The prevalence of fluoroquinolone resistance mechanisms in colonizing Escherichia coli isolates recovered from hospitalized patients

Role of the Water-Metal Ion Bridge in Quinolone Interactions with Escherichia coli Gyrase

Fluoroquinolones are an important class of antibacterials, and rising levels of resistance threaten their clinical efficacy. Gaining a more full understanding of their mechanism of action against their target enzymes-the bacterial type II topoisomerases gyrase and topoisomerase IV-may allow us to rationally design quinolone-based drugs that overcome resistance. As a step toward this goal, we investigated whether the water-metal ion bridge that has been found to mediate the major point of interaction between Escherichia coli topoisomerase IV and Bacillus anthracis topoisomerase IV and gyrase, as well as Mycobacterium tuberculosis gyrase, exists in E. coli gyrase. This is the first investigation of the water-metal ion bridge and its function in a Gram-negative gyrase. Evidence suggests that the water-metal ion bridge does exist in quinolone interactions with this enzyme and, unlike the Gram-positive B. anthracis gyrase, does use both conserved residues (serine and acidic) as bridge anchors. Furthermore, this interaction appears to play a positioning role. These findings raise the possibility that the water-metal ion bridge is a universal point of interaction between quinolones and type II topoisomerases and that it functions primarily as a binding contact in Gram-positive species and primarily as a positioning interaction in Gram-negative species. Future studies will explore this possibility.

Degradation and inactivation of chromosomal and plasmid encoded resistance genes/ARBs and the impact of different matrices on UV and UV/H2O2 based advanced oxidation process

This study reports a structured investigation on the degradation kinetics of different types (gyrA^R,tetA^R, qnrS^R) and conformational forms (chromosomal, plasmids) of ARGs and mobile genetic elements (intl-1, plasmids) as a function of water matrix (DI water, phosphate buffer, wastewater) with UV and UV/H₂O₂ treatments. Extracellular, intracellular and the free-ARGs fate were tracked to infer the impact of various parameters on the degradation efficacy of the treatment process. The degradation profile of e-ARGs (118-454 bp) showed 1-4 log reductions but did not correlate strongly to amplicon size indicating the importance of active sites distribution and/or types of ARGs for UV induced gene damage. The i-ARGs showed similar degradation rates compared to e-ARGs for UV in phosphate buffer (PBS) but showed (1.3-2 times) slower rates for i-ARGs with UV/H₂O₂ due to scavenging of OH radicals by the cellular components. While the ARB inactivation was effective, but ARG damage was not supplemental as i-ARGs and f-ARGs persisted. In the wastewater matrix, generation of radical species was contributing to improved degradation rates from UV/H₂O₂ treatment, specifically for f-ARGs resulting in significantly improved degradation (p<0.05) compared to PBS. These indicates a non-selective nature of attack from radical species generated from UV irradiation on the effluent organic matter (E_fOM) than sequenced based damage to the genes from UV. For the plasmid degradation, conformational differences pertaining to the supercoiled structures and intracellular forms influenced slower (1.2-2.8 times) UV mediated gene damage rate as opposed to chromosomal ARGs. These results can be useful for better assessing UV based treatment processes for effective ARG removal.

Screening for Antimicrobial-Resistant Gram-negative bacteria in hospitalised patients, and risk of progression from colonisation to infection: Systematic review

BACKGROUND

Transmission of antimicrobial-resistant Gram-negative bacteria (AMR-GNB) among hospitalised patients can lead to new cases of carriage, infection and outbreaks, hence the need for early carrier identification. We aim to explore two key elements that may guide control policies for colonisation/infection in hospital settings: screening practices on admission to hospital wards and risk of developing infection from colonisation.

METHODS

We searched on PubMed, Scopus and Cochrane databases for studies published from 2010 up to 2021 reporting on adult patients hospitalised in high-income countries.

RESULTS

The search retrieved 11853 articles. After screening, 100 studies were included. Combining target patient groups and setting type, we identified six screening approaches. The most reported approach was all admitted patients to high-risk (HR) wards (49.4%). The overall prevalence of AMR-GNB was 13.8% (95%CI 9.3-19.0) with significant differences across regions and time. Risk of progression to infection among colonised patients was 11.0% (95%CI 8.0-14.3) and varied according to setting and pathogens' group (p value<0.0001), with higher values reported for Klebsiella species (18.1%; 95%CI 8.9-29.3).

CONCLUSIONS

While providing a comprehensive overview of the screening approaches, our study underlines the considerable burden of AMR-GNB colonisation and risk of progression to infection in hospitals by pathogen, setting and time.

Akim A, Chong PP. Approaches for Mitigating Microbial Biofilm-Related Drug Resistance: A Focus on Micro- and Nanotechnologies

Biofilms play an essential role in chronic and healthcare-associated infections and are more resistant to antimicrobials compared to their planktonic counterparts due to their (1) physiological state, (2) cell density, (3) quorum sensing abilities, (4) presence of extracellular matrix, (5) upregulation of drug efflux pumps, (6) point mutation and overexpression of resistance genes, and (7) presence of persister cells. The genes involved and their implications in antimicrobial resistance are well defined for bacterial biofilms but are understudied in fungal biofilms. Potential therapeutics for biofilm mitigation that have been reported include (1) antimicrobial photodynamic therapy, (2) antimicrobial lock therapy, (3) antimicrobial peptides, (4) electrical methods, and (5) antimicrobial coatings. These approaches exhibit promising characteristics for addressing the impending crisis of antimicrobial resistance (AMR). Recently, advances in the micro- and nanotechnology field have propelled the development of novel biomaterials and approaches to combat biofilms either independently, in combination or as antimicrobial delivery systems. In this review, we will summarize the general principles of clinically important microbial biofilm formation with a focus on fungal biofilms. We will delve into the details of some novel micro- and nanotechnology approaches that have been developed to combat biofilms and the possibility of utilizing them in a clinical setting.

Impact of Beta-Lactam Allergies on Selection of Antimicrobials in an Inpatient Setting Among Veteran Population

Purpose

Beta-lactam antibiotics are among the most common and widely used antibiotics. However, reported allergy to this class of antibiotics is also common, leading to the use of alternative broad-spectrum antibiotics by healthcare providers. This has led to the emergence of various negative health outcomes. The purpose of the study is to investigate the impact of using alternative antibiotics secondary to a beta-lactam allergy among U.S. veterans who have otherwise multiple comorbidities.

Methods

This retrospective observational analysis was conducted over a 5-year period (January 1, 2011 to December 31, 2016) at the Memphis Veterans Affairs Medical Center (VAMC). Admitted patients with a documented beta-lactam allergy were categorized to preferred or non-preferred status based on initial antibiotic therapy antibiotic, allergy history, published guidelines, and local antibiogram. Preferred therapy was defined as the optimal antibiotic treatment for a given indication based on patient allergy history, published Infectious Disease Society of America guidelines, and local antibiogram of Memphis VAMC. The therapy was classified as “non-preferred” if it did not satisfy the preferred therapy criteria. Non-preferred treatments were further assessed for appropriateness based on indication and patient-specific factors. Chi-square and Fisher’s exact tests were conducted to find a difference in rates of negative sequelae among patients receiving preferred vs. non-preferred treatments and appropriate vs. inappropriate treatments.

Findings

Of the 1806 admissions identified, data were collected on 95 unique patients with 147 different antibiotic regimens. There were 68 (52%) preferred treatment regimens and 64 (48%) non-preferred treatment regimens. Of the 64 non-preferred treatments, 43 (67%) were inappropriate. There was a statistically significant decrease in the number of adverse drug events and in the combined negative sequelae outcome among patients receiving preferred therapy vs. non-preferred therapy (2 vs. 12; P &lt; .01 and 11 vs. 23; P &lt; .01, respectively).

Implications

The receipt of non-preferred antibiotic therapy among veterans with a recorded beta-lactam allergy may be associated with an increased risk of developing negative outcomes. Among military personnel, removing unnecessary beta-lactam allergies would improve readiness with optimal antibiotic choices and avoidance of unnecessary risks, expediting return to full duty.

The Impact of Reported Beta-Lactam Allergy in Hospitalized Patients With Hematologic Malignancies Requiring Antibiotics

Background

Patients hospitalized with hematologic malignancy are particularly vulnerable to infection. The impact of reported beta-lactam (BL) allergy in this population remains unknown.

Methods

This was a retrospective cohort study of adult inpatients with hematologic malignancy admitted at 2 tertiary care hospitals from 2010 through 2015. The primary outcome was hospital length of stay (LOS) after administration of the first antibiotic. Secondary outcomes included readmission, mortality, complications, hospital charges, and antibiotic usage. Our goal was to define the impact of BL-only allergy (BLOA) label on clinical outcomes compared to those with no BL allergy (NBLA) in hematologic malignancy inpatients who required systemic antibiotics.

Results

In our cohort (n = 4671), 38.3% had leukemia, 4.9% had Hodgkin lymphoma, 36.1% had non-Hodgkin lymphoma, and 20.7% had multiple myeloma. Among patients, 35.1% reported antibiotic allergy, and 14.1% (n = 660) had BLOA (including 9.3% with penicillin-only allergy and 3.3% cephalosporin-only allergy). Patients with BLOA had longer median LOS compared to patients with NBLA (11.3 vs 7.6 days, P < .001), which remained significant after multivariable adjustment. Patients with BLOA also had significantly worse outcomes in terms of mortality rate at 30 days (7.6% vs 5.3%, P = .017) and 180 days (15.8% vs 12.2%, P = .013), 30-day readmission rate, Clostridium difficile rate, hospital charges ($223 046 vs $173 256, P < .001), antibiotic classes used, and antibiotic duration.

Conclusions

In hospitalized patients with hematologic malignancy, patients with reported BL allergy had worse clinical outcomes and higher healthcare cost than those without BL allergy label.

Don't Get Wound Up: Revised Fluoroquinolone Breakpoints for Enterobacteriaceae and Pseudomonas aeruginosa

Fluoroquinolones remain some of the more commonly prescribed antimicrobial agents in the United States, despite the wide array of reported side effects that are associated with their use. In 2019, the Clinical and Laboratory Standards Institute revised the fluoroquinolone antimicrobial susceptibility testing breakpoints for both Enterobacteriaceae and Pseudomonas aeruginosa This breakpoint revision was deemed necessary on the basis of pharmacokinetic and pharmacodynamic analyses suggesting that the previous breakpoints were too high, in addition to the inability of the previous breakpoints to detect low-level resistance to this antibiotic class. In this minireview, we review the published data in support of this revision, as well as the potential challenges that these breakpoint revisions are likely to pose for clinical laboratories.

High fluoroquinolone MIC is associated with fluoroquinolone treatment failure in urinary tract infections caused by fluoroquinolone susceptible Escherichia coli

Background

Suboptimal clinical response to fluoroquinolone (FQ) therapy has been clearly documented in patients with Salmonella typhi infection with reduced FQ susceptibility. However, the clinical impact of reduced FQ susceptibility on other infections including E. coli urinary tract infections (UTIs) has never been evaluated.

Methods

We conducted a retrospective cohort study of female patients with fluoroquinolone susceptible E. coli (FQSEC) UTIs who received FQ therapy at outpatient services within University of Pennsylvania Health System, Philadelphia. Exposed patients were those with high MIC-FQSEC UTIs (the levofloxacin MIC > 0.12 but ≤ 2 mg/L) while unexposed patients were those with low MIC-FQSEC UTIs (the levofloxacin MIC ≤ 0.12 mg/L). The primary treatment outcome was treatment failure within 10 weeks after initiation of FQ therapy.

Results

From May 2008 to April 2011, we enrolled 29 exposed patients and 246 unexposed patients. Two patients in each group experienced treatment failure; exposed vs. unexposed (6.9 vs. 0.8%; p = 0.06). Risk difference and risk ratio (RR) for treatment failure were 0.06 [95% CI −0.03–0.15; exact-p = 0.06] and 8.48 [95% CI 1.24–57.97; exact-p = 0.06], respectively. After adjusting for underlying cerebrovascular disease, the RR was 7.12 (95% CI 1.20–42.10; MH-p = 0.04).

Conclusion

Our study demonstrated the negative impact of reduced FQ susceptibility on the treatment response to FQ therapy in FQSEC UTIs. This negative impact may be more intensified in other serious infections. Future studies in other clinical situations should be conducted to fill the gap of knowledge.

Rectal Culture-Guided Targeted Antimicrobial Prophylaxis Reduces the Incidence of Post-Operative Infectious Complications in Men at High Risk for Infections Submitted to Transrectal Ultrasound Prostate Biopsy - Results of a Cross-Sectional Study

The role of rectal culture-guided antimicrobial prophylaxis (TAP) in reducing infectious complications (IC) after transrectal-ultrasound prostate biopsy (TRUSPBx) is conflicting. We assessed the prevalence of IC in a cohort of men at high risk for IC submitted to TRUSPBx and treated with either TAP or empirical prophylaxis (EAP). Data from 53 patients at high risk for IC undergoing TRUSPBx were collected. Patients who did not receive a rectal swab (RS) were treated with EAP with fluoroquinolones (FQs). Of those who received the RS, patients with FQ-susceptible organisms received ciprofloxacin while those with FQ-resistant organisms received TAP. Office visits were scheduled to investigate the rate of complication at day 7 and 30 after TRUSPBx. Comorbidities were scored with the Charlson Comorbidity Index (CCI). Descriptive statistics and logistic regression models detailed the association between clinical parameters and IC rate. Out of 53 men, 17 (32.1%) had RS while 36 (67.9%) did not. All RS cultures were positive for E. Coli and 4 (23.5%) reported FQ-resistant pathogens. Considering risk factors for IC, no difference was found in terms of CCI, rate of diabetes, UTIs or recent antibiotic utilization between groups. Overall, 12 (22.6%) men reported IC, with a greater proportion of them belonging to the group treated with EAP (30.6% vs 5.9%; p = 0.045). Of these, 9 (25.0%) patients, all treated with EAP, developed post biopsy UTIs. E. Coli sustained all UTIs and 7 (77.7%) were FQ resistant. At multivariable analysis, CCI≥1, a history of UTIs/prostatitis and recent antibiotic utilization (all p<0.04) were the most powerful predictors for ICs. In conclusion, we found that compared to EAP, TAP significantly reduces ICs, in men at high risk for post TRUSPBx IC. Patients at risk for IC, especially those with recent antibiotic utilization, CCI≥1 and a history of UTIs/prostatitis before biopsy, could benefit from TAP.

Contribution of target alteration, protection and efflux pump in achieving high ciprofloxacin resistance in Enterobacteriaceae

The study aims at revealing the comprehensive contribution of target alteration, target protection and efflux pump to the development of high level of ciprofloxacin (CIP) resistance in Enterobacteriaceae bacteria of environmental, clinical and poultry origins. Antibiotic susceptibility test was used to detect CIP resistant (CIPR) isolates and MIC_CIP was determined by broth microdilution method. The presence of qnrS gene was identified by PCR and Southern blot hybridization (SBH) confirmed their location. Checkerboard titration demonstrated the effect of NMP on CIP action. PCR followed by sequencing and in silico analysis revealed the contribution of mutations in acrR, marR and gyrA to CIPR development. Out of 152 isolates, 101 were detected as CIPR. Randomly selected 53 isolates (MIC_CIP 4–512 µg/mL) were identified as Escherichia spp. (26), Enterobacter spp. (7), Klebsiella spp. (5) and Salmonella spp. (15) and of them 31 isolates carried qnrS. qnrS harboring 18 highly CIPR isolates (MIC_CIP: 256–512 µg/mL) were selected for further study. SBH confirmed 7 isolates harbored qnrS gene in plasmids. The acrA, acrB and tolC were present in all 18 isolates and NMP had an additive (12-isolates) or synergistic (6-isolates) effect on CIP action. Most isolates contained double amino acid (aa) substitutions (S83L and D87N) in QRDR of GyrA resulting in an altered conformation of putative CIP binding pocket. However, some isolates contained single (S83L or S83Y) or no aa substitution but showed high CIPR implicating that the concerted action of three mechanisms is responsible for high CIPR with the most significant role of efflux pump.

Intensity and Mechanisms of Fluoroquinolone Resistance within the H30 and H30Rx Subclones of Escherichia coli Sequence Type 131 Compared with Other Fluoroquinolone-Resistant E. coli

The recent expansion of the H30 subclone of Escherichia coli sequence type 131 (ST131) and its CTX-M-15-associated H30Rx subset remains unexplained. Although ST131 H30 typically exhibits fluoroquinolone resistance, so do multiple other E. coli lineages that have not expanded similarly. To determine whether H30 isolates have more intense fluoroquinolone resistance than other fluoroquinolone-resistant E. coli isolates and to identify possible mechanisms, we determined the MICs for four fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin, and norfloxacin) among 89 well-characterized, genetically diverse fluoroquinolone-resistant E. coli isolates (48 non-H30 and 41 H30 [23 H30Rx and 18 H30 non-Rx]). We compared the MICs with the H30 and H30Rx status, the presence/number of nonsynonymous mutations in gyrA, parC, and parE, the presence of aac(6')-1b-cr (an aminoglycoside/fluoroquinolone agent-modifying enzyme), and the efflux pump activity (measured as organic solvent tolerance [OST]). Among 1,518 recent E. coli clinical isolates, ST131 H30 predominated clonally, both overall and among the fluoroquinolone-resistant isolates. Among the 89 study isolates, compared with non-H30 isolates, H30 isolates exhibited categorically higher MICs for all four fluoroquinolone agents, higher absolute ciprofloxacin and norfloxacin MICs, more nonsynonymous mutations in gyrA, parC, and parE (specifically gyrA D87N, parC E84V, and parE I529L), and a numerically higher prevalence of (H30Rx-associated) aac(6')-1b-cr but lower OST scores. All putative resistance mechanisms were significantly associated with the MICs [for aac(6')-1b-cr: ciprofloxacin and norfloxacin only]. parC D87N corresponded with ST131 H30 and parE I529L with ST131 generally. Thus, more intense fluoroquinolone resistance may provide ST131 H30, especially H30Rx [if aac(6')-1b-cr positive], with subtle fitness advantages over other fluoroquinolone-resistant E. coli strains. This urges both parsimonious fluoroquinolone use and a search for other fitness-enhancing traits within ST131 H30.

The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria

The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.

Risk factors for ambulatory urinary tract infections caused by high-MIC fluoroquinolone-susceptible Escherichia coli in women: results from a large case-control study

OBJECTIVES

The prevalence of high-MIC fluoroquinolone-susceptible Escherichia coli (FQSEC) has been increasing. These isolates are one step closer to full fluoroquinolone (FQ) resistance and may lead to delayed response to FQ therapy. Our study aimed to investigate the epidemiology of high-MIC FQSEC in ambulatory urinary tract infections (UTIs).

PATIENTS AND METHODS

A case-control study was conducted at outpatient services within the University of Pennsylvania Health System, Philadelphia. All female subjects with non-recurrent UTI caused by FQSEC (levofloxacin MIC < 4 mg/L) were enrolled. Cases were subjects with high-MIC FQSEC UTI (levofloxacin MIC >0.12 but < 4 mg/L) and controls were subjects with low-MIC FQSEC UTI (levofloxacin MIC ≤0.12 mg/L). Data on microbiology results and baseline characteristics were extracted from electronic medical records.

RESULTS

During the 3 year study period (May 2008-April 2011), 11 287 episodes of E. coli bacteriuria were identified. The prevalence of FQSEC, FQ-intermediate susceptible E. coli and FQ-resistant E. coli was 75.0%, 0.4% and 24.6%, respectively. A total of 2001 female subjects with FQSEC UTI were enrolled into our study (165 cases and 1836 controls). Independent risk factors for high-MIC FQ susceptibility included Asian race (OR = 2.92; 95% CI = 1.29-6.58; P = 0.02), underlying renal disease (OR = 2.18; 95% CI = 1.15-4.14; P = 0.02) and previous nitrofurantoin exposure (OR = 8.86; 95% CI = 1.95-40.29; P = 0.005).

CONCLUSIONS

Asian race, underlying renal disease and previous exposure to nitrofurantoin were identified as independent risk factors for high-MIC FQSEC. There may be some factors that are more common in Asians, which may result in the selection of high-MIC FQSEC. Further studies are necessary to explore these findings.

Activity of quinolone CP-115,955 against bacterial and human type II topoisomerases is mediated by different interactions

CP-115,955 is a quinolone with a 4-hydroxyphenyl at C7 that displays high activity against both bacterial and human type II topoisomerases. To determine the basis for quinolone cross-reactivity between bacterial and human enzymes, the activity of CP-115,955 and a series of related quinolones and quinazolinediones against Bacillus anthracis topoisomerase IV and human topoisomerase IIα was analyzed. Results indicate that the activity of CP-115,955 against the bacterial and human enzymes is mediated by different interactions. On the basis of the decreased activity of quinazolinediones against wild-type and resistant mutant topoisomerase IV and the low activity of quinolones against resistant mutant enzymes, it appears that the primary interaction of CP-115,955 with the bacterial system is mediated through the C3/C4 keto acid and the water-metal ion bridge. In contrast, the drug interacts with the human enzyme primarily through the C7 4-hydroxyphenyl ring and has no requirement for a substituent at C8 in order to attain high activity. Despite the fact that the human type II enzyme is unable to utilize the water-metal ion bridge, quinolones in the CP-115,955 series display higher activity against topoisomerase IIα in vitro and in cultured human cells than the corresponding quinazolinediones. Thus, quinolones may be a viable platform for the development of novel drugs with anticancer potential.

In vitro selection of resistance to pradofloxacin and ciprofloxacin in canine uropathogenic Escherichia coli isolates

This study explored and compared the mechanisms and selective concentration of resistance between a 3rd (pradofloxacin) and 2nd (ciprofloxacin) generation fluoroquinolone. Pradofloxacin- and ciprofloxacin-resistant mutants were selected by stepwise exposure of Escherichia coli (E. coli) to escalating concentrations of pradofloxacin and ciprofloxacin. The sequence of the quinolone resistance determining region (QRDR) and the transcriptional regulator soxS were analyzed, and efflux pump AcrAB-TolC activity was measured by quantitative real-time reverse transcription-PCR (qRT-PCR). First-step mutants reduced the fluoroquinolone sensitivity and one mutant bore a single substitution in gyrA. Four of six second-step mutants expressed ciprofloxacin resistance, and displayed additional mutations in gyrA and/or parC, while these mutants retained susceptibility to pradofloxacin. All the third-step mutants were fluoroquinolone resistant, and each expressed multidrug resistance (MDR) phenotypes. Further, they displayed resistance to all antibacterials tested except cefotaxime, ceftazidime and meropenem. The number of mutations in QRDR of gyrA and parC correlated with fluoroquinolone MICs. Mutations in parC were not common in pradofloxacin-associated mutants. Moreover, one second- and one third-step ciprofloxacin-associated mutants bore both mutations at position 12 (Ala12Ser) and 78 (Met78Leu) in the soxS gene, yet no mutations in the soxS gene were detected in the pradofloxacin-selected mutants. Altogether, these results demonstrated that resistance emerged relatively more rapidly in 2nd compared to 3rd generation fluoroquinolones. Point mutations in gyrA were a key mechanism of resistance to pradofloxacin, and overexpression of efflux pump gene acrB played a potential role in the emergence of MDR phenotypes identified in this study.

Bacillus anthracis GrlAV96A topoisomerase IV, a quinolone resistance mutation that does not affect the water-metal ion bridge

The rise in quinolone resistance is threatening the clinical use of this important class of broad-spectrum antibacterials. Quinolones kill bacteria by increasing the level of DNA strand breaks generated by the type II topoisomerases gyrase and topoisomerase IV. Most commonly, resistance is caused by mutations in the serine and acidic amino acid residues that anchor a water-metal ion bridge that facilitates quinolone-enzyme interactions. Although other mutations in gyrase and topoisomerase IV have been reported in quinolone-resistant strains, little is known regarding their contributions to cellular quinolone resistance. To address this issue, we characterized the effects of the V96A mutation in the A subunit of Bacillus anthracis topoisomerase IV on quinolone activity. The results indicate that this mutation causes an ∼ 3-fold decrease in quinolone potency and reduces the stability of covalent topoisomerase IV-cleaved DNA complexes. However, based on metal ion usage, the V96A mutation does not disrupt the function of the water-metal ion bridge. A similar level of resistance to quinazolinediones (which do not use the bridge) was seen. V96A is the first topoisomerase IV mutation distal to the water-metal ion bridge demonstrated to decrease quinolone activity. It also represents the first A subunit mutation reported to cause resistance to quinazolinediones. This cross-resistance suggests that the V96A change has a global effect on the structure of the drug-binding pocket of topoisomerase IV.

Role of the water-metal ion bridge in mediating interactions between quinolones and Escherichia coli topoisomerase IV

Although quinolones have been in clinical use for decades, the mechanism underlying drug activity and resistance has remained elusive. However, recent studies indicate that clinically relevant quinolones interact with Bacillus anthracis (Gram-positive) topoisomerase IV through a critical water–metal ion bridge and that the most common quinolone resistance mutations decrease drug activity by disrupting this bridge. As a first step toward determining whether the water–metal ion bridge is a general mechanism of quinolone–topoisomerase interaction, we characterized drug interactions with wild-type Escherichia coli (Gram-negative) topoisomerase IV and a series of ParC enzymes with mutations (S80L, S80I, S80F, and E84K) in the predicted bridge-anchoring residues. Results strongly suggest that the water–metal ion bridge is essential for quinolone activity against E. coli topoisomerase IV. Although the bridge represents a common and critical mechanism that underlies broad-spectrum quinolone function, it appears to play different roles in B. anthracis and E. coli topoisomerase IV. The water–metal ion bridge is the most important binding contact of clinically relevant quinolones with the Gram-positive enzyme. However, it primarily acts to properly align clinically relevant quinolones with E. coli topoisomerase IV. Finally, even though ciprofloxacin is unable to increase levels of DNA cleavage mediated by several of the Ser80 and Glu84 mutant E. coli enzymes, the drug still retains the ability to inhibit the overall catalytic activity of these topoisomerase IV proteins. Inhibition parallels drug binding, suggesting that the presence of the drug in the active site is sufficient to diminish DNA relaxation rates.

Emergence of quinolone resistance in the microbiota of hospitalized patients treated or not with a fluoroquinolone

BACKGROUND

Quinolone resistance is a major global clinical problem. It primarily emerges in microbiota under selective pressure. Studies evaluating the incidence and risk factors for carrying quinolone-resistant bacteria in hospitalized patients treated with fluoroquinolones (FQs) are lacking.

METHODS

We prospectively included hospitalized patients treated with FQs. Nasal, throat and rectal swabs were performed before FQ treatment, at the end of FQ treatment and 30 days later. A 'reference group' of patients not receiving FQs was also included to determine the rates of quinolone resistance acquisition not linked to FQ treatment. Prevalence and incidence of quinolone-resistant strains of nasal coagulase-negative staphylococci (CoNS) and Staphylococcus aureus, pharyngeal α-haemolytic streptococci and faecal Escherichia coli, and risk factors for emergence of quinolone resistance in FQ-treated patients were assessed.

RESULTS

Four-hundred and fifty-one FQ-treated patients were included, as well as 119 subjects in the 'reference group'. Emergence of quinolone resistance occurred in 110/213 (51.6%), 50/336 (14.9%), 53/290 (18.3%) and 46/336 (13.7%) of FQ-treated patients for CoNS, S. aureus, α-haemolytic streptococci and E. coli, respectively, significantly more than for reference patients for CoNS (23/65; P < 0.05), S. aureus (5/91; P < 0.02) and E. coli (4/84; P < 0.05), but not for α-haemolytic streptococci (15/70; P = 0.55). Emergence of resistance was not associated with the type of FQ received, the duration of therapy or the duration of hospital stay, but was associated with host factors such as immunosuppression and altered performance status.

CONCLUSIONS

FQs received during hospitalization account for high rates of emergence of resistance to FQs in clinically relevant bacteria from human microbiota, reflecting the important ecological impact of FQs. Host factors outweighed treatment or hospitalization characteristics as risk factors for carrying quinolone-resistant strains.

Modulation of Bacterial Multidrug Resistance Efflux Pumps of the Major Facilitator Superfamily

Bacterial infections pose a serious public health concern, especially when an infectious disease has a multidrug resistant causative agent. Such multidrug resistant bacteria can compromise the clinical utility of major chemotherapeutic antimicrobial agents. Drug and multidrug resistant bacteria harbor several distinct molecular mechanisms for resistance. Bacterial antimicrobial agent efflux pumps represent a major mechanism of clinical resistance. The major facilitator superfamily (MFS) is one of the largest groups of solute transporters to date and includes a significant number of bacterial drug and multidrug efflux pumps. We review recent work on the modulation of multidrug efflux pumps, paying special attention to those transporters belonging primarily to the MFS.

The effect of a hospital-wide urine culture screening intervention on the incidence of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella species

OBJECTIVE

Optimal strategies for limiting the transmission of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella spp (ESBL-EK) in the hospital setting remain unclear. The objective of this study was to evaluate the impact of a urine culture screening strategy on the incidence of ESBL-EK.

DESIGN

Prospective quasi-experimental study.

SETTING

Two intervention hospitals and one control hospital within a university health system from 2005 to 2009.

PATIENTS AND INTERVENTION

All clinical urine cultures with E. coli or Klebsiella spp were screened for ESBL-EK. Patients determined to be colonized or infected with ESBL-EK were placed in a private room with contact precautions. The primary outcome of interest was nosocomial ESBL-EK incidence in nonurinary clinical cultures (cases occurring more than 48 hours after admission). Changes in monthly ESBL-EK incidence rates were evaluated with mixed-effects Poisson regression models, with adjustment for institution-level characteristics (eg, total admissions).

RESULTS

The overall incidence of ESBL-EK increased from 1.42/10,000 patient-days to 2.16/10,000 patient-days during the study period. The incidence of community-acquired ESBL-EK increased nearly 3-fold, from 0.33/10,000 patient-days to 0.92/10,000 patient-days (P < .001). On multivariable analysis, the intervention was not significantly associated with a reduction in nosocomial ESBL-EK incidence (incidence rate ratio, 1.38 [95% confidence interval, 0.83-2.31]; P - .21).

CONCLUSIONS

Universal screening of clinical urine cultures for ESBL-EK did not result in a reduction in nosocomial ESBL-EK incidence rates, most likely because of increases in importation of ESBL-EK cases from the community. Further studies are needed on elucidating optimal infection control interventions to limit spread of ESBL-producing organisms in the hospital setting.

Exploring the contribution of efflux on the resistance to fluoroquinolones in clinical isolates of Escherichia coli

Resistance to ciprofloxacin in Escherichia coli is increasing parallel to increased use of fluoroquinolones both in The Netherlands and in other European countries. The objective was to investigate the contribution of active efflux and expression of outer membrane proteins (OMPs) in a collection of clinical E. coli isolates collected at a clinical microbiology department in a Dutch hospital. Forty-seven E. coli isolates a wide range of ciprofloxacin minimum inhibitory concentrations and known mutations in the quinolone resistance determining region were included. A fluorometric determination of bisbenzimide efflux was used two different efflux pump inhibitors and compared to quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for the expression levels of acrA, acrB, tolC, yhiV, and mdfA efflux pump genes and the OMPs ompF and ompX. Six isolates (12.7%) showed increased efflux. Although in 35 isolates (76%), overexpression of ≥1 efflux pump genes using qRT-PCR was present. Only the combined overexpression of acrAB-TolC and mdfA correlated with the phenotypic efflux assay using glucose/carbonyl cyanide m-chlorophenylhydrazone with glucose. Thus, efflux was involved in ciprofloxacin resistance in a limited number of E. coli isolates collected at a clinical microbiology department in a Dutch hospital complementing other resistance mechanisms.

Ciprofloxacin Resistance in Enterococcus faecalis Strains Isolated From Male Patients With Complicated Urinary Tract Infection

PURPOSE

Urinary tract infection (UTI) is one of the most prevalent bacterial infections, and fluoroquinolone therapy is a well-known standard regimen for UTI. The prevalence and risk factor analysis of fluoroquinolone resistance in enterococcal UTIs are not well documented. The aim of this study was to evaluate the antimicrobial susceptibility and risk factors for ciprofloxacin resistance in Enterococcus faecalis strains isolated from patients with complicated UTI.

MATERIALS AND METHODS

We evaluated 81 E. faecalis strains isolated from 81 male patients at a single teaching hospital over 3 years. The Vitek 2 automatic system was used for antimicrobial susceptibility analysis.

RESULTS

Antimicrobial resistance rates were rare for ampicillin/sulbactam, imipenem, and vancomycin in E. faecalis. Forty-six percent of the E. faecalis strains were resistant to levofloxacin, 47% were resistant to ciprofloxacin, and 58% were resistant to norfloxacin. E. faecalis strains were highly resistant to erythromycin (92%) and ftetracycline (96%). The risk factor analysis revealed that age intervals, the underlying diseases, catheterization, and the number of admissions did not increase the risk of ciprofloxacin resistance, whereas patients with hospital-acquired infection (odds ratio [OR], 18.15; 95% confidence interval [CI], 3.46 to 95.13; p=0.001), patients who were treated in a urological department (OR, 6.15; 95% CI, 1.5 to 25.41; p=0.012), and patients who were transferred from health care centers (OR, 7.393; 95% CI, 1.32 to 41.22; p=0.023) had an increased risk of ciprofloxacin resistance compared with the matched controls.

CONCLUSIONS

Ciprofloxacin is no longer a recommended therapy for E. faecalis from complicated UTI in men with risk factors. We suggest that ampicillin/sulbactam can be recommended as alternatives for treating ciprofloxacin-resistant E. faecalis strains associated with UTI in Korea.

Defining relatedness in studies of transmission of antimicrobial-resistant organisms: variability in definitions across studies and impact of different approaches on study conclusions

OBJECTIVE

Comparison of studies evaluating patient-to-patient transmission of organisms is difficult, given the lack of standardized criteria. We used fluoroquinolone-resistant Escherichia coli (FQREC) as a model to characterize variability in definitions of relatedness across studies and to evaluate the resultant impact on study conclusions.

DESIGN

Narrative review and cohort study.

METHODS

The narrative review compared relatedness criteria across studies of FQREC. Additionally, an existing database was used to compare relatedness of isolates on the basis of molecular criteria alone versus molecular plus clinical criteria with different temporal cutoffs (hospitalization overlap of ≥1 day or allowance for nonoverlap of hospitalization dates of ≤7 days or ≤30 days).

RESULTS

Forty-six articles met narrative review inclusion criteria. Sixteen studies exclusively utilized molecular criteria to define relatedness. Thirty studies included molecular and clinical criteria. Of these, 6 included temporal data (ie, time period of isolate identification), 10 included patient location, and 14 included proximity and temporal criteria. For the database analysis, 353 patients were colonized with FQREC. There were 2 main clusters containing 48 and 17 related isolates within 49 pulsed-field gel electrophoresis types. Among the clusters, 18.4% of isolates were related by molecular criteria. Incorporating clinical criteria, fewer isolates were considered related: 5.7% of isolates using 30-day criteria, 3.1% using 7-day criteria, and 1.4% using 1-day overlap.

CONCLUSIONS

There is considerable variability in definitions of relatedness of FQREC. Utilizing molecular criteria alone to define relatedness overestimates transmission compared with definitions including clinical criteria. Standard definitions of relatedness in studies of antimicrobial-resistant organisms are needed.

Porter domain opening and closing motions in the multi-drug efflux transporter AcrB

Acriflavine resistance protein B acts as the active transporter in the multi-drug efflux pump Acriflavine resistance proteins A / B - Tolerance to colicins protein in Escherichia coli. Within the same reaction cycle intermediate all Acriflavine resistance protein B X-ray structures display highly similar conformations of the substrate-recruiting and transporting porter domain. To assess if this structural homogeneity is an intrinsic feature of Acriflavine resistance protein B or stems from other causes we performed a series of six independent, unbiased 100 ns molecular dynamics simulations of membrane-embedded, asymmetric, substrate-free wild type Acriflavine resistance protein B in a 150 mM NaCl solution. We find the porter domain more flexible than previously assumed displaying clear opening and closing motions of the proximal binding pocket (L and T-state) and the exit of the drug transport channels (O-intermediate). Concurrently the hydrophobic binding pocket favors a closed conformation in all three protomers. Our findings suggest that the conformational homogeneity seen in the crystal structures is likely an effect of bound but structurally unresolved substrate. Our simulations further imply that each of the known three reaction cycle intermediates occurs in at least two variants, the Thr676 loop independently regulates porter domain access and likely plays a key role in substrate transport. On a 100 ns time scale we find no evidence supporting the proposed LLL resting state in the absence of substrate. If the proximal binding pocket dynamics have an inhibiting effect on Acriflavine resistance protein B pump activity lowering the life time of substrate-accessible conformations, the observed dynamics could provide a structural explanation for the Acriflavine resistance protein B activity-enhancing effect of the adaptor protein Acriflavine resistance protein A stabilizing PC1 and PC2 subdomain orientations.

Diversity of individual dynamic patterns of emergence of resistance to quinolones in Escherichia coli from the fecal flora of healthy volunteers exposed to ciprofloxacin

BACKGROUND

Emergence of quinolone-resistant Escherichia coli (QREC) is an increasing clinical challenge mostly originating in fecal microbiota. The dynamics of the emergence of QREC in feces from individuals exposed to ciprofloxacin is unknown.

METHODS

A total of 48 healthy volunteers received oral ciprofloxacin for 14 days. Fecal specimens were collected on days 0, 8, 14, and 42. Subpopulations of QREC were detected on selective agar, genetically characterized, and compared with quinolone-susceptible E. coli (QSEC) strains collected on different days.

RESULTS

On day 42, 34 subjects carried QSEC, and 14 carried QREC. Of the 14 who carried QREC, 9 carried quinolone-susceptible E. coli on day 0, 1 carried E. coli with a lower level of quinolone resistance on day 0, and 4 carried E. coli with similar levels of resistance and RAPD-genotypes on days 0 and 42. No plasmid acquisition and no selection of resistant mutants from the initial microbiota was evidenced in any case.

CONCLUSIONS

In QREC emerging under ciprofloxacin pressure in the fecal microbiota, no proof of selection of quinolone-resistant mutants from the initial microbiota was evidenced, suggesting that QREC strains on day 42 were either present at undetectable levels in the initial microbiota or that exogenous acquisition of QREC strains occurred. Clinical Trials Registration. NCT00190151.

Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria

Antibiotic resistance mechanisms reported in Gram-negative bacteria are causing a worldwide health problem. The continuous dissemination of 'multidrug-resistant' (MDR) bacteria drastically reduces the efficacy of our antibiotic 'arsenal' and consequently increases the frequency of therapeutic failure. In MDR bacteria, the overexpression of efflux pumps that expel structurally unrelated drugs contributes to the reduced susceptibility by decreasing the intracellular concentration of antibiotics. During the last decade, several clinical data have indicated an increasing involvement of efflux pumps in the emergence and dissemination of resistant Gram-negative bacteria. It is necessary to clearly define the molecular, functional and genetic bases of the efflux pump in order to understand the translocation of antibiotic molecules through the efflux transporter. The recent investigation on the efflux pump AcrB at its structural and physiological levels, including the identification of drug affinity sites and kinetic parameters for various antibiotics, may pave the way towards the rational development of an improved new generation of antibacterial agents as well as efflux inhibitors in order to efficiently combat efflux-based resistance mechanisms.

Prevalence and risk factors for quinolone resistance among Escherichia coli strains isolated from males with community febrile urinary tract infection

The purpose of this study was to evaluate the prevalence and clinical risk factors for quinolone resistance (QR) in E. coli strains from males with febrile urinary tract infection (FUTI). An ambispective cross-sectional study was performed in which we evaluated 153 males with a community FUTI caused by E. coli. Among the 153 FUTI episodes, 101 (66%) were due to quinolone susceptible E. coli strains while 52 (34%) were caused by QR E. coli strains. In the univariate analysis QR was associated with older age, higher Charlson scores, dementia, past UTI, urinary tract abnormalities, previous antibiotic use, particularly with fluoroquinolones (FQ), a healthcare-associated (HA)-UTI (HA-UTI) and to four of the components included in the definition of HA-UTI: hospital admission, nursing home residence, indwelling urethral catheter and invasive urinary instrumentation. In the multivariate analysis, HA-UTI (OR 3.82, 95% CI 1.3-11.24; P 0.015) and use of antimicrobials in the previous month (OR 5.82, 95% CI 2.3-14.88; P < 0.001) mainly with FQ (OR 13.97, 95% CI 2.73-71.53; P 0.002) were associated with QR. To have a HA-UTI and a previous use of FQ in the preceding month were strong risk factors for QR E. coli, and thus empirical antimicrobial treatment with quinolones should be avoided in these patients.

Modelling the impact of antibiotic use on antibiotic-resistant Escherichia coli using population-based data from a large hospital and its surrounding community

OBJECTIVES

To determine the temporal relationship between antibiotic use and incidence of antibiotic-resistant Escherichia coli in both the inpatient and outpatient setting of a large urban area.

METHODS

A retrospective observational time-series analysis was performed to evaluate the incidence of non-duplicate clinical isolates of E. coli resistant to ciprofloxacin, trimethoprim/sulfamethoxazole and cefepime from January 2000 through December 2007, combined with a transfer function model of aggregated data on antibiotic use in both settings obtained from the hospital's pharmacy and outpatient billing offices.

RESULTS

Ciprofloxacin resistance increased from 6.0% (2000) to 15.4% (2007; P<0.0001) and cefepime resistance from 0.9% (2002) to 3.2% (2007; P=0.01). Trimethoprim/sulfamethoxazole resistance remained stable (23.7%-25.8%). Total antibiotic use increased in both settings, while fluoroquinolone use increased significantly only among outpatients. A temporal effect between fluoroquinolone resistance in community E. coli isolates and outpatient use of ciprofloxacin (immediate effect and time lag 1 month) and moxifloxacin (time lag 4 months) was observed, explaining 51% of the variance over time. The incidence of cefepime resistance in E. coli was correlated with ciprofloxacin use in the inpatient (lag 1 month) and outpatient (lag 4 months) settings and with the use of ceftriaxone (lag 0 month), piperacillin/tazobactam (3 months) and cefepime (3 months) in the hospital (R2=51%).

CONCLUSIONS

These results support efforts to reduce prescribing of fluoroquinolones for control of resistant E. coli including extended-spectrum β-lactamase producers and show the added value of time-series analysis to better understand the interaction between community and hospital antibiotic prescribing and its spill-over effect on antibiotic resistance.