Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.

Parallel Evolution to Elucidate the Contributions of PA0625 and parE to Ciprofloxacin Sensitivity in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous pathogen that causes a wide range of acute and chronic infections. Ciprofloxacin, one of the first-line fluoroquinolone class antibiotics, is commonly used for the treatment of P. aeruginosa infections. However, ciprofloxacin-resistant P. aeruginosa is increasingly reported worldwide, making treatment difficult. To determine resistance-related mutations, we conducted an experimental evolution using a previously identified ciprofloxacin-resistant P. aeruginosa clinical isolate, CRP42. The evolved mutants could tolerate a 512-fold higher concentration of ciprofloxacin than CRP42. Genomic DNA reference mapping was performed, which revealed mutations in genes known to be associated with ciprofloxacin resistance as well as in those not previously linked to ciprofloxacin resistance, including the ParE^R586W substitution and PA0625 frameshift insertion. Simulation of the ParE^R586W substitution and PA0625 frameshift insertion by gene editing in CRP42 and the model strain PAO1 demonstrated that while the PA0625 mutation does contribute to resistance, mutation in the ParE^R586W does not contribute to resistance but rather affects tolerance against ciprofloxacin. These findings advance our understanding of ciprofloxacin resistance in P. aeruginosa.

Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland

Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIP^R) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIP^R. High- and low-level ciprofloxacin resistance among CIP^R isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.

Penicillin- and Ciprofloxacin-Resistant Invasive Neisseria meningitidis Isolates from Japan

Neisseria meningitidis causes a life-threatening invasive meningococcal disease (IMD). Isolates resistant to antibiotics, such as penicillin, ceftriaxone, and ciprofloxacin that are recommended for the treatment of IMD patients and their close contacts have been serious public health concerns globally. However, susceptibility profiles to critically important antibiotics and the genetic characteristics of isolates possessing antibiotic resistance are extremely limited as IMD incidence is low in Japan. We assessed the susceptibility profiles of 87 randomly selected, sterile site-derived N. meningitidis strains isolated from hospitals nationwide, recovered between April 1998 and March 2018 in Japan, to seven antibiotics. As a result, we demonstrated, for the first time, that the isolates remained highly susceptible to ceftriaxone, meropenem, azithromycin, ciprofloxacin, chloramphenicol, and rifampin, but not to penicillin. We then characterized the genetic relatedness of six penicillin- and/or ciprofloxacin-resistant isolates obtained in this study with global 112 genomes using core-genome phylogenetic analysis. These results provide the first evidence that invasive lineages such as a penicillin-resistant serogroup W, sequence type (ST)-11 clonal complex (CC), and a ciprofloxacin-resistant serogroup B/C, ST-4821 CC that is considered as a global threat, have been sporadically identified in Japan. Our findings highlight the need to monitor antibiotic resistance in clinical isolates of N. meningitidis, thereby preventing the spread of antibiotic-resistant invasive lineages and maintaining effective treatment for IMD patients and their close contacts. IMPORTANCE Although antibiotics such as penicillin and ceftriaxone can treat invasive meningococcal disease (IMD), the emergence and spread of antibiotic-resistant Neisseria meningitidis have become a global concern. To provide effective treatment, including chemoprophylaxis to IMD patients and their close contacts, we highlighted the importance of recognizing the antibiotic resistance and genetic features of N. meningitidis isolates.

Large-Scale Samples Based Rapid Detection of Ciprofloxacin Resistance in Klebsiella pneumoniae Using Machine Learning Methods

Klebsiella pneumoniae is one of the most common causes of hospital- and community-acquired pneumoniae. Resistance to the extensively used quinolone antibiotic, such as ciprofloxacin, has increased in Klebsiella pneumoniae, which leads to the increase in the risk of initial antibiotic selection for Klebsiella pneumoniae treatment. Rapid and precise identification of ciprofloxacin-resistant Klebsiella pneumoniae (CIRKP) is essential for clinical therapy. Nowadays, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is another approach to discover antibiotic-resistant bacteria due to its shorter inspection time and lower cost than other current methods. Machine learning methods are introduced to assist in discovering significant biomarkers from MALDI-TOF MS data and construct prediction models for rapid antibiotic resistance identification. This study examined 16,997 samples taken from June 2013 to February 2018 as part of a longitudinal investigation done by Change Gung Memorial Hospitals (CGMH) at the Linkou branch. We applied traditional statistical approaches to identify significant biomarkers, and then a comparison was made between high-importance features in machine learning models and statistically selected features. Large-scale data guaranteed the statistical power of selected biomarkers. Besides, clustering analysis analyzed suspicious sub-strains to provide potential information about their influences on antibiotic resistance identification performance. For modeling, to simulate the real antibiotic resistance predicting challenges, we included basic information about patients and the types of specimen carriers into the model construction process and separated the training and testing sets by time. Final performance reached an area under the receiver operating characteristic curve (AUC) of 0.89 for support vector machine (SVM) and extreme gradient boosting (XGB) models. Also, logistic regression and random forest models both achieved AUC around 0.85. In conclusion, models provide sensitive forecasts of CIRKP, which may aid in early antibiotic selection against Klebsiella pneumoniae. The suspicious sub-strains could affect the model performance. Further works could keep on searching for methods to improve both the model accuracy and stability.

Antimicrobial Resistance of Acetobacter and Komagataeibacter Species Originating from Vinegars

Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After ingesting vinegar, the bacteria come into close contact with the human microbiota, creating the possibility of horizontal gene transfer, including genetic determinants for antibiotic resistance. Due to the global spread of antimicrobial resistance (AMR), we analyzed the AMR of Acetobacter and Komagataeibacter species originating mainly from vinegars. Six antibiotics from different structural groups and mechanisms of action were selected for testing. The AMR was assessed with the disk diffusion method using various growth media. Although the number of resistant strains differed among the growth media, 97.4%, 74.4%, 56.4%, and 33.3% of strains were resistant to trimethoprim, erythromycin, ciprofloxacin, and chloramphenicol, respectively, on all three media. Moreover, 17.9% and 53.8% of all strains were resistant to four and three antibiotics of different antimicrobial classes, respectively. We then looked for antimicrobial resistance genes in the genome sequences of the reference strains. The most common genetic determinant potentially involved in AMR encodes an efflux pump. Since these genes pass through the gastrointestinal tract and may be transferred to human microbiota, further experiments are needed to analyze the probability of this scenario in more detail.

A Novel Non-Coding RNA CsiR Regulates the Ciprofloxacin Resistance in Proteus vulgaris by Interacting with emrB mRNA

Bacterial non-coding RNAs (ncRNAs) play important regulatory roles in various physiological metabolic pathways. In this study, a novel ncRNA CsiR (ciprofloxacin stress-induced ncRNA) involved in the regulation of ciprofloxacin resistance in the foodborne multidrug-resistant Proteus vulgaris (P. vulgaris) strain P3M was identified. The survival rate of the CsiR-deficient strain was higher than that of the wild-type strain P3M under the ciprofloxacin treatment condition, indicating that CsiR played a negative regulatory role, and its target gene emrB was identified through further target prediction, quantitative real-time PCR (qRT-PCR), and microscale thermophoresis (MST). Further studies showed that the interaction between CsiR and emrB mRNA affected the stability of the latter at the post-transcriptional level to a large degree, and ultimately affected the ciprofloxacin resistance of P3M. Notably, the base-pairing sites between CsiR and emrB mRNAs were highly conserved in other sequenced P. vulgaris strains, suggesting that this regulatory mechanism may be ubiquitous in this species. To the best of our knowledge, this is the first identification of a novel ncRNA involved in the regulation of ciprofloxacin resistance in P. vulgaris species, which lays a solid foundation for comprehensively expounding the antibiotic resistance mechanism of P. vulgaris.

Fosfomycin susceptibility of uropathogens at Charlotte Maxeke Johannesburg Academic Hospital

Background

Multidrug-resistant uropathogens are becoming widespread both in community and hospital setting. Safe yet effective treatments are a priority. Fosfomycin is an antibacterial that displays good activity against most bacteria causing urinary tract infections (UTIs), including multidrug-resistant bacteria. The aim of this study was to evaluate fosfomycin susceptibility for uropathogens isolated from a microbiology laboratory at a tertiary academic hospital. In addition, this was compared to the susceptibility of other oral antimicrobials.

Methods

We conducted a retrospective analysis of laboratory reports for uropathogens isolated at Charlotte Maxeke Johannesburg Academic Hospital from September 2015 to August 2017. Antimicrobial susceptibility testing of the isolates was performed using the Kirby–Bauer disk diffusion method or the Vitek^® 2 system according to the Clinical and Laboratory Standards Institute.

Results

Overall susceptibility of fosfomycin for the 4700 Enterobacteriaceae isolates was 95.7%; 95% confidence interval (CI) 95.1–96.2. The overall susceptibility for fosfomycin against the gram-positives was 98.6%. There were 37.9% multidrug-resistant Enterobacteriaceae (MDRE) isolated during the study period. Fosfomycin displayed activity against 94.4% of extended-spectrum β-lactamase (ESBL) producers and 90.7% for carbapenem-resistant Enterobacteriaceae (CRE). None of the methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus isolates tested was fosfomycin resistant. The overall in vitro susceptibility was significantly higher for fosfomycin (p = 0.0001) compared to amoxicillin/clavulanic acid, cephalexin, cefuroxime, ciprofloxacin, trimethoprim/sulfamethoxazole and nitrofurantoin.

Conclusion

This study confirmed the high susceptibility of fosfomycin against UTI pathogens isolated at our institution. In an era of increasing antimicrobial resistance, fosfomycin represents a potential option for the treatment of UTIs at Charlotte Maxeke Johannesburg Academic Hospital.

Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda

Misuse and overuse of antibiotics drive the selection and spread of antibiotic-resistant bacteria. Although genetic mutations have been well defined for different types of antibiotic resistance, ways to revert antibiotic resistance are largely unexplored. Here, we adopted a proteomics approach to investigate the mechanism underlying ciprofloxacin resistance in Edwardsiella tarda, a representative pathogen that infects both economic animal species and human beings. By comparing the protein expression profiles of ciprofloxacin-sensitive and -resistant E. tarda, a total of 233 proteins of differential abundance were identified, where 53 proteins belong to the functional categories of metabolism, featuring a disrupted pyruvate cycle and decreased energy metabolism but increased fatty acid biosynthesis. The altered pyruvate cycle and energy metabolism were confirmed by gene expression and biochemical assays. Furthermore, the role of fatty acid biosynthesis and quinolone resistance were explored. The expression level and enzymatic activity of acetyl coenzyme A (acetyl-CoA) carboxylase, the first step of fatty acid biosynthesis, were increased in ciprofloxacin-resistant E. tarda. Treatment of ciprofloxacin-resistant E. tarda with acetyl-CoA carboxylase and 3-oxoacyl-[acyl carrier protein] synthase II inhibitors, 2-aminooxazole and triclosan, respectively, reduced the expression of fatty acid biosynthesis and promoted quinolone-mediated killing efficacy to antibiotic-resistant bacteria. Similar results were obtained in clinically isolated E. tarda strains. Our study suggests that energy metabolism has been reprogramed in ciprofloxacin-resistant bacteria that favor the biosynthesis of fatty acid, presenting a novel target to tackle antibiotic-resistant bacteria.

IMPORTANCEEdwardsiella tarda is the causative agent of edwardsiellosis, which imposes huge challenges on clinics and aquaculture. Due to the overuse of antibiotics, the emergence and spread of antibiotic-resistant E. tarda threaten human health and animal farming. However, the mechanism of ciprofloxacin resistance in E. tarda is still lacking. Here, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics was performed to identify a differential proteome between ciprofloxacin-sensitive and -resistant E. tarda. The fluctuated pyruvate cycle and reduced energy metabolism and elevated fatty acid biosynthesis are metabolic signatures of ciprofloxacin resistance. Moreover, inhibition of biosynthesis of fatty acids promotes quinolone-mediated killing efficacy in both lab-evolved and clinically isolated strains. This study reveals that a ciprofloxacin resistance mechanism is mediated by the elevated biosynthesis of fatty acids and the depressed pyruvate metabolism and energy metabolism in E. tarda. These findings provide a novel understanding for the ciprofloxacin resistance mechanism in E. tarda.

Epidemiologic Associations Vary Between Tetracycline and Fluoroquinolone Resistant Campylobacter jejuni Infections

Campylobacter jejuni is the leading cause of bacterial gastroenteritis and antibiotic resistant C. jejuni are a serious threat to public health. Herein, we sought to evaluate trends in C. jejuni infections, quantify resistance frequencies, and identify epidemiological factors associated with infection. Campylobacter jejuni isolates (n = 214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. The minimum inhibitory concentration for nine antibiotics was determined using microbroth dilution, while demographic and clinical data were used for the univariate and multivariate analyses. Over the 4-year period, a significant increase in the recovery of C. jejuni was observed (p ≤ 0.0001). Differences in infection rates were observed by hospital and several factors were linked to more severe disease. Patients residing in urban areas, for instance, were significantly more likely to be hospitalized than rural residents as were patients over 40 years of age and those self-identifying as non-White, highlighting potential disparities in disease outcomes. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n = 120; 56.1%) followed by resistance to ciprofloxacin (n = 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Resistance to two antibiotic classes was observed in 38 (17.8%) isolates, while multidrug resistance, or resistance to three or more classes, was observed in four (1.9%). Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). Relative to patients with only tetracycline resistant infections, those with ciprofloxacin resistance were more likely to travel internationally, be hospitalized and have an infection during the fall or summer. Together, these findings show increasing rates of infection and resistance and highlight specific factors that impact both outcomes. Enhancing understanding of factors linked to C. jejuni resistance and more severe infections is critical for disease prevention, particularly since many clinical laboratories have switched to the use of culture-independent tests for the detection of Campylobacter.

Gene-Gene Interactions Dictate Ciprofloxacin Resistance in Pseudomonas aeruginosa and Facilitate Prediction of Resistance Phenotype from Genome Sequence Data

Ciprofloxacin is one of the most widely used antibiotics for treating Pseudomonas aeruginosa infections. However, P. aeruginosa acquires mutations that confer ciprofloxacin resistance, making treatment more difficult. Resistance is multifactorial, with mutations in multiple genes influencing the resistance phenotype. However, the contributions of individual mutations and mutation combinations to the amounts of ciprofloxacin that P. aeruginosa can tolerate are not well understood. Engineering P. aeruginosa strain PAO1 to contain mutations in any one of the resistance-associated genes gyrA, nfxB, rnfC, parC, and parE showed that only gyrA mutations increased the MIC for ciprofloxacin. Mutations in parC and parE increased the MIC of a gyrA mutant, making the bacteria ciprofloxacin resistant. Mutations in nfxB and rnfC increased the MIC, conferring resistance, only if both were mutated in a gyrA background. Mutations in all of gyrA, nfxB, rnfC, and parC/E further increased the MIC. These findings reveal an epistatic network of gene-gene interactions in ciprofloxacin resistance. We used this information to predict ciprofloxacin resistance/susceptibility for 274 isolates of P. aeruginosa from their genome sequences. Antibiotic susceptibility profiles were predicted correctly for 84% of the isolates. The majority of isolates for which prediction was unsuccessful were ciprofloxacin resistant, demonstrating the involvement of additional as yet unidentified genes and mutations in resistance. Our data show that gene-gene interactions can play an important role in antibiotic resistance and can be successfully incorporated into models predicting resistance phenotype.

Antibacterial Activity of Propolis Extracts from the Central Region of Romania against Neisseria gonorrhoeae

(1) Background: Sexually transmitted infections (STIs) are among the most common infections worldwide, many of these being caused by Neisseria gonorrhoeae (NG). Increased antimicrobial NG resistance has been reported in recent decades, highlighting the need for new sources of natural compounds with valuable antimicrobial activity. This study aims to determine the effect of propolis extracts on NG strains, including antibiotic-resistant strains. (2) Methods: First void urine samples from presumed positive STI subjects were harvested. DNA was extracted, purified, and amplified via PCR for the simultaneous detection of 6 STIs. The presence of the dcmH, gyrA, and parC genes was checked in the DNA samples from NG-positive patients. The antimicrobial activity of 5 aqueous propolis extracts from central Romania was investigated in vitro against some isolated NG strains. ANOVA tests were employed to assess differences and interactions between the inhibition zone for NG strains and propolis extracts. (3) Results: 7.07% of the patients presented NG infections, some strains being resistant or intermediate-resistant to ciprofloxacin. All propolis samples exhibited an antibacterial effect, including on resistant strains. (4) Conclusions: Statistical analysis demonstrated that the diameter of the inhibition zone was influenced both by the NG strain type and the source of the propolis extracts.

Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species

Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.

Mechanisms for Development of Ciprofloxacin Resistance in a Clinical Isolate of Pseudomonas aeruginosa

Treatment of infections by Pseudomonas aeruginosa is difficult due to its high intrinsic and acquired antibiotic resistance. Upon colonization in the human hosts, P. aeruginosa accumulates genetic mutations that confer the bacterium antibiotic resistance and ability to better live in the host environment. Characterizing the evolutionary traits would provide important insights into the development of effective combinatory antibiotic therapies to cure P. aeruginosa infections. In this work, we performed a detailed analysis of the molecular mechanisms by which a clinical isolate (CSP18) yields a ciprofloxacin-resistant derivative (CRP42). Genomic DNA re-sequencing and RNAseq were carried out to compare the genomic mutational signature and transcriptional profiles between the two isolates. The results indicated that D87G mutation in GyrA, together with MexEF-OprN hyper-expression caused by F7S mutation in MexS, was responsible for the increased resistance to ciprofloxacin in the isolate CRP42. Further simulation of CRP42 by gene editing in CSP18 demonstrated that D87G mutation in GyrA rendered CSP18 a fourfold increase in minimum inhibitory concentration against ciprofloxacin, while F7S mutation in MexS conferred an additional eightfold increase. Our experimental results demonstrate for the first time that the clinically relevant F7S point mutation in MexS results in hyper-expression of the mexEF-oprN and thus confers P. aeruginosa resistance to ciprofloxacin.

Extra-intestinal Salmonellosis in a Tertiary Care Center in Saudi Arabia

Introduction: Salmonella infection is one of the most common causes of gastroenteritis worldwide. It is associated with high morbidity and mortality if not treated properly. It has developed resistance to multiple antibiotics. These developments are concerning. This study sought to observe common patterns of invasive Salmonella infections, such as the common serotypes involved, presentation, sensitive investigations, and effective treatment. This study also aimed to examine the risk factors that can worsen the infection and increase morbidity and mortality. Methodology: This retrospective analysis included all patients who were diagnosed with invasive Salmonella infection at King Khalid University Hospital from May 2017 to December 2018. Most patients in this report were immunocompromised; however, a few previously healthy patients. Different types of specimens were collected. Twenty-two patients with invasive Salmonella were included in this study. Results: Sixteen of them had underlying conditions. The most common presenting symptoms of illness were fever (n = 13), vomiting (n = 6), and diarrhea (n = 4). Most blood samples (94%) were positive for Salmonella. All patients were discharged except three who died; these were all older patients with comorbidities. Although four different antimicrobial resistance patterns were noticed in this study, ciprofloxacin was the highest significant percentage (62.5%). Of five patients initially treated with ciprofloxacin, three of them expressed resistance to this antibiotic. Conclusion: The findings of this study support that immunocompromised patients and people with extreme ages are more likely to have serious medical illnesses and at higher risk of infection with Salmonella spp. Therefore, this study emphasises the importance of antimicrobial judicious utilisation. Tackling the escalating antibiotic resistance could be approached by implementing advanced public education levels to maintain high standards of food and water safety. Moreover, the urge to investigating newer drugs against Salmonella with an acceptable safety profile is a cornerstone to attenuate the rapidly acquired bacterial resistance precisely for those who are immunocompromised. Furthermore, predicting the mortality, morbidity and the clinical response is feasible according to the patient parameters and comorbidities.

Evolution of Ciprofloxacin Resistance-Encoding Genetic Elements in Salmonella

The incidence of ciprofloxacin resistance in Salmonella has increased dramatically in the past decade. To track the evolutionary trend of ciprofloxacin resistance-encoding genetic elements during this period, we surveyed the prevalence of Salmonella in food products in Shenzhen, China, during the period of 2012 to 2017 and performed whole-genome sequencing and genetic analysis of 566 ciprofloxacin-resistant clinical Salmonella strains collected during this survey. We observed that target gene mutations have become much less common, with single gyrA mutation currently detectable in Salmonella enterica serovar Typhimurium only. Multiple plasmid-mediated quinolone resistance (PMQR) genes located in the chromosome and plasmids are now frequently detectable in ciprofloxacin-resistant Salmonella strains of various serotypes. Among them, the qnrS1 gene was often harbored by multiple plasmids, with p10k-like plasmids being the most dominant. Importantly, p10k-like plasmids initially were not conjugative but became transmissible with the help of a helper plasmid. Ciprofloxacin resistance due to combined effect of carriage of the qnrS1 gene and other resistance mechanisms is common. In S Typhimurium, carriage of qnrS1 is often associated with a single gyrA mutation; in other serotypes, combination of qnrS1 and other PMQR genes located in the chromosomal fragment or plasmid is observed. Another major mechanism of ciprofloxacin resistance, mainly observable in S Derby, involves a chromosomal fragment harboring the qnrS2-aac(6')lb-cr-oqxAB elements. Intriguingly, this chromosomal fragment, flanked by IS26, could form a circular intermediate and became transferrable. To conclude, the increase in the incidence of various PMQR mobile genetic elements and their interactions with other resistance mechanism contribute to a sharp increase in the prevalence of ciprofloxacin-resistant clinical Salmonella strains in recent years.IMPORTANCE Resistance of nontyphoidal Salmonella to fluoroquinolones such as ciprofloxacin is known to be mediated by target mutations. This study surveyed the prevalence of Salmonella strains recovered from 2,989 food products in Shenzhen, China, during the period 2012 to 2017 and characterized the genetic features of several PMQR gene-bearing plasmids and ciprofloxacin resistance-encoding DNA fragments. The emergence of such genetic elements has caused a shift in the genetic location of ciprofloxacin resistance determinants from the chromosomal mutations to various mobile genetic elements. The distribution of these PMQR plasmids showed that they exhibited high serotype specificity, except for the p10k-like plasmids, which can be widely detected and efficiently transmitted among Salmonella strains of various serotypes by fusing to a new conjugative helper plasmid. The sharp increase in the prevalence of ciprofloxacin resistance in recent years may cause a predisposition to the emergence of multidrug-resistant Salmonella strains and pose huge challenges to public health and infection control efforts.

Ciprofloxacin Pharmacokinetics/Pharmacodynamics against Susceptible and Low-Level Resistant Escherichia coli Isolates in an Experimental Ascending Urinary Tract Infection Model in Mice

The mouse ascending urinary tract infection model was used to study the pharmacokinetic/pharmacodynamic (PKPD) relationships of the effect of ciprofloxacin in subcutaneous treatment for 3 days with varying doses and dosing intervals against a susceptible Escherichia coli strain (MIC, 0.032 mg/liter). Further, a humanized dose of ciprofloxacin was administered for 3 days against three E. coli strains with low-level resistance, i.e., MICs of 0.06, 0.25, and 1 mg/liter, respectively. Against the susceptible isolate, ciprofloxacin was highly effective in clearing the urine with daily doses from 10 mg/kg, but the dosing regimen had to be divided into at least two doses for optimal effect. Ciprofloxacin could not clear the urine or kidneys for the low-level-resistant strains. PKPD correlations with all strains combined showed that for the AUC₂₄/MIC there was a slightly higher correlation with effect in urine and kidneys (R ², 0.71 and 0.69, respectively) than the %T_>MIC (R ², 0.41 and 0.61, respectively). Equal correlations for the two PKPD indices were found for reduction of colony counts (CFU) in the bladder tissue, but not even the highest dose of 28 mg/kg × 6 could clear the bladder tissue. In conclusion, ciprofloxacin is highly effective in clearing the urine and kidney tissue for fully susceptible E. coli, while even low-level resistance in E. coli obscures this effect. While the effect of ciprofloxacin is mostly AUC/MIC driven against E. coli infection in the urinary tract, the effect in urine depends on the presence of ciprofloxacin in the urine during most of a 24-h period.

Transmission of Chromosomal MDR DNA Fragment Encoding Ciprofloxacin Resistance by a Conjugative Helper Plasmid in Salmonella

Resistance to ciprofloxacin, a treatment choice for Salmonella infections, has increased dramatically in recent years in particular in serotype Salmonella Derby with most of strains carrying chromosome-encoded multiple plasmid-mediated quinolone resistance (PMQR) genes. In this work, we discovered a conjugative plasmid, pSa64-96kb, in a Salmonella Derby isolate, namely Sa64, which could extract and fuse to a multiple drug resistance (MDR) DNA fragment containing two PMQR genes, aac(6')-Ib-cr, and qnrS2 located on the chromosome of the Salmonella strain. This process led to the formation of a new 188 kb fusion plasmid, which could be then subsequently transmitted to recipient strain Escherichia coli J53. The chromosomal MDR DNA fragment was shown to be flanked by one copy of IS26 element at each end and could be excised from the chromosome to form circular intermediate, which was then fused to pSa64-96kb and form a single plasmid through IS26 mediated homologous recombination. The role of IS26 on enhancing the efficacy of fusion and transmission of this chromosomal MDR DNA fragment was further proven in other Salmonella strains. These findings showed that dynamic interaction between specific chromosomal fragment and plasmids may significantly enhance resistance development and transferability of mobile resistance-encoding elements among bacterial pathogens.

Involvement of the AcrAB Efflux Pump in Ciprofloxacin Resistance in Clinical Klebsiella Pneumoniae Isolates

BACKGROUND

Increasing prevalence of multiple antibiotic resistance in Klebsiella pneumoniae strains confines the therapeutic options used to treat bacterial infections.

OBJECTIVE

We aimed in this study to investigate the role of AcrAB and qepA efflux pumps and AAC(6')-Ib-cr enzyme in ciprofloxacin resistance and to detect the RAPD-PCR fingerprint of K. pneumoniae isolates.

METHODS

A total of , 117 K. pneumoniae isolates were collected from hospitalized patients in three hospitals in Tehran, Iran, from August 2013 to March 2014. Antimicrobial susceptibility tests were performed by the disk diffusion method. Molecular identification and expression level of encoding quinolone resistance genes, acrA, acrB, qepA, and aac(6')-Ib-cr, were performed by PCR and real-- time PCR assays, respectively. All the K. pneumoniae isolates containing the mentioned genes were used simultaneously for RAPD-PCR typing.

RESULTS

Colistin and carbapenems were the most efficient antibiotics against the clinical isolates of K. pneumoniae. PCR assay demonstrated that among the 117 isolates, 110 (94%) and 102 (87%) were positive for acrA and acrB gene and 5 (4%) and 100 (85%) isolates showed to have qepA and aac(6')-Ib-cr genes, respectively. Determination for AcrAB pump expression in 21% of strains demonstrated an increased expression, and the mean increase expression for acrB genes was 0.5-81. The results of RAPD-PCR reflected that in 95% CI, all isolates belonged to a clone.

CONCLUSION

A high prevalence of genes encoding quinolone resistance in K. pneumoniae was detected in clinical samples. Therefore, the control of infection and prevention of drug-resistant bacteria spread need careful management of medication and identification of resistant isolates.

ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

The ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas spp. All Pseudomonas complete genomes were downloaded from NCBI’s Refseq library and were inspected for the presence of the crpP gene. The mobile elements carrying this gene were further characterized. The crpP gene was identified only in P. aeruginosa, in more than half of the complete chromosomes (61.9%, n = 133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136 crpP-harboring integrative and conjugative elements (ICEs), with 93.4% belonging to the mating-pair formation G (MPF_G) family. The ICEs were integrated at the end of a tRNA^Lys gene and were all flanked by highly conserved 45-bp direct repeats. The crpP-carrying ICEs contain 26 core genes (2.2% of all 1193 genes found in all the ICEs together), which are present in 99% or more of the crpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work suggests that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying crpP gene in P. aeruginosa.

Profiles of gyrA Mutations and Plasmid-Mediated Quinolone Resistance Genes in Shigella Isolates with Different Levels of Fluoroquinolone Susceptibility

Purpose

Fluoroquinolone-resistant Shigella is considered a serious public health problem and has been put on the WHO global priority list of antibiotic-resistant bacteria. This study was aimed to investigate the fluoroquinolone resistance in Shigella and its relevant genetic mechanisms.

Materials and Methods

Shigella isolates that were isolated from diarrheal patient’s feces in Ningbo China from 2011 to 2018 were tested for susceptibility to ampicillin, gentamicin, tetracycline, nalidixic acid, ciprofloxacin, and cefotaxime. Genes related to quinolone resistance were amplified by PCR.

Results

A total of 118 Shigella isolates were collected, including 76 S. flexneri isolates, 40 S. sonnei isolates, and 2 S. boydii isolates. Ciprofloxacin susceptibility test identified 10 (9%) susceptible, 65 (55%) intermediate, and 43 (36%) resistant isolates. Of 76 S. flexneri isolates, 37 were ciprofloxacin resistant, a prevalence significantly higher than 6 of 40 S. sonnei isolates (P=0.01). The isolates collected during 2014–2018 displayed a significant increase in the prevalence of ciprofloxacin resistance (P=0.05) than those collected during 2011–2013. All the ciprofloxacin-intermediate and resistant isolates had mutations of gyrA(S83L) and parC (S80I), whereas only the ciprofloxacin-resistant isolates had gyrA (D87N) mutation and qnrB gene. Additionally, 30% of the ciprofloxacin-resistant isolates were positive for aac(6´)-Ib-cr gene.

Conclusion

This study shows the currently increasing prevalence of ciprofloxacin resistance. The reduced fluoroquinolone susceptibility is highly associated with gyrA (S83L) and parC (S80I) mutations, while the fluoroquinolone resistance is highly associated with gyrA (D87N) mutation, qnrB gene and perhaps aac(6´)-Ib-cr gene.

Estimating the burden of enteric fever in Chhattisgarh: A single-center study on culture-positive cases from a newly built tertiary care hospital

BACKGROUND

Enteric fever is the most common cause of community acquired blood stream infections in under developed and developing countries. The enteric fever is exclusive to humans and transmitted through the faeco-oral route. Though India is an endemic zone for enteric fever, the data is very scarce from Central India. The present study was undertaken to determine the prevalence of enteric fever in this region and to know the antimicrobial susceptibility pattern of the isolated typhoidal Salmonellae.

MATERIAL AND METHOD

We conducted a retrospective analysis of blood culture positive cases of enteric fever over a period of two years (December 2015 to December 2017). All blood cultures submitted for suspected enteric fever and associated symptoms were included in the study. Relevant demographic, clinical and laboratory data were analyzed.

RESULT

A total of 51 cases (3.56%) were of typhoidal Salmonella from a total of 1430 blood culture submission. Salmonella Typhi were 70.5% while Salmonella Paratyphi A were 29.5% of the total isolated Salmonellae. The most vulnerable age group was 10-19years (41.2%). The mean minimum inhibitory concentration of ciprofloxacin for Salmonella Typhi and Salmonella Paratyphi A are 1.20 and 1.97 μg/ml respectively. All the isolates were susceptible to ceftriaxone. Highest isolation was in the July - September quarter (35.3%).

CONCLUSION

There is a high prevalence of the disease which needs urgent focus on safe water, sanitation services and also to establish guidelines for empiric therapy for enteric fever.

Detection of Chromosomal and Plasmid-Mediated Quinolone Resistance Among Escherichia coli Isolated from Urinary Tract Infection Cases; Zagazig University Hospitals, Egypt

Introduction

Resistance to fluoroquinolones (FQ) in uropathogenic Escherichia coli (UPEC) has emerged as a growing problem. Chromosomal mutations and plasmid-mediated quinolone resistance (PMQR) determinants have been implicated. Data concerning the prevalence of these determinants in UPEC in our hospital are quite limited.

Purpose

To investigate the occurrence and genetic determinants of FQ resistance in UPEC isolated from urinary tract infection (UTI) cases in Zagazig University Hospitals.

Patients and Methods

Following their isolation, the identification and susceptibility of UPEC isolates were performed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer (MALDI-TOF MS). FQ resistance was detected by the disc diffusion method. Ciprofloxacin minimal inhibitory concentration (MIC) was determined using E-test. Chromosomal mutations in the gyrA gene were detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and for detection of PMQR, a couple of multiplex PCR reactions were used.

Results

Among a total of 192 UPEC isolates, 46.9% (n=90) were FQ resistant. More than half of the isolates (57.8%) exhibited high-level ciprofloxacin resistance (MIC > 32 µg/mL). Mutations in gyrA were detected in 76.7% of isolates, with 34.4% having mutations at more than one site. PMQR determinants were detected in 80.1% of UPEC isolates, with aac(6ʹ)-Ib-cr gene being the most frequent found in 61.1% of isolates.

Conclusion

There is a high prevalence of both gyrA mutations and PMQR determinants among UPEC isolates in our hospital which contribute to high-level ciprofloxacin resistance, a finding that may require the revision of the antibiotics used for empirical treatment of UTI.

Identification of Essential Residues for Ciprofloxacin Resistance of Ciprofloxacin-Modifying Enzyme (CrpP) of pUM505

The ciprofloxacin-resistance crpP gene, encoded by the pUM505 plasmid, isolated from a P. aeruginosa clinical isolate, confers an enzymatic mechanism of antibiotic phosphorylation, which is ATP-dependent, that decreases ciprofloxacin susceptibility. Homologous crpP genes are distributed across extended spectrum beta-lactamase (ESBL)-producing isolates obtained from Mexican hospitals and which confer decreased susceptibility to CIP. The analysis of sequences of the CrpP of proteins showed that the residues Gly7, Thr8, Asp9, Lys33 and Gly34 (located at the N-terminal region) and Cys40 (located at the C-terminal region) are conserved in all proteins, suggesting that these residues could be essential for CrpP function. The aim of this study was to investigate the amino acids essential to ciprofloxacin resistance, which is conferred by the CrpP protein of pUM505 plasmid. Mutations in the codons encoding Gly7, Asp9, Lys33 and Cys40 of CrpP protein from pUM505 were generated by PCR fusion. The results showed that all mutations generated in CrpP proteins increased ciprofloxacin susceptibility in Escherichia coli. In addition, the CrpP modified proteins were purified and their enzymatic activity on ciprofloxacin was assayed, showing that these modified proteins do not exert catalytic activity on ciprofloxacin. Moreover, by infrared assays it was determined that the modified proteins were are not able to modify the ciprofloxacin molecule. Our findings are the first report that indicate that the amino acids, namely Gly7, Asp9, Lys33 and Cys40, which are conserved in the CrpP proteins, possess an essential role for the enzymatic mechanism that confers ciprofloxacin resistance.

Can Ciprofloxacin be Used for Precision Treatment of Gonorrhea in Public STD Clinics? Assessment of Ciprofloxacin Susceptibility and an Opportunity for Point-of-Care Testing

Background: Given the lack of new antimicrobials to treat Neisseria gonorrhoeae (NG) infections, reusing previously recommended antimicrobials has been proposed as a strategy to control the spread of multi-drug-resistant NG. We assessed ciprofloxacin susceptibility in a large sample set of NG isolates and identified correlates associated with ciprofloxacin-resistant NG infections. Methods: NG isolates collected in Baltimore, Maryland between 2014 and 2016 were evaluated by Gyrase A (gyrA) PCR and E-test for susceptibility to ciprofloxacin. Clinical characteristics and demographics were evaluated by multivariate regression analysis to identify correlates of ciprofloxacin-resistant NG infections. Results: 510 NG isolates from predominately African American (96.5%), heterosexual (85.7%), and HIV-negative (92.5%) male subjects were included in the study. The overall percentage of isolates with mutant gyrA sequences, indicative of ciprofloxacin resistance, was 32.4%, and significantly increased from 24.7% in 2014 to 45.2% in 2016 (p < 0.001). Participants older than 35 years of age were 2.35 times more likely to have a gyrA mutant NG infection than younger participants (p < 0.001). Race, sexual orientation, symptomology, or co-infection the HIV or syphilis were not associated with a particular NG gyrA genotype. Conclusions: Resistance to ciprofloxacin in Baltimore is lower than other regions and indicates that in this environment, use of ciprofloxacin may be appropriate for targeted treatment provided utilization of enhanced surveillance tools. The targeted use of ciprofloxacin may be more beneficial for individuals under 35 years of age. Point-of-care tests for NG diagnosis and susceptibility testing are urgently needed to identify individuals who can be treated with this targeted approach.

Transmission of ciprofloxacin resistance in Salmonella mediated by a novel type of conjugative helper plasmids

Ciprofloxacin resistance in Salmonella has been increasingly reported due to the emergence and dissemination of multiple Plasmid-Mediated Quinolone Resistance (PMQR) determinants, which are mainly located in non-conjugative plasmids or chromosome. In this study, we aimed to depict the molecular mechanisms underlying the rare phenomenon of horizontal transfer of ciprofloxacin resistance phenotype in Salmonella by conjugation experiments, S1-PFGE and complete plasmid sequencing. Two types of non-conjugative plasmids, namely an IncX1 type carrying a qnrS1 gene, and an IncH1 plasmid carrying the oqxAB-qnrS gene, both ciprofloxacin resistance determinants in Salmonella, were recovered from two Salmonella strains. Importantly, these non-conjugative plasmids could be fused with a novel Incl1 type conjugative helper plasmid, which could target insertion sequence (IS) elements located in the non-conjugative, ciprofloxacin-resistance-encoding plasmid through replicative transcription, eventually forming a hybrid conjugative plasmid transmissible among members of Enterobacteriaceae. Since our data showed that such conjugative helper plasmids are commonly detectable among clinical Salmonella strains, particularly S. Typhimurium, fusion events leading to generation and enhanced dissemination of conjugative ciprofloxacin resistance-encoding plasmids in Salmonella are expected to result in a sharp increase in the incidence of resistance to fluoroquinolone, the key choice for treating life-threatening Salmonella infections, thereby posing a serious public health threat.

Evolution and transmission of a conjugative plasmid encoding both ciprofloxacin and ceftriaxone resistance in Salmonella

Ceftriaxone and ciprofloxacin are the drugs of choice in treatment of invasive Salmonella infections. This study discovered a novel type of plasmid, pSa44-CIP-CRO, which was recovered from a S. London strain isolated from meat product and comprised genetic determinants that encoded resistance to both ciprofloxacin and ceftriaxone. This plasmid could be resolved into two daughter plasmids and co-exist with such daughter plasmids in a dynamic form in Salmonella; yet it was only present as a single plasmid in Escherichia coli. One daughter plasmid, pSa44-CRO, was found to carry the bla_CTX-M-130 gene, which encodes resistance to ceftriaxone, whereas the other plasmid, pSa44-CIP, carried multiple PMQR genes such as qnrB6-aac(6')-Ib-cr, which mediated resistance to ciprofloxacin. These two daughter plasmids could be integrated into one single plasmid through ISPa40 mediated homologous recombination. Mouse infection and treatment experiments showed that carriage of plasmid, pSa44-CIP-CRO by S. typhimurium led to the impairment of treatment by ciprofloxacin or cefitiofur, a veterinary drug with similar properties as ceftriaxone. In conclusion, dissemination of such conjugative plasmids impairs current choices of treatment for life-threatening Salmonella infection and hence constitutes a serious public health threat.

Pseudomonas aeruginosa Polynucleotide Phosphorylase Contributes to Ciprofloxacin Resistance by Regulating PrtR

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that causes various acute and chronic infections. It is intrinsically resistant to a variety of antibiotics. However, production of pyocins during SOS response sensitizes P. aeruginosa to quinolone antibiotics by inducing cell lysis. The polynucleotide phosphorylase (PNPase) is a conserved phosphate-dependent 3′–5′ exonuclease that plays an important role in bacterial response to environmental stresses and pathogenesis by influencing mRNA and small RNA stabilities. Previously, we demonstrated that PNPase controls the type III and type VI secretion systems in P. aeruginosa. In this study, we found that mutation of the PNPase coding gene (pnp) increases the bacterial resistance to ciprofloxacin. Gene expression analyses revealed that the expression of pyocin biosynthesis genes is decreased in the pnp mutant. PrtR, a negative regulator of pyocin biosynthesis genes, is upregulated in the pnp mutant. We further demonstrated that PNPase represses the expression of PrtR on the post-transcriptional level. A fragment containing 43 nucleotides of the 5′ untranslated region was found to be involved in the PNPase mediated regulation of PrtR. Overall, our results reveled a novel layer of regulation on the pyocin biosynthesis by the PNPase in P. aeruginosa.

Characterization of ciprofloxacin-resistant and ESBL-producing Salmonella enteric serotype Derby in Eastern China

Background

Fluoroquinolone resistance and ESBL-production are concurrently found in a limited number of Salmonella serotypes. The present study was aimed to characterize fluoroquinolone-resistant and ESBL-producing Salmonella enteric serotype Derby (S. Derby) isolates in terms of antimicrobial susceptibility, relevant genetic mechanisms, and PFGE.

Results

From 2013 to 2017 in Ningbo China, 52 S. Derby isolates were identified out of 826 non-typhoidal Salmonella isolates from patient feces, food, and environmental water samples. Three S. derby isolates were identified to be fluoroquinolone-resistant and ESBL-producing with cefotaxime MIC of 64 μg/mL and ciprofloxacin MIC of 4 μg/mL. The three isolates contained the same genetic structure of quinolone resistance, including a silent gyrA mutation S (TCC) 83S (TCT) and three PMQR genes qnrB, qnrS and aac(6′)-Ib-cr. As withβ-lactams resistance mechanisms, two isolates contained bla_TEM, bla_OXA, and bla_CTX-M genes and one isolate contained bla_OXA and bla_CTX-M genes. Additionally, two isolates displayed more identical PFGE pattern than the third isolate, whereas three isolates showed the same plasmid profile of I1, W and P by PCR-based replicon typing. The conjugation experiment showed no dissemination of β-lactam resistance by direct contact among isolates; the transformation experiment failed to transfer plasmid conferring ampicillin resistance to E. coli DH5a.

Conclusion

The present study demonstrates the emerging fluoroquinolone-resistant and ESBL-producing S. Derby in both humans and the environment. Seeing that S. Derby has become one of the most common Salmonella serotypes, this situation gives rise to a new major risk of food-borne diseases.

Characterization of Ciprofloxacin Resistance in Laboratory-Derived Mutants of Vibrio parahaemolyticus with qnr Gene

Ciprofloxacin, a broad-spectrum fluoroquinolone, is a bactericidal antibiotic targeting DNA gyrase and DNA topoisomerase IV encoded by the gyrA and parC genes. Resistance to fluoroquinolones requires the accumulation of multiple mutations including those that alter target genes and increase drug efflux. To examine the development of fluoroquinolones resistance in Vibrio parahaemolyticus, ciprofloxacin induction and selection was used to obtain several resistant V. parahaemolyticus mutants, which showed decreased susceptibilities to quinolones, and increased or decreased susceptibility to other structurally unrelated antibiotics. Quinolone resistance-determining region mutations were characterized, and it was found that gyrA mutations occurred in some of the high-level resistant mutants although qnr was present in both wild-type susceptible and resistant mutant strains. The mutants showed increased qnr expression and exposure to sub-inhibitory concentrations of ciprofloxacin caused a further increase in qnr expression independently of the SOS system. Two mutants demonstrated increased expression of the VmeCD-VpoC pump gene that promotes quinolone efflux. In addition, some of the high-level resistance mutants significantly decreased bacterial fitness. These data suggested that multiple genes contributed to the enhanced ciprofloxacin resistance appeared in V. parahaemolyticus and that acquisition of ciprofloxacin resistance impaired bacterial fitness.

Identification and Characterization of Conjugative Plasmids That Encode Ciprofloxacin Resistance in Salmonella

This study aimed to characterize novel conjugative plasmids that encode transferable ciprofloxacin resistance in Salmonella In this study, 157 nonduplicated Salmonella isolates were recovered from food products, of which 55 were found to be resistant to ciprofloxacin. Interestingly, 37 of the 55 Cip^rSalmonella isolates (67%) did not harbor any mutations in the quinolone resistance-determining regions (QRDR). Six Salmonella isolates were shown to carry two novel types of conjugative plasmids that could transfer the ciprofloxacin resistance phenotype to Escherichia coli J53 (azithromycin resistant [Azi^r]). The first type of conjugative plasmid belonged to the ∼110-kb IncFIB-type conjugative plasmids carrying qnrB-bearing and aac(6')-Ib-cr-bearing mobile elements. Transfer of the plasmid between E. coli and Salmonella could confer a ciprofloxacin MIC of 1 to 2 μg/ml. The second type of conjugative plasmid belonged to ∼240-kb IncH1/IncF plasmids carrying a single PMQR gene, qnrS Importantly, this type of conjugative ciprofloxacin resistance plasmid could be detected in clinical Salmonella isolates. The dissemination of these conjugative plasmids that confer ciprofloxacin resistance poses serious challenges to public health and Salmonella infection control.

Molecular Characterization of qnrVC Genes and Their Novel Alleles in Vibrio spp. Isolated from Food Products in China

This study reports the prevalences of qnrVC genes in 74 ciprofloxacin-resistant Vibrio sp. isolates. Two novel functional qnrVC alleles, qnrVC8 and qnrVC9, sharing 98% and 99% nucleotide similarity with qnrVC6 and qnrVC7, respectively, were identified. Our findings suggested that carriage of qnrVC alleles, together with target mutations in gyrA and parC genes, may contribute to the development of fluoroquinolone resistance in Vibrio species, posing a serious threat to public health.

The Molecular Mechanisms of Ciprofloxacin Resistance in Clinical Campylobacter jejuni and Their Genotyping Characteristics in Beijing, China

We assessed the susceptibility of 182 Campylobacter jejuni isolates from patients with diarrhea to eight antibiotics and analyzed the molecular mechanisms of ciprofloxacin resistance as well as the genetic characteristics based on multilocus sequence typing (MLST). The C257T mutation was found on the quinolone resistance-determining region (QRDR) of the gyrA gene in all ciprofloxacin-resistant strains. Mutations on the QRDR of the gyrB gene were silent. A total of 74 strains had 7 inverted repeat (IR) (a 16-bp IR on the intergenic region between cmeR and cmeABC) mutation polymorphisms. Compared with strains without the IR mutations, strains with the IR mutations had higher resistance rates to ciprofloxacin (94.6% vs. 83.3%), nalidixic acid (94.6% vs. 83.3%), tetracycline (98.6% vs. 85.2%), doxycycline (91.9% vs. 71.3%), florfenicol (59.5% vs. 17.6%), chloramphenicol (25.7% vs. 4.6%), gentamicin (16.2% vs. 3.7%), and multidrug resistance than those without IR mutations (all p < 0.05). With C257T mutation alone, 89.9% strains with minimum inhibitory concentration (MIC) values focused on 16, 32, and 64 μg/mL, whereas strains with C257T mutation in combination with the IR mutations had a higher ciprofloxacin resistance level with 88.6% MIC values focused on 64, 128, and 512 μg/mL (p < 0.0001). The strains in this study showed a high genetic variability based on MLST with 117 sequence types (STs), 37 of which were novel. CC-21 was the most common clonal complex (CC) followed by CC-353 and CC-45. No association was found between STs and ciprofloxacin resistance. In conclusion, the C257T mutation on gyrA was the major mechanism for ciprofloxacin resistance, and the C257T mutation in combination with the IR mutations might result in more severe ciprofloxacin resistance to C. jejuni.

Arcobacter butzleri Ciprofloxacin Resistance: Point Mutations in DNA Gyrase A and Role on Fitness Cost

Arcobacter butzleri is a widely distributed emerging pathogen resistant to various classes of antimicrobial agents, namely fluoroquinolones. A. butzleri resistance to fluoroquinolones is conferred by point mutations at the antibiotic target. The aim of this study was to evaluate mutations at gyrA associated with ciprofloxacin resistance and evaluate whether acquisition of resistance impacts on fitness and stress tolerance of A. butzleri. A. butzleri ciprofloxacin mutants were generated by laboratory induction. Identification of mutations associated with ciprofloxacin resistance was performed by gyrA sequencing. Growth kinetics, cost of fitness, biofilm formation ability, and stress tolerance were assessed. Two amino acid substitutions in the quinolone resistance-determining region of GyrA were identified in the mutant strains, one previously described (Thr-85-Ile) and a new substitution (Asp-89-Tyr). No differences in growth kinetics were recorded between parental and mutant strains; however, fitness cost was variable, according to the genetic background of the strains, and independently of ciprofloxacin resistance. Overall, the ciprofloxacin resistance development did not significantly affect stress tolerance, motility, or biofilm-forming ability. In conclusion, acquisition of ciprofloxacin resistance in A. butzleri is associated with mutations in gyrA and is likely well compensated, with cost of fitness reflecting the diversity in genetic background of this bacterium.

Fluoroquinolone Resistance Mechanisms by Molecular Epidemiologic Study of Ciprofloxacin-Nonsusceptible Escherichia coli Sequence Types Isolated from Clinical Specimens in a Tertiary Care University Hospital in Korea: Emergence of Clone ST131, 2006-2008

To investigate the sequence types (STs) and fluoroquinolone resistance related mutations among ciprofloxacin (CIP)-non-susceptible extended-spectrum β-lactamase (ESBL)-producing E. coli isolated from Korean patients from 2006-2008. The prevalence of fluoroquinolone resistance-determining region (QRDR) mutations in gyrA, gyrB, parC, and parE and plasmid-mediated quinolone resistance (PMQR) genes were also studied. Multilocus sequence typing (MLST) was performed to identify STs. The most common ST was ST131 (33/51, 64.7%). All isolates, except one isolate, showed three mutations at codons 83 (S83L) and 87 (S87N) in gyrA and 80 (S80I) in parC The prevalence of ST131 in our hospital was much higher than reported in other Asian studies during a similar time period. The mutations found in ST131 were concordant with other studies.

A study on the aac-(61)-lb-cr gene prevalence among ciprofloxacin-resistant strains of uropathogenic Enterobacteriaceae

INTRODUCTION

Urinary tract infections (UTIs) are very common. Indiscriminate use of antibiotics has led to the development of resistance to most of the commonly used antibiotics including quinolones.

AIM

This study aimed to find out the prevalence of ciprofloxacin resistance among the uropathogenic Enterobacteriaceae, to determine the virulence factors of these isolates, and to detect the aac-(6¹)-lb-cr gene among those isolates with minimal inhibitory concentrations (MICs) of ciprofloxacin >256 mcg/ml.

MATERIALS AND METHODS

Urine samples reaching the microbiology laboratory were processed, pathogens belonging to the Enterobacteriaceae family were isolated from those with significant bacteriuria, and antibiotic sensitivity testing was performed according to the CLSI guidelines. MIC of ciprofloxacin for the isolates resistant to ciprofloxacin was determined by using the E-test, and virulence factors such as hemagglutination, hemolysis, and mucoid colonies were analyzed. aac-(6¹)-lb-cr gene was analyzed by polymerase chain reaction for those isolates with MIC > 256 mcg/ml.

RESULTS

Escherichia coli was the most common isolate (62%) with the highest ciprofloxacin resistance (68%). Fourteen percent of them had MIC > 256 mcg/ml and all of these isolates harbored the aac-(6¹)-lb-cr gene.

CONCLUSION

Plasmid-mediated drug resistance can rapidly spread and lead to selection of drug-resistant mutants if not controlled.

High genetic similarity of ciprofloxacin-resistant Campylobacter jejuni in central Europe

Campylobacteriosis is the leading zoonosis in the European Union with the majority of cases attributed to Campylobacter jejuni. Although the disease is usually self-limiting, some severe cases need to be treated with antibiotics, primarily macrolides and quinolones. However, the resistance to the latter is reaching alarming levels in most of the EU countries. To shed light on the expansion of antibiotic resistance in central Europe, we have investigated genetic similarity across 178 ciprofloxacin-resistant C. jejuni mostly isolated in Slovenia, Austria and Germany. We performed comparative genetic similarity analyses using allelic types of seven multilocus sequence typing housekeeping genes, and single nucleotide polymorphisms of a quinolone resistance determining region located within the DNA gyrase subunit A gene. This analysis revealed high genetic similarity of isolates from clonal complex ST-21 that carry gyrA allelic type 1 in all three of these central-European countries, suggesting these ciprofloxacin resistant isolates arose from a recent common ancestor and are spread clonally.

Rapid change in the ciprofloxacin resistance pattern among Neisseria gonorrhoeae strains in Nuuk, Greenland: time to reconsider preventive and treatment strategies

OBJECTIVES

Sexually transmitted infections (STIs), including infections with Neisseria gonorrhoeae (GC), are highly incident in Greenland. Since January 2011, GC testing has been performed on urine with nucleic acid amplification tests (NAATs) by strand displacement amplification (Becton Dickinson ProbeTec). Monitoring of GC antibiotic susceptibility by culture was introduced in Nuuk in 2012. Until 2014, no cases of ciprofloxacin-resistant GC strains were reported. In this paper, we report the finding of ciprofloxacin-resistant GC and describe the most recent incidence of GC infections in Greenland.

METHODS

The number of urine NAATs and culture-positive swabs from January to October 2014 were obtained from the Central Laboratory at Queens Ingrid's Hospital in Nuuk and stratified on gender, place and period of testing. Incidence rates were estimated as number of urine NAAT * (12/10) per 100,000 inhabitants. Men in Nuuk with a positive NAAT for GC were encouraged to provide a urethral swab for culture and susceptibility testing.

RESULTS

From January to October 2014, a total of 5,436 urine GC NAATs were performed on patients from Nuuk and 9,031 from the rest of Greenland. Of these, 422 (8%) and 820 (9%) were positive, respectively. From January to August, 6 (15%) cultures from Nuuk were ciprofloxacin resistant while in September and October, 26 (59%) were ciprofloxacin resistant (p<0.01). In total, 35 (40%) of 88 culture-positive isolates showed ciprofloxacin resistance. GC incidence in Nuuk was 3,017 per 100,000 inhabitants per year, compared to 2,491 per 100,000 inhabitants per year in the rest of Greenland.

CONCLUSION

Within a short period, a rapid and dramatic change in ciprofloxacin susceptibility among GC strains isolated in Nuuk was documented and recommendation for first line treatments has changed. Continued monitoring and rethinking of primary and secondary preventive initiatives is highly recommended in this high GC incidence setting.

Ciprofloxacin resistance and gonorrhea incidence rates in 17 cities, United States, 1991-2006

Antimicrobial drug resistance can hinder gonorrhea prevention and control efforts. In this study, we analyzed historical ciprofloxacin resistance data and gonorrhea incidence data to examine the possible effect of antimicrobial drug resistance on gonorrhea incidence at the population level. We analyzed data from the Gonococcal Isolate Surveillance Project and city-level gonorrhea incidence rates from surveillance data for 17 cities during 1991–2006. We found a strong positive association between ciprofloxacin resistance and gonorrhea incidence rates at the city level during this period. Their association was consistent with predictions of mathematical models in which resistance to treatment can increase gonorrhea incidence rates through factors such as increased duration of infection. These findings highlight the possibility of future increases in gonorrhea incidence caused by emerging cephalosporin resistance.

PMQR genes oqxAB and aac(6')Ib-cr accelerate the development of fluoroquinolone resistance in Salmonella typhimurium

Emergence of multidrug-resistant Salmonella typhimurium strains, especially the ACSSuT and nalidixic acid R types, has significantly compromised the effectiveness of current strategies to control Salmonella infections, resulting in increased morbidity and mortality. Clinical S. typhimurium isolates recovered in Hong Kong during the period of 2005–2011 were increasingly resistant to ciprofloxacin (CIP) and antibiotics of the ACSSuT group. Our data revealed that oqxAB and aac(6′)Ib-cr were encoded on plasmids of various sizes and the presence of these two elements together with a single gyrA mutation in S. typhimurium were sufficient to mediate resistance to CIP. Acquisition of the oqxAB and aac(6′)Ib-cr encoding plasmids by S. typhimurium caused a fourfold increase in CIP minimal inhibitory concentration. Furthermore, the presence of oqxAB and aac(6′)Ib-cr in Salmonella dramatically increased the mutation prevention concentration of CIP which may due to mutational changes in the drug target genes. In conclusion, possession of oqxAB and aac(6′)Ib-cr encoding plasmid facilitate the selection of CIP resistant S. typhimurium, thereby causing a remarkable increase of CIP resistance among clinical Salmonella strains in Hong Kong.

Detection of highly ciprofloxacin resistance acinetobacter baumannii isolated from patients with burn wound infections in presence and absence of efflux pump inhibitor

The emergence of fluoroquinolone resistance among A. baumannii isolates is now of particular concern. Phenotypic and genotypic characteristics of resistance to ciprofloxacin among 50 Acinetobacter baumannii isolated from burn wound infections of Tehran were evaluated by E-test and broth microdilution in presence and absence of efflux pump inhibitor phenylalanine- arginine β-naphthylamide (PAβN) and PCR-sequencing methods. All isolates were then typed by REP-PCR fingerprinting to find the clonal relationship between resistant isolates. Our results indicated that resistance to ciprofloxacin among A. baumannii isolated from burn infections in Tehran are high with resistance rate of 100% and ciprofloxacin resistant isolates have a mutation of Serine 83 →Leucine in the quinolone resistance determining region (QRDR) of DNA gyrase subunit A (GyrA). 38% of the isolates showed MIC ranges of 64 to ≥512μg/ml and were considered as highly resistant. We could not detect Par C mutations and plasmid-mediated quinolone resistance A (qnrA) among ciprofloxacin resistant isolates. When we used the efflux pump inhibitor PAbN, MIC of ciprofloxacin was reduced two-to four folds. REP-type A (25/50; 50%), B (20/50; 30%) and C (10/50; 20%) were the most common REP-types among A. baumannii isolates. It seems that mutation in GyrA is the main mechanism of resistant to ciprofloxacin among A. baumannii isolates from burn infections and presence of efflux pumps is just secondary target for ciprofloxacin resistant among A. baumannii in Iran. Regarding with limitation of REP-types detected in this study, we found good correlation between resistance to ciprofloxacin and REP-types A-C.

Contribution of AcrAB efflux pump to ciprofloxacin resistance in Klebsiella pneumoniae isolated from burn patients

Resistance to fluoroquinolones has been recently increased among bacterial strains isolated from outpatients. Multidrug-resistant K. pneumoniae is one of the major organisms isolated from burn patients and the AcrAB efflux pump is the principal pump contributing to the intrinsic resistance in K. pneumoniae against multiple antimicrobial agents including ciprofloxacin and other fluoroquinolones.

Fifty-two K. pneumoniae isolated from burn patients in Shahid Motahari hospital and confirmed by conventional biochemical tests. Antimicrobial susceptibility testing was done according to CLSI 2011 guidelines, to determine the antimicrobial resistance pattern of isolates. AcrA gene was detected among ciprofloxacin-resistant isolates by PCR assay. MICs to ciprofloxacin were measured with and without carbonyl cyanide 3-chlorophenylhydrazone (CCCP). Forty out of the 52 K. pneumoniae isolated from burn patients in Shahid Motahari hospital were resistant to ciprofloxacin according to breakpoint of CLSI guideline. PCR assay for acrA gene demonstrated that all ciprofloxacin-resistant isolates harbored acrA gene coding the membrane fusion protein AcrA and is a part of AcrAB efflux system. Among these isolates, 19 strains (47.5%) showed 2 to 32 fold reduction in MICs after using CCCP as an efflux pump inhibitor. The other 21 strains (52.5%) showed no disparity in MICs before and after using CCCP. In conclusion, the AcrAB efflux system is one of the principal mechanisms contribute in ciprofloxacin resistance among K. pneumoniae isolates but there are some other mechanisms interfere with ciprofloxacin resistance such as mutation in target proteins of DNA gyrase of topoisomerase IV enzymes.

Ciprofloxacin-resistant Salmonella enterica serovar Kentucky in Canada

We report emergence of ciprofloxacin-resistant Salmonella enterica serovar Kentucky in Canada during 2003-2009. All isolates had similar macrorestriction patterns and were multilocus sequence type ST198, which has been observed in Europe and Africa. Ciprofloxacin-resistant S. enterica serovar Kentucky represents 66% of all ciprofloxacin-resistant nontyphoidal Salmonella sp. isolates observed in Canada since 2003.

ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198

A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Among a panel of representative isolates (n = 27), covering the epidemic, only three showed distinct mutations in ramR resulting in enhanced expression of genes encoding the AcrAB-TolC efflux system and low increase in ciprofloxacin MIC. No mutations were detected in other regulatory regions of this efflux system. Ciprofloxacin resistance in serovar Kentucky ST198 is thus currently mainly due to multiple target gene mutations.

Molecular basis of high-level ciprofloxacin resistance in Neisseria gonorrhoeae strains from Shandong Province, China

In the study, the ciprofloxacin resistance rate was 100%. High-level ciprofloxacin resistance rate was 63.55%. Sixteen different mutation patterns involved in the formation of ciprofloxacin resistance were identified. The most prevalent were patterns P7 (25.2%), P8 (15.0%), P9 (11.2%), P1 (10.3%), and P5 (10.3%). All of the 107 NG isolates analyzed for mutations in the study have demonstrated a change of Ser-91 → Phe in the gyrA gene, and all except one have demonstrated a change in position 95 of the amino acid sequence. All of the 68 high-level QRNG isolates had double mutations in gyrA gene combined with a single or two mutations in parC gene. It is most important that a new mutation site of Ile-97 → Met in gyrA and a new mutation of Leu-106 → Ile in parC were found in the study, both leading to high-level ciprofloxacin resistance (MIC values, 8 μg/mL, 32 μg/mL, respectively). Therefore, we confim that gyrA mutations are necessary for the fluoroquinolone resistance phenotype and parC mutations are correlated intimately with high-level fluoroquinolone resistance. In China fluoroquinolone resistance in Neisseria gonorrhoeae strains is very serious and the new mutation sites in the fluoroquinolone resistance-determining regions emerge more and more quickly. Hence, in China fluoroquinolones, which are used to treat gonorrhoea presently, should be substituted by a new antibiotics.

Geographical variation in antibiotic-resistant Escherichia coli isolates from stool, cow-dung and drinking water

Little information is available on relationships between the biophysical environment and antibiotic resistance. This study was conducted to investigate the antibiotic resistance pattern of Escherichia coli isolated from child stool samples, cow-dung and drinking water from the non-coastal (230 households) and coastal (187 households) regions of Odisha, India. Susceptibility testing of E. coli isolates (n = 696) to the following antibiotics: tetracycline, ampicillin/sulbactam, cefuroxime, cefotaxime, cefixime, cotrimoxazole, amikacin, ciprofloxacin, norfloxacin and nalidixic acid was performed by the disk diffusion method. Ciprofloxacin minimum inhibitory concentration (MIC) values were determined for ciprofloxacin-resistant isolates (n = 83). Resistance to at least one antibiotic was detected in 90% or more of the E. coli isolates. Ciprofloxacin MIC values ranged from 8 to 32 µg/mL. The odds ratio (OR) of resistance in E. coli isolates from children’s stool (OR = 3.1, 95% CI 1.18–8.01), cow-dung (OR = 3.6, 95% CI 1.59–8.03, P = 0.002) and drinking water (OR = 3.8, 95% CI 1.00–14.44, P = 0.049) were higher in non-coastal compared to coastal region. Similarly, the co-resistance in cow-dung (OR = 2.5, 95% CI 1.39–4.37, P = 0.002) and drinking water (OR = 3.2, 95% CI 1.36–7.41, P = 0.008) as well as the multi-resistance in cow-dung (OR = 2.2, 95% CI 1.12–4.34, P = 0.022) and drinking water (OR = 2.7, 95% CI 1.06–7.07, P = 0.036) were also higher in the non-coastal compared to the coastal region.

Change of antimicrobial susceptibility among Escherichia coli strains isolated from female patients with community-onset acute pyelonephritis

PURPOSE

There is a concern on which antimicrobials are appropriate as empirical agents for community-onset acute pyelonephritis (APN) in regions where the fluoroquinolone resistance rate is high, such as in Korea.

MATERIALS AND METHODS

Three hundred and two strains of E. coli in 2001-2002 and 349 strains in 2008-2009 were isolated from the urine cultures of female adult APN patients, and the antimicrobial susceptibility was compared according to each study period. All the patients were classified as uncomplicated or complicated APN, and a subgroup analysis was done thereafter.

RESULTS

The E. coli strains isolated in 2008-2009 showed improved susceptibility to trimethoprim-sulfamethoxazole compared to those isolated in 2001-2002. However, the third generation cephalosporin and gentamicin susceptibility was worsened. Of the 232 isolates from the uncomplicated APN patients, there was no difference between the two different time periods. On the other hand, of the 419 isolates from the complicated APN patients, the susceptibility to third generation cephalosporin, gentamicin and ciprofloxacin was significantly worsened.

CONCLUSION

The antimicrobial susceptibility of E. coli changed over the study period, however, this change occurred mainly in the complicated APN patients. In Korea, ciprofloxacin is still useful as an empirical agent for uncomplicated APN patients, but this is not the case for patients with complicated APN because of high resistance rate to ciprofloxacin in these patients. For the complicated APN patients, the rate of resistance to ciprofloxacin is already more than 30%.