-positive samples yielded an isolate resistant to ceftriaxone, ciprofloxacin, enrofloxacin, or levofloxacin. Although none of the samples yielded an isolate simultaneously resistant to three or four antimicrobials, a total of eight samples yielded at least one isolate resistant to five or more antimicrobials tested. Included among the 18 group B-positive samples were three samples that, individually, yielded at least one Salmonella Typhimurium var. Copenhagen DT104 isolate resistant to at least six antimicrobials tested. Results from this study support current prudent therapeutic and subtherapeutic antimicrobial use recommendations.

Antimicrobial drug resistance in non-typhoidal salmonellas from humans in England and Wales in 1999: decrease in multiple resistance in Salmonella enterica serotypes Typhimurium, Virchow, and Hadar

In 1999 the incidence of multiple drug resistance (to four or more antimicrobials) in non-typhoidal salmonellas from humans in England and Wales fell in isolations of Salmonella enterica serotypes Typhimurium, Virchow, and Hadar. This fall has been most noticeable in S. Typhimurium, where 59% of isolates were multiresistant compared to 81% in 1996. The main reason for this has been a 75% decline in isolations of multiply-resistant S. Typhimurium definitive phage type (DT) 104 (MR DT104) since 1996. Nevertheless MR DT104 remains second to S. Enteritidis phage type 4 as the most common strain in cases of human salmonellosis in England and Wales. Multiple resistance has also remained high in S. Hadar, with 49% of isolates resistant to four drugs or more compared to 56% in 1996. Isolates with decreased sensitivity to ciprofloxacin (minimal inhibitory concentration: 0.25-1.0 mg/L) have increased in incidence in S. Enteritidis, S. Virchow, and S. Hadar; in S. Hadar 70% of isolates were resistant to ciprofloxacin at this level. It is hoped that Codes of Practice introduced by some pharmaceutical companies, governments, professional organisations, and others to combat the unnecessary prophylactic use of fluoroquinolones in animal husbandry will not result in a reduction in the incidence of resistance to ciprofloxacin in salmonella organisms causing infections in humans.

Antimicrobial susceptibility of nontyphoidal Salmonella isolated from humans in Belgium

Human nontyphoidal Salmonella infections are the primary cause of foodborne disease in developed countries, resulting in considerable morbidity and occasionally death, especially in immunocompromised patients. Strains of Salmonella that are resistant to antimicrobial agents have become a world-wide health problem. Fluoroquinolones are drugs of choice for treatment of human invasive salmonellosis, and have been useful for the treatment of infections caused by multi-resistant strains. However, strains resistant to ciprofloxacin have been noted. A random sample of 378 Salmonella strains of human origin was collected during 1998. Their susceptibility to 11 antimicrobial agents was determined by the agar dilution method according to NCCLS standards. In total, 38 serotypes were represented of which S. Enteritidis (20.4%), S. Typhimurium (20.4%), S. Hadar (9.0%), S. Brandenburg (7.9%), S. Infantis (7.7%), and S. Virchow (5.3%) were the most common. All strains were susceptible to ceftriaxone and ciprofloxacin. For nalidixic acid the rate of resistance was 19.0%. Of the 72 strains resistant to nalidixic acid, 31 were S. Hadar, and thus 91.2% (31/34) of the S. Hadar isolates showed resistance to nalidixic acid. Most of the S. Hadar strains were also resistant to ampicillin, tetracycline and sulphamethoxazole, and an elevated MIC50 (0.25 microgram/ml) and MIC90 (1 microgram/ml) was observed for ciprofloxacin. The high rate of resistance to nalidixic acid can be a first step towards the development of resistance to ciprofloxacin.

Use of a LightCycler gyrA mutation assay for rapid identification of mutations conferring decreased susceptibility to ciprofloxacin in multiresistant Salmonella enterica serotype Typhimurium DT104 isolates

A LightCycler-based PCR-hybridization gyrA mutation assay (GAMA) was developed to rapidly detect gyrA point mutations in multiresistant (MR) Salmonella enterica serotype Typhimurium DT104 with decreased susceptibility to ciprofloxacin (MIC, 0.25 to 1.0 mg/liter). Ninety-two isolates (49 human, 43 animal) were tested with three individual oligonucleotide probes directed against an Asp-87-to-Asn (GAC-->AAC) mutation, an Asp-87-to-Gly (GAC-->GGC) mutation, and a Ser-83-to-Phe (TCC-->TTC) mutation. Strains homologous to the probes could be distinguished from strains that had different mutations by their probe-target melting temperatures. Thirty-seven human and 30 animal isolates had an Asp-87-to-Asn substitution, 6 human and 6 animal isolates had a Ser-83-to-Phe substitution, and 5 human and 2 animal isolates had an Asp-87-to-Gly substitution. The remaining six strains all had mismatches with the three probes and therefore different gyrA mutations. The sequencing of gyrA from these six isolates showed that one human strain and two animal strains had an Asp-87-to-Tyr (GAC-->TAC) substitution and two animal strains had a Ser-83-to-Tyr (TCC-->TAC) substitution. One animal strain had no gyrA mutation, suggesting that this isolate had a different mechanism of resistance. Fifty-eight of the strains tested were indistinguishable by several different typing methods including antibiograms, pulsed-field gel gel electrophoresis, and plasmid profiling, although they could be further subdivided according to gyrA mutation. This study confirmed that MR DT104 with decreased susceptibility to ciprofloxacin from humans and food animals in England and Wales may have arisen independently against a background of clonal spread of MR DT104.

Evidence for an efflux pump mediating multiple antibiotic resistance in Salmonella enterica serovar Typhimurium

The mechanism of multiple antibiotic resistance in six isolates of Salmonella enterica serovar Typhimurium recovered from a patient treated with ciprofloxacin was studied to investigate the role of efflux in the resistance phenotype. Compared to the patient's pretherapy isolate (L3), five of six isolates accumulated less ciprofloxacin, three of six isolates accumulated less chloramphenicol, and all six accumulated less tetracycline. The accumulation of one or more antibiotics was increased by carbonyl cyanide m-chlorophenylhydrazone to concentrations similar to those accumulated by L3 for all isolates except one, in which accumulation of all three agents remained approximately half that of L3. All isolates had the published wild-type sequences of marO and marR. No increased expression of marA, tolC, or soxS was observed by Northern blotting; however, three isolates showed increased expression of acrB, which was confirmed by quantitative competitive reverse transcription-PCR. However, there were no mutations within acrR or the promoter region of acrAB in any of the isolates.

Quinolone resistance mutations in the gyrA gene of clinical isolates of Salmonella

S. typhimurium AlhR, S. enteritidis OulR, and S. hadar GueR resistant to fluoroquinolones (QR), ciprofloxacin MICs, 0.25 to 1 microgram/ml; norfloxacin MICs, 0.5 to 4 micrograms/ml; nalidixic acid MIC, 256 micrograms/ml were isolated from urinary tract infections (AlhR and OulR) during FQ therapy in immunocompromised patients infected by the parent FQ-susceptible strains (AlhS and OulS) (ciprofloxacin MICs, 0.032-0.063; norfloxacin MICs, 0.125-0.25; nalidixic acid MICs, 4-8) or from intestinal infection (GueR). Transformation of AlhR, OulR, and GueR by plasmid pJSW101 carrying the wild-type gyrA gene of Escherichia coli resulted in complementation (nalidixic acid MICs, 4 to 8), proving that these strains had a gyrA mutation. A 800-bp fragment of gyrA from the five strains was amplified by PCR. Direct DNA sequencing of 252-bp region of this fragment identified a single point mutation leading to a substitution Ser-83 to Tyr in AlhR and to a substitution Ser-83 to Phe in OulR and in GueR. These results emphasize the potential risk of selection of FQ-resistant Salmonella during FQ therapy in immunocompromised patients and suggest that these strains differ from the parent strains at least by one mutation in the gyrA gene. They also confirm the role of substitutions in position 83 of gyrA in FQ-resistant clinical isolates of Salmonella.

Resistance to ciprofloxacin in non-typhoidal salmonellas from humans in England and Wales-the current situation

OBJECTIVE: To report on the prevalence of isolates with ciprofloxacin resistance in non-typhoidal salmonellas from humans in England and Wales in 1997. METHODS: All non-typhoidal salmonellas referred to the Laboratory of Enteric Pathogens in 1997 were screened for resistance to ciprofloxacin at 0.125 and 1.0 mg/L and nalidixic acid at 16 mg/L, and results were compared to those for 1994. Full minimal inhibitory concentrations (MICs) of these antimicrobials were also determined for a selection of isolates resistant to ciprofloxacin at 0.125 mg/L but sensitive at 1.0 mg/L, and for all isolates resistant at 1.0 mg/L. RESULTS: Since 1994 there have been increases in the occurrence of resistance to ciprofloxacin (MICs: 0.25-1.0 mg/L) in Salmonella enterica serotypes Enteritidis, Typhimurium, Virchow and Hadar. Of particular importance have been increases in the occurrence of resistance in multiresistant S. Typhimurium DT 104, and also in S. virchow, a serotype with a propensity for causing extraintestinal infections in humans. High-level resistance (MIC >/=2.0 mg/L) was uncommon and was identified in only a few strains, all from patients with a history of recent foreign travel. CONCLUSIONS: There is a strong temporal association between increases in the occurrence of ciprofloxacin resistance in Salmonella serotypes Typhimurium, Virchow and Hadar from humans in England and Wales and with the licensing for use in food animals in the UK of the related fluoroquinolone antibiotic enrofloxacin; in contrast, for S. enteritidis ciprofloxacin resistance was most common in a phage type associated with foreign travel. It is hoped that recent recommendations for the use of fluoroquinolone antimicrobials in food animals in the UK will result in a reduction in the occurrence of resistance to ciprofloxacin in zoonotic salmonellas causing infections in humans.

Increasing fluoroquinolone resistance in salmonella serotypes in Finland during 1995-1997

Antimicrobial resistance trends were examined for 811 salmonella isolates from humans collected in Finland during 1995-1997. The material was divided into domestic and foreign isolates according to the origin of infection. A total of 2.3% of the 387 domestic and 7.8% of the 424 foreign isolates were quinolone-resistant (P < 0.001). Among the domestic isolates we detected an emergence of ciprofloxacin resistance (MIC > or = 0.25 mg/L) with the proportion of resistant isolates increasing from 0 to 2.2% (P = 0.2). Among the foreign isolates this increase was even more dramatic, from 2.0% to 8.4% (P = 0.037) during the study period.

Resistance to ciprofloxacin in pathogenic Enterobacteriaceae in England and Wales in 1996

In 1996, 6% of Escherichia coli from extraintestinal infections were resistant to ciprofloxacin with minimum inhibitory concentrations (MICs) > or = 2 mg/l (high level resistance). Low level resistance (MIC 0.125-1 mg/l) was also identified in 7% of Salmonella typhi, 4% of S paratyphi A, and 4% of non-typhoidal salmonellas. However, resistance to ciprofloxacin was rarely identified in shigellas. For E coli, physicians should be aware that treatment failures may occur when patients with invasive illness are treated with ciprofloxacin before the results of laboratory sensitivity tests are available. For salmonellas an increasing number of treatment failures have been recorded for patients infected with strains with low level resistance. Because of the increasing incidence of Enterobacteriaceae with low level resistance to ciprofloxacin, it is recommended that for this group of organisms a breakpoint of 0.125 mg/l should be included in laboratory sensitivity tests.

Mutations in gyrA gene of quinolone-resistant Salmonella serotypes isolated from humans and animals

The quinolone resistance-determining regions (QRDRs) of the gyrA genes of quinolone-resistant clinical and veterinary salmonella isolates were sequenced. Substitutions analogous to a substitution of a Ser to a Phe at position 83 (Ser83-->Phe) and Asp87-->Gly or Tyr in Escherichia coli were found, as was a single novel mutation outside of the QRDR resulting in Ala119-->Glu. The data suggest that gyrA mutations are associated with quinolone resistance in veterinary and clinical salmonella isolates and that the limits of the QRDR may require revision.

Selection of multiple resistance in Salmonella enteritidis during treatment with ciprofloxacin

We report on a strain of Salmonella enteritidis which was found to be resistant to both ciprofloxacin and beta-lactams and chloramphenicol in a patient treated with ciprofloxacin for a splenic abscess. We conclude that in invasive infections such as a splenic abscess caused by Salmonella, early surgical intervention is important. Multiple-drug-resistant strains of Salmonella may be selected by treatment with ciprofloxacin alone.

Emergence of ciprofloxacin resistance during treatment of Salmonella osteomyelitis in three patients with sickle cell disease

The treatment of salmonella osteomyelitis in sickle cell disease (SCD) is difficult and the emergence of antibiotic resistance in Salmonella spp presents further problems for clinicians treating SCD. Three patients presented with salmonella bacteraemia. Treatment with several intravenous antibiotics did not prevent the subsequent development of osteomyelitis. Emergence of resistance to multiple antibiotics, including ciprofloxacin, during the treatment of salmonella osteomyelitis in SCD patients is reported here for the first time. Ceftriaxone 2 g once daily given for 3 months to 3 years was an effective and convenient treatment for osteomyelitis caused by multiply-resistant salmonella. Two of these patients gave a definite history of diarrhoea, and stool cultures confirmed the presence of Salmonella spp in one. Our experience shows that salmonella osteomyelitis may not be prevented by early treatment of bacteraemia in SCD patients. Other measures to reduce the risk of salmonella infection are therefore necessary.

Role of quinolones in the treatment of diarrhoeal diseases

Diarrhoeal diseases are still an important health problem in both developing and developed countries, and resistance to commonly used antibiotics among enteric pathogens is a major issue. Quinolones have become important agents in the treatment of diarrhoeal diseases because of their excellent in vitro activity against pathogens and their pharmacological features. In many clinical studies, they appeared to be effective in the treatment of shigellosis and the prevention and treatment of diarrhoea in travellers. Several studies have demonstrated that single-dose therapy with these agents is sufficient in many cases. Their role in the treatment of acute salmonellosis is still controversial, because of their lack of efficacy in eliminating salmonella from the faeces.

Ciprofloxacin resistance in clinical isolates of Salmonella typhimurium obtained from two patients

Two patients (patients A and B) infected with Salmonella typhimurium failed ciprofloxacin therapy, and the posttherapy isolates had reduced susceptibilities to quinolones; 6 of 11 isolates from patient B were also cross-resistant to chemically unrelated agents. No transferable resistance, chloramphenicol-acetylating enzymes, or beta-lactamases were detected. For 13 of 14 isolates, the concentrations of ciprofloxacin that inhibited DNA synthesis by 50% were similar to the MICs, suggesting a mutation in gyrA. Insertion of pNJR3-2 (gyrA) in the posttherapy isolate from patient A and 5 of 11 of the posttherapy isolates from patient B resulted in lower quinolone MICs, also suggesting that resistance was due to a mutation in gyrA. Three of the five isolates also had reduced levels of accumulation of quinolones. All six cross-resistant isolates from patient B had reduced levels of accumulation of quinolones, but only one isolate had increased susceptibility when pNJR3-2 was inserted. Despite the lack of OmpF seen in five isolates from patient B, there was no correlation with decreased levels of quinolone accumulation. All isolates had identical smooth lipopolysaccharide profiles. The mechanism of apparently reduced accumulation has yet to be determined.

Quinolones in Salmonella typhi infection

The quinolones possess a high degree of in vitro activity against enteric bacteria, including Salmonella. This observation, coupled with the limitations of current antityphoid agents, has resulted in the evaluation of quinolones in the therapy of S. typhi infection, including both enteric fever and chronic intestinal carriage. In open uncontrolled trials, norfloxacin, ciprofloxacin, ofloxacin and pefloxacin have been used successfully to treat more than 200 patients with culture-proven typhoid fever. In comparative clinical trials, ciprofloxacin, ofloxacin, pefloxacin or fleroxacin were equivalent or superior to standard antityphoid therapy. In separate studies, norfloxacin and ciprofloxacin were each effective in eliminating intestinal excretion of S. typhi in chronic carriers. Because of increasing resistance worldwide to conventional antityphoid drugs, and in view of the efficacy of the quinolones in the therapy of both typhoid fever and typhoid intestinal carriage, these drugs may become the treatment of choice for these important enteric infections.

Quinolones in the treatment of acute bacterial diarrhoeal diseases

Acute bacterial diarrhoea is still an important disease, especially in developing countries. Resistance to antibiotics among enteric pathogens is relatively common in many parts of the world. The quinolones are active in vitro against these organisms, and achieve high stool concentrations. Because of these features, quinolones have been used in the treatment of acute diarrhoeal diseases caused by various bacteria. They appear to be effective in the therapy of shigellosis and travellers' diarrhoea, as well as in the prevention of diarrhoeal disease in travellers. However, their role in the treatment of salmonella gastroenteritis has not been established yet.

Susceptibilities of ampicillin-resistant strains of Salmonella other than S. typhi to 10 antimicrobial agents

Ampicillin-resistant strains of Salmonella other than S. typhi constitute a health problem. We tested the antimicrobial susceptibilities to 10 antibiotics of 57 of these strains isolated in a 30-month period. The rates of resistance were as follows: chloramphenicol, 40.3%; tetracycline, 33.3%; gentamicin, 5.3%; co-trimoxazole, 5.3%; nalidixic acid, 1.8%; and amoxicillin-clavulanic acid, cefotaxime, ceftriaxone, aztreonam, and ciprofloxacin, 0%. In our experience, there are alternative antibiotics with excellent in vitro activities.

In vitro activity of lomefloxacin and other antimicrobials against bacterial enteritis pathogens

Lomefloxacin is a new, difluoroquinolone. In this study, the in vitro activity of lomefloxacin against clinical isolates of a variety of bacterial species associated with acute diarrheal disease was determined and compared with that of ciprofloxacin, ofloxacin, amoxicillin, sulphamethoxazole, trimethoprim, tetracycline, and chloramphenicol. Bacterial isolates were obtained from different geographical areas, including Western Europe and the United Kingdom, Southern Europe, Africa, the Middle East, South and Southeast Asia, and South America, and were included to reflect the range of susceptibility seen throughout the world. Minimum inhibitory concentrations (MICs) were determined using an agar incorporation technique in Mueller-Hinton medium supplemented when necessary with saponin-lysed horse blood at a final concentration of 10% vol/vol. Lomefloxacin was highly active against all the species examined which included Salmonella spp., Shigella spp., Escherichia coli enterotoxigenic [(ETEC), enteroinvasive (EIEC), and enteropathogenic (EPEC) strains], Yersinia enterocolitica, Campylobacter jejuni, Vibrio spp., and Aeromonas hydrophila, with all isolates inhibited by 1 mg/L or less. This activity was similar to ofloxacin and slightly less than that of ciprofloxacin. By contrast, many of the isolates were resistant to one or more of the other, unrelated animicrobials. No cross-resistance between lomefloxacin and any of the nonfluoroquinolone antimicrobials examined in the study was observed.

Ofloxacin. A reappraisal of its antimicrobial activity, pharmacology and therapeutic use

Ofloxacin is a fluoroquinolone whose primary mechanism of action is inhibition of bacterial DNA gyrase. In vitro it has a broad spectrum of activity against aerobic Gram-negative and Gram-positive bacteria, although it is poorly active against anaerobes. Ofloxacin, unlike most other broad spectrum antibacterial drugs, can be administered orally as well as intravenously. Penetration into body tissues and fluids is highly efficient. Clinical trials with orally and intravenously administered ofloxacin have confirmed its potential for use in a wide range of infections, where it has generally proved as effective as standard treatments. Ofloxacin in well tolerated, and in comparison with other available fluoroquinolones is less likely to cause clinically relevant drug interactions. Ofloxacin thus offers a valuable oral treatment (with an option for intravenous administration if necessary) for use in a wide range of clinical infections, but with a particular advantage in more severe or chronic infections when recourse to parenteral broad spectrum agents would normally be required, thereby providing cost savings and additionally allowing outpatient treatment.