Urinary Tract Physiological Conditions Promote Ciprofloxacin Resistance in Low-Level-Quinolone-Resistant Escherichia coli

Tackling catheter-associated urinary tract infections with next-generation antimicrobial technologies

Urinary catheters and other medical devices associated with the urinary tract such as stents are major contributors to nosocomial urinary tract infections (UTIs) as they provide an access path for pathogens to enter the bladder. Considering that catheter-associated urinary tract infections (CAUTIs) account for approximately 75% of UTIs and that UTIs represent the most common type of healthcare-associated infections, novel anti-infective device technologies are urgently required. The rapid rise of antimicrobial resistance in the context of CAUTIs further highlights the importance of such preventative strategies. In this review, the risk factors for pathogen colonization in the urinary tract are dissected, taking into account the nature and mechanistics of this unique environment. Moreover, the most promising next-generation preventative strategies are critically assessed, focusing in particular on anti-infective surface coatings. Finally, emerging approaches in this field and their likely clinical impact are examined.

Acidic Urine pH and Clinical Outcome of Lower Urinary Tract Infection in Kidney Transplant Recipients Treated with Ciprofloxacin and Fosfomycin

Different factors, including antimicrobial resistance, may diminish the effectiveness of antibiotic therapy, challenging the management of post-transplant urinary tract infection (UTI). The association of acidic urine pH with microbiological and clinical outcomes was evaluated after fosfomycin or ciprofloxacin therapy in 184 kidney transplant recipients (KTRs) with UTI episodes by Escherichia coli (N = 115) and Klebsiella pneumoniae (N = 69). Initial urine pH, antimicrobial therapy, and clinical and microbiological outcomes, and one- and six-month follow-up were assessed. Fosfomycin was prescribed in 88 (76.5%) E. coli and 46 (66.7%) K. pneumoniae UTI episodes in the total cohort. When the urine pH ≤ 6, fosfomycin was prescribed in 60 (52.2%) E. coli and 29 (42.0%) K. pneumoniae. Initial urine pH ≤ 6 in E. coli UTI was associated with symptomatic episodes (8/60 vs. 0/55, p = 0.04) at one-month follow-up, with a similar trend in those patients receiving fosfomycin (7/47 vs. 0/41, p = 0.09). Acidic urine pH was not associated with microbiological or clinical cure in K. pneumoniae UTI. At pH 5, the ciprofloxacin MIC90 increased from 8 to >8 mg/L in E. coli and from 4 to >8 mg/L in K. pneumoniae. At pH 5, the fosfomycin MIC90 decreased from 8 to 4 mg/L in E. coli and from 512 to 128 mg/L in K. pneumoniae. Acidic urine is not associated with the microbiological efficacy of fosfomycin and ciprofloxacin in KTRs with UTI, but it is associated with symptomatic UTI episodes at one-month follow-up in E. coli episodes.

Urinary pH and antibiotics, choose carefully. A systematic review

Uncomplicated urinary tract infection (UTI) is the most common bacterial infection in women. Since 1948, the relationship between urinary pH and antibiotics (ABs) has been established. We aimed to search for the best urinary pH for each family of antibiotics and to assess whether pH changes bacterial susceptibility to them. We included in vitro research and in vivo studies including one or more bacterial species and tested the effect of one or more ABs at different pH values. We also included randomized controlled clinical trials (RCTs) in uncomplicated UTI (EAU guidelines 2019 definition), choosing the ABs based on urinary pH or using an antibiotic plus urinary pH modifiers (L-methionine, vitamin C…) vs. an antibiotic and a placebo. Quadas-2 tool was used as a quality assessment of the studies and PRISMA set of items for systematic reviews. Two authors independently screened and evaluated the papers, while two additional authors individually repeated the search. A fifth researcher acted as an arbiter, and another author collaborated as a hospital pharmaceutical consultant. Alkaline-friendly antibiotics are most fluoroquinolones, aminoglycosides, trimethoprim. Acidic-friendly antibiotics are fosfomycin, tetracycline, nitrofurantoin and some β-lactams. We suggest performing urine cultures with antibiogram tests, in both acidic and alkaline media, to define the bacterial susceptibility profile. There is insufficient in vivo evidence to support whether choosing an antibiotic based on a patient's urinary pH or adding urinary pH modifiers will lead to a higher cure rate.

QUIRMIA-A Phenotype-Based Algorithm for the Inference of Quinolone Resistance Mechanisms in Escherichia coli

OBJECTIVES

Quinolone resistance in Escherichia coli occurs mainly as a result of mutations in the quinolone-resistance-determining regions of gyrA and parC, which encode the drugs' primary targets. Mutational alterations affecting drug permeability or efflux as well as plasmid-based resistance mechanisms can also contribute to resistance, albeit to a lesser extent. Simplifying and generalizing complex evolutionary trajectories, low-level resistance towards fluoroquinolones arises from a single mutation in gyrA, while clinical high-level resistance is associated with two mutations in gyrA plus one mutation in parC. Both low- and high-level resistance can be detected phenotypically using nalidixic acid and fluoroquinolones such as ciprofloxacin, respectively. The aim of this study was to develop a decision tree based on disc diffusion data and to define epidemiological cut-offs to infer resistance mechanisms and to predict clinical resistance in E. coli. This diagnostic algorithm should provide a coherent genotype/phenotype classification, which separates the wildtype from any non-wildtype and further differentiates within the non-wildtype.

METHODS

Phenotypic susceptibility of 553 clinical E. coli isolates towards nalidixic acid, ciprofloxacin, norfloxacin and levofloxacin was determined by disc diffusion, and the genomes were sequenced. Based on epidemiological cut-offs, we developed a QUInolone Resistance Mechanisms Inference Algorithm (QUIRMIA) to infer the underlying resistance mechanisms responsible for the corresponding phenotypes, resulting in the categorization as "susceptible" (wildtype), "low-level resistance" (non-wildtype) and "high-level resistance" (non-wildtype). The congruence of phenotypes and whole genome sequencing (WGS)-derived genotypes was then assigned using QUIRMIA- and EUCAST-based AST interpretation.

RESULTS

QUIRMIA-based inference of resistance mechanisms and sequencing data were highly congruent (542/553, 98%). In contrast, EUCAST-based classification with its binary classification into "susceptible" and "resistant" isolates failed to recognize and properly categorize low-level resistant isolates.

CONCLUSIONS

QUIRMIA provides a coherent genotype/phenotype categorization and may be integrated in the EUCAST expert rule set, thereby enabling reliable detection of low-level resistant isolates, which may help to better predict outcome and to prevent the emergence of clinical resistance.

Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms

The contribution of biofilms to virulence and as a barrier to treatment is well-established for Staphylococcus aureus and Enterococcus faecalis, both nosocomial pathogens frequently isolated from biofilm-associated infections. Despite frequent co-isolation, their interactions in biofilms have not been well-characterized. We report that in combination, these two species can give rise to augmented biofilms biomass that is dependent on the activation of E. faecalis aerobic respiration. In E. faecalis, respiration requires both exogenous heme to activate the cydAB-encoded heme-dependent cytochrome bd, and the availability of O₂. We determined that the ABC transporter encoded by cydDC contributes to heme import. In dual species biofilms, S. aureus provides the heme to activate E. faecalis respiration. S. aureus mutants deficient in heme biosynthesis were unable to augment biofilms whereas heme alone is sufficient to augment E. faecalis mono-species biofilms. Our results demonstrate that S. aureus-derived heme, likely in the form of released hemoproteins, promotes E. faecalis biofilm formation, and that E. faecalis gelatinase activity facilitates heme extraction from hemoproteins. This interspecies interaction and metabolic cross-feeding may explain the frequent co-occurrence of these microbes in biofilm-associated infections.

Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis

Background

Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream.

Case presentation

The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants.

Objectives

To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches.

Results

Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin.

Conclusions

Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00521-7.

Machine learning based urinary pH sensing using polyaniline deposited paper device and integration of smart web app interface: Theory to application

The present study employs density functional theory-based first principle calculation to investigate the electron transport properties of polyaniline following exposure to acidic and alkaline pH. In-situ deposited polyaniline-based paper device maintains emeraldine salt form while it is exposed to acidic pH and converts to emeraldine base when it is subjected to alkaline pH solutions. These structural changes at acidic and alkaline pH are validated experimentally by Raman spectra. Furthermore, the Raman spectra computed from density functional theory are validated with the experimental spectra. The changes in the theoretical energy band gap of polyaniline obtained from first principle calculations were correlated with the changes in the experimental impedimetric response of the sensor after exposure to acidic and alkaline solutions. Finally, the impedimetric responses were used to predict urine pH through a machine learning based smart and interactive web application. Different machine learning based regression models were implemented to acquire the best possible outcome. Gradient Boosting Regressor with least square loss model was selected as it showed lowest mean square, mean absolute, and root mean square error than other models. The smart sensing platform successfully predicts the unknown pH of urine samples with an average accuracy of more than 98%. The locally deployed smart web app can be accessed within a local area network by the end-user, which holds promise towards effective detection of urinary pH.

Alkaline Urine in the Emergency Department Predicts Nitrofurantoin Resistance

BACKGROUND

The Proteeae group (i.e., Proteus species, Morganella morganii, and Providencia species) frequently causes urinary tract infections (UTIs) and is generally resistant to nitrofurantoin. Proteeae species can produce urease, which can increase urine pH.

OBJECTIVE

Our aim was to determine whether higher urine pH in the emergency department is associated with nitrofurantoin resistance.

METHODS

A single health system database of emergency department patients aged 18 years and older who received urinalysis between April 18, 2014, and March 7, 2017, was examined using χ² test and multivariable regression analysis.

RESULTS

Of 67,271 urine samples analyzed, 13,456 samples grew a single bacterial species. Urine cultures growing the Proteeae group were associated with significantly more alkaline urine than other bacteriuria cultures (odds ratio [OR] 2.20, 95% confidence interval [CI] 2.06-2.36; p < 0.001). The Proteeae species represented 4.4% of urine samples at pH 5-7, 24.4% at pH 8-9, and 40.0% at pH 9. At urine pH 5-7, 80.4% of urine samples were sensitive to nitrofurantoin; however, this percentage decreased to 66.1% for urine pH 8-9 and 54.6% for urine pH 9. Nitrofurantoin had the highest OR (2.10, 95% CI 1.85-2.39) among cefazolin, ciprofloxacin, and trimethoprim/sulfamethoxazole for bacteriuria sensitive to those antibiotics at urine pH 5-7. At urine pH 8-9 and 9, nitrofurantoin had the lowest OR among the antibiotics: 0.48 (95% CI 0.42-0.54) and 0.31 (95% CI 0.24-0.40), respectively (p < 0.001 for both).

CONCLUSIONS

Urine pH of 8 or higher is associated with high rates of nitrofurantoin resistance.

Genome-Wide Screening and Characterization of Genes Involved in Response to High Dose of Ciprofloxacin in Escherichia coli

The global emergence of antibiotic resistance, especially in Gram-negative bacteria, is an urgent threat to public health. Inevitably, considering its extensive use and misuse, resistance toward ciprofloxacin has increased in almost all clinically relevant bacteria. This study aimed to investigate the transcriptome changes at a high concentration of ciprofloxacin in Escherichia coli. In brief, 1,418 differentially expressed genes (DEGs) were identified, from which 773 genes were upregulated by ciprofloxacin, whereas 651 genes were downregulated. Enriched biological pathways reflected the upregulation of biological processes such as DNA damage and repair system, toxin/antitoxin systems, formaldehyde detoxification system. With kyoto encyclopedia of genes and genomes pathway analysis, higher expressed DEGs were associated with "LPS biosynthesis," "streptomycin biosynthesis," and "polyketide sugar unit biosynthesis." Lower expressed DEGs were associated with "biosynthesis of amino acids" and "flagellar assembly" pathways. After treatment of ciprofloxacin, lipopolysaccharide (LPS) release was increased by two times, and the gene expression level of LPS synthesis was elevated (p < 0.05) in both reference and clinical strains. Our results demonstrated that transient exposure to high-dose ciprofloxacin is a double-edged sword. Cautions should be taken when administering high-dose antibiotic treatment for infectious diseases.

Antibacterial activity of apramycin at acidic pH warrants wide therapeutic window in the treatment of complicated urinary tract infections and acute pyelonephritis

Background

The clinical-stage drug candidate EBL-1003 (apramycin) represents a distinct new subclass of aminoglycoside antibiotics for the treatment of drug-resistant infections. It has demonstrated best-in-class coverage of resistant isolates, and preclinical efficacy in lung infection models. However, preclinical evidence for its utility in other disease indications has yet to be provided. Here we studied the therapeutic potential of EBL-1003 in the treatment of complicated urinary tract infection and acute pyelonephritis (cUTI/AP).

Methods

A combination of data-base mining, antimicrobial susceptibility testing, time-kill experiments, and four murine infection models was used in a comprehensive assessment of the microbiological coverage and efficacy of EBL-1003 against Gram-negative uropathogens. The pharmacokinetics and renal toxicology of EBL-1003 in rats was studied to assess the therapeutic window of EBL-1003 in the treatment of cUTI/AP.

Findings

EBL-1003 demonstrated broad-spectrum activity and rapid multi-log CFU reduction against a phenotypic variety of bacterial uropathogens including aminoglycoside-resistant clinical isolates. The basicity of amines in the apramycin molecule suggested a higher increase in positive charge at urinary pH when compared to gentamicin or amikacin, resulting in sustained drug uptake and bactericidal activity, and consequently in potent efficacy in mouse infection models. Renal pharmacokinetics, biomarkers for toxicity, and kidney histopathology in adult rats all indicated a significantly lower nephrotoxicity of EBL-1003 than of gentamicin.

Interpretation

This study provides preclinical proof-of-concept for the efficacy of EBL-1003 in cUTI/AP. Similar efficacy but lower nephrotoxicity of EBL-1003 in comparison to gentamicin may thus translate into a higher safety margin and a wider therapeutic window in the treatment of cUTI/API.

Funding

A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.

Characterization of Plasmid-Mediated Quinolone Resistance and Serogroup Distributions of Uropathogenic Escherichia coli among Iranian Kidney Transplant Patients

Introduction

Urinary tract infection (UTI) is one of the most frequent infections in kidney transplant patients (KTPs). This infection is mainly caused by uropathogenic Escherichia coli (UPEC). Plasmid-mediated quinolone resistance (PMQR) was also increasingly identified in UPEC. This study proposed to investigate the frequency of quinolone-resistance plasmid genes and the O-antigen serogroup among UPEC isolated from KTPs and non-KTP with UTI.

Methods

Totally, 114 UPEC isolates from 49 KTPs and 65 non-KTPs patients diagnosed with an UPEC-associated UTI were obtained from June 2019 to December 2019 at three laboratory centers in Isfahan, Iran. The isolates were confirmed through phenotypic and genotypic methods. Moreover, the antimicrobial susceptibility test to nalidixic acid, ciprofloxacin, norfloxacin, and ofloxacin was performed using a disk diffusion method. The presence of the qnr gene as well as the serogroup distribution was identified using the PCR method.

Result

According to data, the distribution of O1, O2, O4, O16, and O25 serogroups were 3.5%, 2.6, 3.5, 3.5, and 20.2%, respectively. Antibiotic susceptibility pattern revealed that the highest and lowest resistance rates were to nalidixic acid (69.3%) and norfloxacin (43.9%), respectively. Also, the frequency of qnrS and qnrB genes were 33.3% and 15.8%, respectively, while none of the isolates was found to be positive for the qnrA gene. There was no significant association between the presence of qnr genes and higher antibiotic resistance.

Conclusion

This study recognized that the qnrS gene, O25 serotype, and resistance to nalidixic acid had the highest frequencies in UPEC strains isolated from UTI patients.

Plasmidic Fluoroquinolone Resistance Genes in Fluoroquinolone-Resistant and/or Extended Spectrum Beta-Lactamase-Producing Escherichia coli Strains Isolated from Pediatric and Adult Patients Diagnosed with Urinary Tract Infection

Escherichia coli is the leading etiological agent of community-acquired urinary tract infection (UTI). Fluoroquinolones have long been the choice of empirical treatment for UTIs. Plasmid-mediated fluoroquinolone-resistance (PMFR) is important not only for conferring resistance to fluoroquinolones but also because of the presence of PMFR genes on plasmids carrying genes encoding resistance to other antimicrobials. In this study, we aimed at investigating the frequency of PMFR genes in fluoroquinolone-resistant and/or expanded spectrum beta-lactamase (ESBL)-producing E. coli strains isolated from pediatric and adult patients diagnosed with UTI. E. coli strains isolated from urine cultures of 141 adult and 117 pediatric outpatients were evaluated. Antimicrobial susceptibilities were interpreted according to the EUCAST criteria. The presence of PMFR genes (qnrA, qnrB, qnrC, qnrS, qepA, aac(6')-Ib, and aac(6')-Ib-cr) was investigated by multiplex PCR analysis. One hundred-three (73.05%) adult and 92 (78.63%) pediatric isolates were fluoroquinolone resistant and/or ESBL producers. One third (92/258) of all isolates carried at least one PMFR gene, the most prevalent one being qnrS (67.4%). None of the isolates carried qnrC and qepA genes. PMFR determinants were found to be widespread among adult and pediatric isolates. Rational antimicrobial use is crucial for prevention of resistance in both adult and pediatric populations.

Urinary Tract Conditions Affect Fosfomycin Activity against Escherichia coli Strains Harboring Chromosomal Mutations Involved in Fosfomycin Uptake

The steps by which Escherichia coli strains harboring mutations related to fosfomycin (FOS) resistance arise and spread during urinary tract infections (UTIs) are far from being understood. The aim of this study was to evaluate the effects of urine, pH, and anaerobiosis on FOS activity against a set of isogenic strains carrying the most prevalent chromosomal mutations conferring FOS resistance (ΔuhpT, ΔglpT, ΔcyaA, and ΔptsI), either singly or in combination. We also studied fosfomycin-resistant E. coli clinical isolates from patients with UTI. Our results demonstrate that urinary tract physiological conditions might have a profound impact on FOS activity against strains with chromosomal FOS resistance mutations. Specifically, acidic pH values and anaerobiosis convert most of the strains categorized as resistant to fosfomycin according to the international guidelines to a susceptible status. Therefore, urinary pH values may have practical interest in the management of UTIs. Finally, our results, together with the high fitness cost associated with FOS resistance mutations, might explain the low prevalence of fosfomycin-resistant E. coli variants in UTIs.

Pharmacodynamics of Finafloxacin, Ciprofloxacin, and Levofloxacin in Serum and Urine against TEM- and SHV-Type Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae Isolates from Patients with Urinary Tract Infections

The pharmacodynamics of finafloxacin, ciprofloxacin, and levofloxacin against extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae isolates were compared. Since quinolones lose activity in acidic media, and particularly in urine, their activities were tested in parallel under conventional conditions and in acidic artificial urine. For this purpose, TEM- and SHV-type ESBL-producing Escherichia coli and Klebsiella pneumoniae strains and their wild-type counterparts were exposed in a modified Grasso model to simulated concentrations of drugs in serum and urine following oral doses of either finafloxacin at 800 mg once a day (q.d.), immediate-release ciprofloxacin at 500 mg twice a day (b.i.d.), extended-release ciprofloxacin at 1,000 mg q.d., or levofloxacin at 500 or 750 mg q.d. The concentrations of the drugs in urine were fitted by compartmental modeling. Bacteria were cultivated in Mueller-Hinton broth (MHB) at pH 7.2 or 5.8 or in artificial urine at pH 5.8. Bacteria were counted every 2 h until 10 h and at 24 h; the areas under the bacterial-count-versus-time curves were calculated. It was found that finafloxacin eliminated all strains within 2 h under all the conditions studied. At all doses studied, ciprofloxacin and levofloxacin were highly active against wild-type strains in MHB at pH 7.2 but lost activity in MHB, and particularly in urine, at pH 5.8. Viable counts of ESBL producers were reduced for 6 to 8 h by 3 log10 titers, but the bacteria regrew thereafter. Ciprofloxacin and levofloxacin were almost inactive against the SHV producer grown in artificial urine. We conclude that pharmacodynamic models using artificial urine may mirror the physiology of urinary tract infections more closely than those using conventional media. In contrast to ciprofloxacin and levofloxacin, finafloxacin gained activity in this model at an acidic pH, maintained activity in artificial urine, and was active against TEM and SHV producers.

Plasmidic qnr Genes Confer Clinical Resistance to Ciprofloxacin under Urinary Tract Physiological Conditions

Escherichia coli variants expressing plasmid-mediated qnr genes are usually susceptible to fluoroquinolones by standard susceptibility testing. Here we show that, under specific urinary tract physiological conditions, susceptible laboratory and clinical strains harboring qnr determinants become fully resistant to ciprofloxacin (CIP). Therefore, physiological conditions, mainly urine pH values, should be considered when performing susceptibility testing of CIP activity against E. coli in treating urinary tract infection (UTI) and for selecting appropriate antibiotics for UTI treatment.