Search

Background: In this study, the mechanisms implicated in delafloxacin resistance in Klebsiella pneumoniae strains were investigated. Delafloxacin is a novel, broad-spectrum fluoroquinolone that has been approved for clinical application. Methods: In our study, 43 K. pneumoniae strains were assessed, antimicrobial susceptibility testing was performed via the broth microdilution method, and the minimum inhibitory concentration (MIC) values for ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, and imipenem were determined. Four delafloxacin-resistant K. pneumoniae strains were selected for whole-genome sequencing (WGS). Results: The MIC50 values for the 43 K. pneumoniae strains were as follows: ciprofloxacin 0.5 mg/L, levofloxacin 0.25 mg/L, moxifloxacin 0.5 mg/L, and delafloxacin 0.25 mg/L. All four selected delafloxacin-resistant K. pneumoniae strains showed extended-spectrum beta-lactamase production, and one strain exhibited carbapenem resistance. WGS enabled us to determine the sequence types (STs) of these strains, namely, ST307 (two strains), ST377, and ST147. Multiple mutations in quinolone-resistance-determining regions (QRDRs) were detected in all the delafloxacin-resistant K. pneumoniae strains; specifically, gyrA Ser83Ile and parC Ser80Ile were uniformly present in the strains of ST307 and ST147. However, in the ST377 strain, gyrA Ser83Tyr, Asp87Ala, and parC Ser80Ile, amino acid substitutions were detected. We also identified OqxAB and AcrAB efflux pumps in all delafloxacin-resistant K. pneumoniae strains. The association between beta-lactamase production and delafloxacin resistance was determined; specifically, CTX-M-15 production was detected in the ST147, ST307, and ST377 strains. Moreover, NDM-1 was detected in ST147. Conclusions: We conclude that multiple mutations in QRDRs, in combination with OqxAB and AcrAB efflux pumps, achieved delafloxacin resistance in K. pneumoniae. In our study, we report on NDM-1-producing K. pneumoniae ST147 in Hungary. [ABSTRACT FROM AUTHOR]

Abstract Purpose Corynebacterium species are commensals of human skin and mucous membranes and are recognized as important pathogens in ocular infections. This study investigated the clinical characteristics of Corynebacterium keratitis. Methods We retrospectively reviewed cases of bacterial keratitis in which Corynebacterium species were solely isolated from corneal scraping cultures collected at Ehime University Hospital between January 2010 and February 2024. The clinical findings of Corynebacterium keratitis were divided into two types: adherent and infiltrative, which are defined as adhesion to the corneal surface or stromal infiltration, respectively. Results Of the 232 culture-positive cases of bacterial keratitis, 23 (9.9%) were positive for Corynebacterium species alone. The mean patient age was 60.1 ± 21.0 years, and the cohort included 12 males and 11 females. Adherent type was found in 13 patients (56.5%) and infiltrative type was observed in 10 patients (43.5%). Fluoroquinolone eye drops were used by 14 (60.9%) patients and steroid eye drops by 12 (52.2%). Corynebacterium macginleyi was the most commonly identified species (85.7%). 91% of Corynebacterium isolates were resistant to fluoroquinolones. All of C. macginleyi isolates were fluoroquinolone-resistant, and 93.3% of the isolates were highly resistant (minimal inhibitory concentrations > 32 µg/mL). All cases were treated with frequent antimicrobial eye drops, mainly cephalosporins, and the mean treatment duration was 21.6 days. Although no patient required therapeutic keratoplasty, five adherent types required multiple therapeutic debridements to physically remove the bacteria. Conclusions Corynebacterium keratitis presented as adherent and infiltrative types of lesions. The main characteristics of the patient included the use of fluoroquinolone and steroid eye drops.

The global tuberculosis (TB) epidemic is becoming progressively more complex due to the increasing prevalence of multidrug-resistant TB (MDR-TB), particularly with resistance to fluoroquinolones (FQs). This study focuses on identifying genetic mutations in the gyrA and gyrB genes of Mycobacterium tuberculosis that drive FQ resistance. Sputum samples from suspected pulmonary TB patients were analyzed using PCR and sequencing to detect mutations within the quinolone resistance-determining regions (QRDR). The analysis revealed that mutations in gyrA, especially S95T, are prevalent and play a key role in FQ resistance. Additionally, less frequent mutations in gyrB, such as E501D and A533P, were also detected. These findings shed light on the molecular mechanisms contributing to FQ resistance in MDR-TB strains and underscore the need for enhanced diagnostic methods to identify resistance patterns more accurately. The insights gained from this research offer a foundation for improving TB treatment approaches and addressing the growing challenge of drug-resistant TB worldwide.

Abstract Fluoroquinolone-resistant (FQs-R) microorganisms causing infectious complications after ultrasound-guided needle biopsy of the prostate (TRUS-BP) have become an important challenge in healthcare settings globally, questioning the continued utility of FQ as the preferred prophylactic agent. This study aimed to characterize molecular mechanisms of resistance on FQs-R E. coli isolated from the enteric microbiota of patients undergoing (TRUS-BP) and to highlight their impact on Minimum Inhibitory Concentrations (MICs). From February 2016 to December 2018, the incidence of rectal carriage of Qs-FQs resistant Enterobacterales detected from rectal swabs of patients before undergoing (TRUS-BP) was 61.06% (80/131) all related to E. coli species. Based on the MICs range of Qs (24–256 mg/L) and FQs (0.24–128 mg/L) breakpoint by EUCAST, we categorized these E. coli isolates into three resistance profiles (I, II, and III) associated with the patterns of chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC and the plasmid-mediated quinolone resistance encoding genes (PMQRs) detected by PCR-based assay and sequencing; MICs increase in an escalation step according to the co-occurrence of multiple molecular mechanisms. The mutation of the gyrA gene was the most frequent on codons (Ser83Leu/Thr/Tyr/Trp and Asp87Asn); mutation on the parC gene was the least on codons (Ser80Iso/Leu and Glu84 Val/Gly/Lys). PMQRs genes (4 qnrB ,7 qnrS, and one aac(6’)-Ib-cr) were determined within 15% of the isolates. Allelic variation allows us to report earliest the qnrB81 determinant in an E. coli isolate. Among isolates (35%) belonged to the notorious ST131 lineage. The phylogenetic group showed a predominance of B2 group (51, 25%), however (PFGE) revealed a high level of clonal variability. Worrying incidence of FQs-R E. coli isolates in the rectal flora of our local population showed the potential to cause post-infection. FQ resistance is a complex interplay between mutations in the QRDRs and PMQR determinants that impact MICs. The importance of intestinal microbiota as a reservoir of resistant strains and pandemic clones encourages driving mitigation challenges to characterize molecular mechanisms of antimicrobial resistance to adapt prophylactic therapy, control infection, and ensure epidemiological monitoring.

Abstract In this study delafloxacin resistance mechanisms in Escherichia coli strains were analyzed. Delafloxacin is a new fluoroquinolone, that is approved for clinical application however, resistance against this agent is scarcely reported. In our study 37 E. coli strains were included and antimicrobial susceptibility testing was performed for ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, imipenem. Six delafloxacin resistant E. coli strains were selected for whole-genome sequencing and all of them exhibited resistance to other fluoroquinonlones and showed an extended-spectrum beta-lactamase phenotype. The six delafloxacin resistant E. coli strains belonged to different sequence types (STs) namely, ST131 (2 strains), ST57 (2 strains), ST162 and ST15840. Each delafloxacin resistant strain possessed multiple mutations in quinolone resistance-determining regions (QRDRs). Notably, three mutations in gyrA Ser83Leu, Asp87Asn and parC Ser80Ile were in strains of ST162, ST57 and ST15840. However, the two strains of ST131 carried five combined mutations namely, gyrA Ser83Leu, Asp87Asn, parC Ser80Ile, Glu84Val, parE Ile549Leu. Association of delafloxacin resistance and production of CTX-M-15 in ST131, CMY-2 in ST162 and ST15840 was detected. In this study a new ST, ST15840 of clonal complex 69 was identified. Our results demonstrate, that at least three mutations in QRDRs are required for delafloxacin resistance in E. coli.

Background: New Zealand has among the highest rates of antimicrobial resistance in Mycoplasma genitalium in the world. The aim of this study was to correlate treatment outcomes with 23S rRNA and parC mutations associated with macrolide and fluroquinolone resistance, respectively, in a cohort of sexual health clinic patients. Methods: Laboratory and clinical data were collected for patients with M. genitalium infections attending Auckland Sexual Health Service between 1 January 2018 and 31 December 2022, who had a test-of-cure performed within 21–90 days of a treatment episode. Treatment outcomes were correlated with the presence or absence of resistance mutations and treatment regimen utilised. Results: A total of 95 infections from 93 patients met the study inclusion criteria. Eighty of 93 (86%) infections with available data were macrolide resistant, with 20 of 74 (27%) having both macrolide resistance and parC mutations. Sixteen of 20 (80%) of parC mutations were G248T (S83I), three of 20 (15%) G259T (D87Y) and one of 20 (5%) A247C (S83R). All macrolide-susceptible infections treated with doxycycline and azithromycin were cured (12/12), as were all macrolide-resistant infections without parC mutations treated with doxycycline and moxifloxacin (37/37). Cure rates for macrolide-resistant infections with parC mutations were lower, with variable and often multiple treatment courses; eight of 16 (50%) were cured using one course of sequential doxycycline and moxifloxacin, seven of nine (78%) with one course of minocycline, zero of two (0%) with pristinamycin and one of one (100%) with doxycycline and sitafloxacin. Conclusions: Our findings highlight the differing treatment outcomes for infections with and without parC mutations, offering opportunities to refine management of M. genitalium infections. New Zealand has high rates of antimicrobial resistance in Mycoplasma genitalium. We correlated treatment outcomes with resistance markers and found excellent outcomes for macrolide-sensitive infections, or those without par C mutations, with first-line resistance-guided therapies. There were lower cure rates for infections with both macrolide and par C mutations, offering opportunities to refine management of M. genitalium infections. [ABSTRACT FROM AUTHOR]

The global tuberculosis (TB) epidemic is becoming progressively more complex due to the increasing prevalence of multidrug-resistant TB (MDR-TB), particularly with resistance to fluoroquinolones (FQs). This study focuses on identifying genetic mutations in the gyrA and gyrB genes of Mycobacterium tuberculosis that drive FQ resistance. Sputum samples from suspected pulmonary TB patients were analyzed using PCR and sequencing to detect mutations within the quinolone resistance-determining regions (QRDR). The analysis revealed that mutations in gyrA, especially S95T, are prevalent and play a key role in FQ resistance. Additionally, less frequent mutations in gyrB, such as E501D and A533P, were also detected. These findings shed light on the molecular mechanisms contributing to FQ resistance in MDR-TB strains and underscore the need for enhanced diagnostic methods to identify resistance patterns more accurately. The insights gained from this research offer a foundation for improving TB treatment approaches and addressing the growing challenge of drug-resistant TB worldwide. [ABSTRACT FROM AUTHOR]

Fluoroquinolone-resistant (FQs-R) microorganisms causing infectious complications after ultrasound-guided needle biopsy of the prostate (TRUS-BP) have become an important challenge in healthcare settings globally, questioning the continued utility of FQ as the preferred prophylactic agent. This study aimed to characterize molecular mechanisms of resistance on FQs-R E. coli isolated from the enteric microbiota of patients undergoing (TRUS-BP) and to highlight their impact on Minimum Inhibitory Concentrations (MICs). From February 2016 to December 2018, the incidence of rectal carriage of Qs-FQs resistant Enterobacterales detected from rectal swabs of patients before undergoing (TRUS-BP) was 61.06% (80/131) all related to E. coli species. Based on the MICs range of Qs (24–256 mg/L) and FQs (0.24–128 mg/L) breakpoint by EUCAST, we categorized these E. coli isolates into three resistance profiles (I, II, and III) associated with the patterns of chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC and the plasmid-mediated quinolone resistance encoding genes (PMQRs) detected by PCR-based assay and sequencing; MICs increase in an escalation step according to the co-occurrence of multiple molecular mechanisms. The mutation of the gyrA gene was the most frequent on codons (Ser83Leu/Thr/Tyr/Trp and Asp87Asn); mutation on the parC gene was the least on codons (Ser80Iso/Leu and Glu84 Val/Gly/Lys). PMQRs genes (4 qnrB ,7 qnrS, and one aac(6’)-Ib-cr) were determined within 15% of the isolates. Allelic variation allows us to report earliest the qnrB81 determinant in an E. coli isolate. Among isolates (35%) belonged to the notorious ST131 lineage. The phylogenetic group showed a predominance of B2 group (51, 25%), however (PFGE) revealed a high level of clonal variability. Worrying incidence of FQs-R E. coli isolates in the rectal flora of our local population showed the potential to cause post-infection. FQ resistance is a complex interplay between mutations in the QRDRs and PMQR determinants that impact MICs. The importance of intestinal microbiota as a reservoir of resistant strains and pandemic clones encourages driving mitigation challenges to characterize molecular mechanisms of antimicrobial resistance to adapt prophylactic therapy, control infection, and ensure epidemiological monitoring. [ABSTRACT FROM AUTHOR]

Community-acquired urinary tract infections account for 15% of all outpatient use of antibiotics, and women are primarily affected; the major causative microorganism is uropathogenic Escherichia coli (E. coli). Treatment is indicated for cystitis and pyelonephritis and includes B-lactams (amoxicillin-clavulanic acid or third-generation cephalosporins), fluoroquinolones (ciprofloxacin or levofloxacin), nitrofurantoin, fosfomycin, and trimethoprim–sulfamethoxazole. Resistance to antibiotic treatment is of concern; several mechanisms have been associated with the acquisition of genes that confer antimicrobial resistance to fluoroquinolones, which are often associated with other patterns of resistance, especially in extended-spectrum beta-lactamase (ESBL) producers. Several studies have addressed the prevalence of uropathogens producing ESBLs, but only a few have focused on fluoroquinolone resistance, and, to our knowledge, none have addressed the prevalence of phylotypes or genes responsible for antimicrobial resistance to fluoroquinolones. The focus of the present review was to analyze recently published papers that described the E. coli phylotype causing community-acquired UTIs in association with fluoroquinolone resistance. [ABSTRACT FROM AUTHOR]

In this study delafloxacin resistance mechanisms in Escherichia coli strains were analyzed. Delafloxacin is a new fluoroquinolone, that is approved for clinical application however, resistance against this agent is scarcely reported. In our study 37 E. coli strains were included and antimicrobial susceptibility testing was performed for ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, imipenem. Six delafloxacin resistant E. coli strains were selected for whole-genome sequencing and all of them exhibited resistance to other fluoroquinonlones and showed an extended-spectrum beta-lactamase phenotype. The six delafloxacin resistant E. coli strains belonged to different sequence types (STs) namely, ST131 (2 strains), ST57 (2 strains), ST162 and ST15840. Each delafloxacin resistant strain possessed multiple mutations in quinolone resistance-determining regions (QRDRs). Notably, three mutations in gyrA Ser83Leu, Asp87Asn and parC Ser80Ile were in strains of ST162, ST57 and ST15840. However, the two strains of ST131 carried five combined mutations namely, gyrA Ser83Leu, Asp87Asn, parC Ser80Ile, Glu84Val, parE Ile549Leu. Association of delafloxacin resistance and production of CTX-M-15 in ST131, CMY-2 in ST162 and ST15840 was detected. In this study a new ST, ST15840 of clonal complex 69 was identified. Our results demonstrate, that at least three mutations in QRDRs are required for delafloxacin resistance in E. coli. [ABSTRACT FROM AUTHOR]

Campylobacter species are the leading cause of bacterial diarrhoea worldwide and consumption of contaminated chicken meat is the most common route of infection. Chickens can be infected with multiple strains of Campylobacter and during the infection cycle this pathogen must survive a wide variety of environments. Numerous studies have reported a high degree of genetic variability in this pathogen that can use antigenic and phase variation to alter the expression of key phenotypes. In this study the phenotypic profile of isolates from freshly slaughtered chickens, chicken products in the supermarket and stool samples from infected patients were compared to identify phenotypic changes during the passage of the bacteria through the infection cycle. Isolates from different stages of the infection cycle had altered phenotypic profiles with isolates from human stool samples showing a lower ability to form a biofilm and an increased ability to associate with epithelial cells in vitro. Resistance to fluoroquinolones was found in all cohorts but at a much higher occurrence (94%) in isolates from supermarket chicken. Isolates displaying high levels of resistance to fluoroquinolones also were more likely to display a higher tolerance to growth in the presence of oxygen. In conclusion, isolates with specific phenotypes appear to be overly represented at different stages of the infection cycle suggesting that environmental stresses may be enriched for strains with these phenotypes.

Aim to investigate the pathogens distribution and drug resistance of gram-negative bacteria causing bloodstream infection (BSIs) in Infectious Disease Surveillance of Pediatric from 2016 to 2022. The prevalence of four important drug resistance phenotypes was studied: difficult-to-treat resistance, fluoroquinolone resistance, carbapenem resistance, and extended-spectrum cephalosporin resistance, and to provide reference basis for preventing and treating BSIs diseases in children. Methods: Strain identification and antimicrobial susceptibility tests were independently performed at each hospital. Data were analyzed using Whonet 5.6 and GraphPad Prism 8 software. The Mann–Whitney U-test was used to examine and compare temporal changes. Results: A total of 39977 BSIs strains were isolated, with 27.1% of the negative bacteria causing BSIs (10824 strains). The highest bacteria detected were E. coli and S. maltophilia in the neonatal and pediatric groups. The detection rate of carbapenem-resistant-K. pneumoniae (CRKPN) in neonate group was 31.4%, significantly increased compared with pediatric group, whose detection rate was 24.7%. The rates of resistance to levofloxacin and trimethoprim/sulfamethoxazole were significantly lower in neonatal groups than pediatric groups in BSIs caused by K. pneumoniae. To imipenem and meropenem were 3.6% and 3.9% among neonatal isolates, which was lower than 4.7% and 5.8 among pediatric BSIs caused by E. coli. Isolated from neonatal BSIs caused by A. baumannii showed lower resistance ratios to all the agents tested than those from pediatric. However, only the prevalence of piperacillin/tazobactam resistance was statistically lower than that in pediatric BSIs caused by P. aeruginosa. The average detection rates of carbapenem resistance, extended-spectrum cephalosporin resistance, and fluoroquinolone resistance for K. pneumoniae and E. coli were 28.1%,41.4%,11.6% and 4.0%,24.3%,31.1%, respectively. Conclusion: The detection rate of gram-negative pathogens showed an increasing trend among the bloodstream infection. The detection rate of CRKPN assumed a downward trend in 2018. There are differences types of pathogens between the neonatal group and the pediatric group, The detection rate of CRKPN in the neonate group was significantly higher than pediatric group. The first average detection rates for carbapenem resistance, extended-spectrum cephalosporin resistance, and fluoroquinolone resistance were obtained for A. baumannii, K. pneumoniae, and Escherichia coli, respectively. Those data showed a high level of antimicrobial resistance, which has posed an urgent threat to Children's health, suggested that effective monitoring of antimicrobial resistance and antimicrobial stewardship among children in China are required. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the benefit of targeted antibiotic prophylaxis (TAP) based on rectal swab culture in comparison with standard empiric antimicrobial prophylaxis in patients undergoing transrectal ultrasound-guided needle biopsy of the prostate (TRUS-BP), as well as to assess rate of fecal carriage of Fluoroquinolone-resistant Enterobacterales FQRE. Patients and methods: We prospectively analyzed data that randomized 157 patients within two groups: (G1) TAP according to rectal swab performed 10 days before PB; (G2): empirical antibiotic prophylaxis with ciprofloxacin. Prevalence of FQRE digestive carriage and risk factors were investigated. Incidence of infectious complications after (TRUS-BP) in each group was compared. Results: G2 included 80 patients versus 77 in G1. There was no difference between the two groups regarding age, diabetes, prostate volume, PSA, number of biopsy cores, and risk factors for FQRE. In G2, the prevalence of FQRE digestive carriage was 56.3% all related to E. coli species. In the case of digestive carriage of FQRE, TAP according to the rectal swab culture with third-generation cephalosporins was performed in 73.3%. Patients with FQRE had history of FQ use within the last 6 months in 17.8% (p = 0.03). Rate of febrile urinary tract infection after PB was 13% in G1 and 3.8% in G2 (p = 0.02). Conclusions: Incidence of FQ resistance in the intestinal flora of our local population was prevalent. Risk factor for resistance was the use of FQ within the last 6 months. TAP adapted to rectal swab, mainly with third-generation cephalosporins, significantly reduced the rate of infectious complications after (TRUS-BP). [ABSTRACT FROM AUTHOR]

Background/Objectives: Antimicrobial resistance of the E. coli O25 ST131 clonal lineage poses a significant therapeutic challenge worldwide, often involving resistance to fluoroquinolones and extended-spectrum beta-lactamase (ESBL) production. This retrospective study compared the dissemination of multidrug-resistant E. coli O25 ST131 isolated from the urine of outpatients at the largest Croatian clinical microbiology department across six years over two study periods. Methods: The E. coli O25 ST131 clonal lineage was detected via a rapid PCR method using pabB and trpA primers after positive agglutination with E. coli serogroup O25 antisera. ESBL phenotypes and antibiotic susceptibility were investigated according to EUCAST guidelines and breakpoint tables. Results: In the first period, there were a total of 45 isolates of E. coli O25 ST131, among which 30 were isolates with proven ESBL production. In the second period, a total of 114 isolates of E. coli O25 ST131 were detected, among which 75 (65.8%) were ESBL-positive (p > 0.05). In ESBL-negative strains, the multidrug-resistant (MDR) phenotype was characterized by simultaneous resistance to ampicillin, co-trimoxazole, and fluoroquinolones (with an equal proportion of 3/15 isolates in the first period and 7/39 isolates in the second period, p > 0.05). There was no statistically significant difference in the frequency of MDR detection across the two study periods (36/45 and 98/114, p > 0.05). This is the first detection of E. coli O25 ST131 in the outpatient population in Zagreb. Conclusions: There was no statistically significant difference in the frequency of detecting the E. coli O25 ST 131 clone across the two study periods. The high frequency of MDR phenotype among ESBL-negative isolates of E. coli O25 ST131 and an equally high proportion of MDR strains among ESBL producers in this clonal lineage, with the total detection of MDR isolates ≥ 80% in both study periods, are the reasons why this bacterial clone poses a public health threat and why further investigation into its metabolic and virulence characteristics is needed in order to estimate its spreading potential among the outpatient population in Zagreb.

Background: In this study, the mechanisms implicated in delafloxacin resistance in Klebsiella pneumoniae strains were investigated. Delafloxacin is a novel, broad-spectrum fluoroquinolone that has been approved for clinical application. Methods: In our study, 43 K. pneumoniae strains were assessed, antimicrobial susceptibility testing was performed via the broth microdilution method, and the minimum inhibitory concentration (MIC) values for ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, and imipenem were determined. Four delafloxacin-resistant K. pneumoniae strains were selected for whole-genome sequencing (WGS). Results: The MIC50 values for the 43 K. pneumoniae strains were as follows: ciprofloxacin 0.5 mg/L, levofloxacin 0.25 mg/L, moxifloxacin 0.5 mg/L, and delafloxacin 0.25 mg/L. All four selected delafloxacin-resistant K. pneumoniae strains showed extended-spectrum beta-lactamase production, and one strain exhibited carbapenem resistance. WGS enabled us to determine the sequence types (STs) of these strains, namely, ST307 (two strains), ST377, and ST147. Multiple mutations in quinolone-resistance-determining regions (QRDRs) were detected in all the delafloxacin-resistant K. pneumoniae strains; specifically, gyrA Ser83Ile and parC Ser80Ile were uniformly present in the strains of ST307 and ST147. However, in the ST377 strain, gyrA Ser83Tyr, Asp87Ala, and parC Ser80Ile, amino acid substitutions were detected. We also identified OqxAB and AcrAB efflux pumps in all delafloxacin-resistant K. pneumoniae strains. The association between beta-lactamase production and delafloxacin resistance was determined; specifically, CTX-M-15 production was detected in the ST147, ST307, and ST377 strains. Moreover, NDM-1 was detected in ST147. Conclusions: We conclude that multiple mutations in QRDRs, in combination with OqxAB and AcrAB efflux pumps, achieved delafloxacin resistance in K. pneumoniae. In our study, we report on NDM-1-producing K. pneumoniae ST147 in Hungary.

Introduction: Extraintestinal Escherichia coli infections represent a growing public health threat, However, current studies often overlook important factors such as temporal patterns of infection, phylogenetic and clonal background, or the host gut E. coli population, despite their likely significance. Methods: In this study, we analyzed >7000 clinical E. coli isolates from patients at the Minneapolis Veterans Affairs Health Care System (2012-2019), and concurrent fecal E. coli from uninfected veterans. We assessed phylogenetic group distribution, membership in selected sequence types (STs), and subsets thereof--including the pandemic, resistance-associated ST131-H30R, and ST1193 lineages--and strain type, as defined by pulsed-field gel electrophoresis. We then analyzed these features alongside the temporal patterns of infection in individual hosts. Results: The H30R lineage emerged as the leading lineage, both overall and among fluoroquinolone-resistant isolates, with ST1193 following among fluoroquinolone-resistant isolates. Recurrences were common, occurring in 31% of subjects and 41% of episodes, and often multiple and delayed/prolonged (up to 23 episodes per subject; up to 2655d post-index). Remarkably, these recurrences typically involved the subject's index strain (63% of recurrences), even when affecting extra-urinary sites. ST131, H30R, ST1193, and fluoroquinoloneresistant strains generally caused significantly more recurrences than did other strains, despite similar recurrence intervals. ST131 strain types shifted significantly over the study period. Infection-causing strains were commonly detectable in host feces at times other than during an infection episode; the likelihood of detection varied with surveillance intensity and proximity to the infection. H30R and ST1193 were prominent causes of fecal-clinical clonal overlap. Discussion: These findings provide novel insights into the temporal and clonal characteristics of E. coli infections in veterans and support efforts to develop anti-colonization interventions. [ABSTRACT FROM AUTHOR]

Objective: To investigate the antibiotic resistance patterns and genetic factors associated with ExPEC strains isolated from UTI patients. Study Design: Cross sectional Study. Setting: Microbiology Lab in Lahore, Pakistan. Period: December 2021 to June 2022. Methods: A total of 300 urine samples were collected from patients with UTIs, sourced from various hospitals and labs. E. coli identification was confirmed using biochemical tests and the API 20 E standardized method. Results: Antimicrobial susceptibility testing was performed using the disc diffusion technique following CLSI guidelines. The findings revealed varying levels of resistance among the isolates. High resistance rates were observed for ampicillin (92.6%), amoxicillin (93.6%), ceftriaxone (88.9%), and ciprofloxacin (82.4%). Lower resistance rates were found for gentamycin (66%), meropenem (8.2%), tigecycline (4%), imipenem (12.4%), and colistin (0.0%). However, no significant association was detected between the AER gene and fluoroquinolone resistance. Conclusion: This study sheds light on the prevalence of antibiotic resistance in ExPEC strains causing UTIs. The high resistance rates to commonly prescribed antibiotics highlight the need for judicious antibiotic use and alternative treatment strategies. Moreover, the absence of a clear link between the AER gene and fluoroquinolone resistance suggests the involvement of other mechanisms in conferring resistance. Understanding the resistance patterns and genetic factors associated with ExPEC strains is crucial for devising effective treatment strategies and combating the growing problem of multi-drug resistance in UTIs caused by E. coli. [ABSTRACT FROM AUTHOR]

We investigated the carriage of PMQR determinants by E. coli from surface water and their antibiotypes. Water samples were collected and analysed from two surface water: Agbowo (AG) and Arulogun (AR) in South-west Nigeria for E. coli, which were identified using PCR detection of uidA. Susceptibility to antibiotics was done using the disc-diffusion method. Detection of PMQR genes in isolates showing complete resistance or intermediate susceptibility to the fluoroquinolone antibiotics was done using primer-specific PCR. Thirty-six E. coli isolates were obtained [AG (20) and AR (16)]. The isolates showed different levels of resistance to the tested antibiotics, with 100% resistance to amoxicillin-clavulanate. None of the isolates was positive for extended spectrum β-lactamase (ESBL) production, but 25 showed complete resistance or intermediate susceptibility to the fluoroquinolone antibiotics. Two isolates each from AG and AR carried qnrA, one isolate carried qnrS, with one each from AG and AR carrying aac(6′)-lb-cr. Four isolates carried oqxAB, but, qnrB and qepA were not detected in any isolate. This study revealed that polluted surface water is a 'hub' of antibiotic-resistant E. coli harbouring PMQR genes. [ABSTRACT FROM AUTHOR]

Abstract Background Fluoroquinolone resistance is an issue of concern amongst physicians worldwide. In urology, fluoroquinolones are often used in the treatment of acute pyelonephritis and prostatitis, as well as infections caused by multidrug‐resistant pathogens. Aims We aim to highlight the importance of antimicrobial stewardship and the need for ongoing biomedical research to discover novel agents in our losing battle against resistant pathogens. Materials and methods In this review, we survey the literature and summarise fluoroquinolone resistance as it pertains to pyelonephritis and prostatitis, as well as alternative treatment strategies and prevention of multidrug resistance. Results The rise of fluoroquinolone resistance in bacteria has reduced the available treatment options, often necessitating hospital admission for intravenous antibiotics, which places an additional burden on both patients and the healthcare system. Many countries such as Australia have attempted to limit fluoroquinolone resistance by imposing strict prescribing criteria, though these efforts have not been entirely successful. Solutions to overcome resistance include prevention, combination therapy and the development of novel antimicrobial agents. Conclusions Prevention of the proliferation of resistant organisms by antimicrobial stewardship is paramount, and urologists are obliged to be aware of responsible prescribing practices such as referring to local guidelines when prescribing. By reserving fluoroquinolones for infections in which they are truly indicated and by prescribing based on both patient and local environmental factors, we can preserve this effective resource for future use.

Community-acquired urinary tract infections account for 15% of all outpatient use of antibiotics, and women are primarily affected; the major causative microorganism is uropathogenic Escherichia coli (E. coli). Treatment is indicated for cystitis and pyelonephritis and includes B-lactams (amoxicillin-clavulanic acid or third-generation cephalosporins), fluoroquinolones (ciprofloxacin or levofloxacin), nitrofurantoin, fosfomycin, and trimethoprim–sulfamethoxazole. Resistance to antibiotic treatment is of concern; several mechanisms have been associated with the acquisition of genes that confer antimicrobial resistance to fluoroquinolones, which are often associated with other patterns of resistance, especially in extended-spectrum beta-lactamase (ESBL) producers. Several studies have addressed the prevalence of uropathogens producing ESBLs, but only a few have focused on fluoroquinolone resistance, and, to our knowledge, none have addressed the prevalence of phylotypes or genes responsible for antimicrobial resistance to fluoroquinolones. The focus of the present review was to analyze recently published papers that described the E. coli phylotype causing community-acquired UTIs in association with fluoroquinolone resistance.

IntroductionExtraintestinal Escherichia coli infections represent a growing public health threat, However, current studies often overlook important factors such as temporal patterns of infection, phylogenetic and clonal background, or the host gut E. coli population, despite their likely significance.MethodsIn this study, we analyzed >7000 clinical E. coli isolates from patients at the Minneapolis Veterans Affairs Health Care System (2012–2019), and concurrent fecal E. coli from uninfected veterans. We assessed phylogenetic group distribution, membership in selected sequence types (STs), and subsets thereof—including the pandemic, resistance-associated ST131-H30R, and ST1193 lineages—and strain type, as defined by pulsed-field gel electrophoresis. We then analyzed these features alongside the temporal patterns of infection in individual hosts.ResultsThe H30R lineage emerged as the leading lineage, both overall and among fluoroquinolone-resistant isolates, with ST1193 following among fluoroquinolone-resistant isolates. Recurrences were common, occurring in 31% of subjects and 41% of episodes, and often multiple and delayed/prolonged (up to 23 episodes per subject; up to 2655d post-index). Remarkably, these recurrences typically involved the subject’s index strain (63% of recurrences), even when affecting extra-urinary sites. ST131, H30R, ST1193, and fluoroquinolone-resistant strains generally caused significantly more recurrences than did other strains, despite similar recurrence intervals. ST131 strain types shifted significantly over the study period. Infection-causing strains were commonly detectable in host feces at times other than during an infection episode; the likelihood of detection varied with surveillance intensity and proximity to the infection. H30R and ST1193 were prominent causes of fecal-clinical clonal overlap.DiscussionThese findings provide novel insights into the temporal and clonal characteristics of E. coli infections in veterans and support efforts to develop anti-colonization interventions.

Transmission of antimicrobial-resistant bacteria among humans, animals, and the environment is a growing concern worldwide. The distribution of an international high-risk fluoroquinolone-resistant Escherichia coli clone, ST131, has been documented in clinical settings. However, the transmission of ST131 from humans to surrounding environments remains poorly elucidated. To comprehend the current situation and identify the source of ST131 in nature, we analyzed the genetic features of ST131 isolates from the aquatic environment (lake/river water) and wildlife (fox, raccoon, raccoon dog, and deer) and compared them with the features of isolates from humans in Japan using accessory and core genome single nucleotide polymorphism (SNP) analyses. We identified ST131 isolates belonging to the same phylotype and genome clusters (four of eight clusters were concomitant) with low SNP distance between the human isolates and those from the aquatic environment and wildlife. These findings warn of ST131 transmission between humans and the surrounding environment in Japan.

ABSTRACTMycoplasma genitalium is fastidious to culture, and its detection in human clinical specimens relies mainly on molecular methods. Phenotypic determination of antibiotic susceptibility for this bacterium is not a timely or feasible option for most clinical laboratories. This study sought to determine whether next-generation sequencing technologies can effectively be employed in determining genetic mutations associated with drug resistance in M. genitalium samples collected in Aptima Hologic tubes and possibly integrating them into viable workflows in public health laboratories. Following analysis by a custom-designed bioinformatics pipeline, at least one mutation/sample has been identified in 94/98 specimens in at least one of seven loci (macrolides: rrl, rplD, rplV; fluoroquinolones: parC, parE, gyrA, gyrB) described previously to be connected to antibiotic resistance. This method identified a total of 469 single nucleotide polymorphisms (SNPs) (452 mutations): 134 of 23S rRNA SNPs and 318 amino acid mutations: 114 substitutions and 204 synonymous; the turnaround time (sample to analyzed sequence) was typically 3 days. The assays and workflows described in this work demonstrated that the determination of a drug resistance profile for macrolides and fluoroquinolones of M. genitalium samples by using next-generation sequencing in clinical samples is a feasible approach that can be implemented in clinical laboratories, following thorough and extensive validation studies.IMPORTANCEThe mechanisms of drug resistance in Mycoplasma genitalium are complex and involve several genetic loci. The molecular methods for accurately characterizing resistance to fluoroquinolones and macrolides in this organism are often not available or approved for patient use and do not cover all genetic determinants. To this end, we propose a next-generation sequencing-based method with a turnaround time of 3 days that includes the investigation of all drug resistance loci of M. genitalium. Following adaptation, validation, and verification for routine clinical use, assays based on this method may yield molecular results that can be used to guide proper treatment regimens and for surveillance of drug resistance in the general population.

Purpose: This study analyzed the relationship between patient age and the prevalence and fluoroquinolone susceptibility of gram-positive cocci from the ocular surface flora before ophthalmic surgery. Methods: This surveillance study included scraped samples from the conjunctival sac of 8923 eyes of 5490 patients (70.0 ± 13.7 years) without ocular infection before ophthalmologic surgery between August 2018 and December 2020. A review of microbiological records regarding patient age was used to determine the number of isolates and gram-positive species obtained, as well as their fluoroquinolone susceptibility. Fluoroquinolone susceptibility was determined using the Clinical and Laboratory Standards Institute protocols of broth microdilution. Statistical analysis was performed using a generalized additive model and a log-linear model. Results: In total, 9,894 bacterial isolates obtained from scraped samples from the patients were analyzed. The detected species were Staphylococcus epidermidis (31.0%), Staphylococcus aureus (6.1%), Staphylococcus lugdunensis (3.9%), Enterococcus faecalis (5.8%), Corynebacterium species (31.7%), and Cutibacterium acnes (7.5%) and others. The number of species isolated from the ocular surface was increased at the rate of 1.018 per 10 years of age (p < 0.0001). S. epidermidis, S. lugdunensis, E. faecalis, and Corynebacterium species were isolated more often with an increase in patient age. The levofloxacin resistance ratio of methicillin-sensitive S. epidermidis and Corynebacterium species increased at the rate of 1.204 and 1.087 respectively with a 10-year increase in age (both p < 0.0001). Conclusion: Gram-positive bacteria in the ocular surface flora (OSF) exhibited gradual changes in diversity and fluoroquinolone resistance with an increase in patient age. It is important to monitor the OSF of the patients before ophthalmologic surgery to prevent refractory ocular postoperative infection. [ABSTRACT FROM AUTHOR]

Background. Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern. Objectives. To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS. Methods. Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short-and long-read platforms. Results. ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene. Conclusions. This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism. [ABSTRACT FROM AUTHOR]

Introduction: Fluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug-resistant (MDR) Enterobacterales (Ent) infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with an overall goal to devise treatment and prevention strategies. Methods: A case--control study of children (0-18 years) at three Chicago hospitals was performed. Cases had infections by FQ-susceptible, β-lactamase-producing (bla) Ent harboring a non- or low-level expression of PMFQR genes (PMFQS Ent). Controls had FQR infections due to bla Ent with expressed PMFQR genes (PMFQR Ent). We sought bla genes by PCR or DNA (BD Max Check-Points assay®) and PMFQR genes by PCR. We performed rep-PCR, MLST, and E. coli phylogenetic grouping. Whole genome sequencing was additionally performed on PMFQS Ent positive isolates. Demographics, comorbidities, and device, antibiotic, and healthcare exposures were evaluated. Predictors of infection were assessed. Results: Of 170 β-lactamase-producing Ent isolates, 85 (50%) were FQS; 23 (27%) had PMFQR genes (PMFQS cases). Eighty-five (50%) were FQR; 53 (62%) had PMFQR genes (PMFQR controls). The median age for children with PMFQS Ent and PMFQR Ent was 4.3 and 6.2 years, respectively (p = NS). Of 23 PMFQS Ent, 56% were Klebsiella spp., and of 53 PMFQR Ent, 76% were E. coli. The most common bla and PMFQR genes detected in PMFQS Ent were blaSHV ESBL (44%) and oqxAB (57%), and the corresponding genes detected in PMFQR Ent were blaCTX-M-1-group ESBL (79%) and aac(6')-Ib-cr (83%). Whole genome sequencing of PMFQS Ent revealed the additional presence of mcr-9, a transferable polymyxin resistance gene, in 47% of isolates, along with multiple plasmids and mobile genetic elements propagating drug resistance. Multivariable regression analysis showed that children with PMFQS Ent infections were more likely to have hospital onset infection (OR 5.7, 95% CI 1.6-22) and isolates containing multiple bla genes (OR 3.8, 95% CI 1.1-14.5). The presence of invasive devices mediated the effects of healthcare setting in the final model. Differences in demographics, comorbidities, or antibiotic use were not found. Conclusions: Paradoxically, PMFQS Ent infections were often hospital onset and PMFQR Ent infections were community onset. PMFQS Ent commonly coharbored multiple bla and PMFQR genes, and additional silent, yet transferrable antibiotic resistance genes such as mcr-9, affecting therapeutic options and suggesting the need to address infection prevention strategies to control spread. Control of PMFQS Ent infections will require validating community and healthcare-based sources and risk factors associated with acquisition. [ABSTRACT FROM AUTHOR]

A Klebsiella quasipneumoniae subsp. similipneumoniae strain, named S915, belonging to the ST1859 O5:KL35, and harboring the plasmid-mediated quinolone resistance qnrE1 gene, was isolated from a soil sample cultivated with lettuce in Brazil. The core genome multilocus sequence typing analysis revealed that S915 strain was most related to a clinical strain of Brazil. Comparative genomic analysis showed that ST1859 O5:KL35 strains have been circulating in clinical settings and are closely related to multidrug resistance and multimetal tolerance. Strain S915 presented a plasmid contig co-harboring the qnrE1 gene and tellurite tolerance operon. The region harboring the qnrE1 gene (ISEcp1-qnrE1-araJ-ahp) shared high similarity with others from infected humans, ready-to-eat dish, and food-producing animals in Brazil. This is the first report of the plasmid-mediated qnrE1 gene in the environment. Our findings evidence the initial dissemination of the qnrE1 gene in the environment by the introduction of a clinical strain, which may be spread to different sectors, representing a One Health challenge. [ABSTRACT FROM AUTHOR]

ABSTRACT: Objectives: The aim of this study was to perform a genomic investigation of a multiple fluoroquinolone-resistant Leclercia adecarboxylata strain isolated from a synanthropic pigeon in São Paulo, Brazil. Methods: Whole-genome sequencing was performed using an Illumina platform, and in silico deep analyses of the resistome were performed. Comparative phylogenomics was conducted using a global collection of publicly available genomes of L. adecarboxylata strains isolated from human and animal hosts. Results: L. adecarboxylata strain P62P1 displayed resistance to human (norfloxacin, ofloxacin, ciprofloxacin, and levofloxacin) and veterinary (enrofloxacin) fluoroquinolones. This multiple quinolone-resistant profile was associated with mutations in the gyrA (S83I) and parC (S80I) genes and the presence of the qnrS gene within an ISKpn19-orf-qnrS1-ΔIS3-blaLAP-2 module, previously identified in L. adecarboxylata strains isolated from pig feed and faeces in China. Genes associated with arsenic, silver, copper, and mercury resistance were also predicted. Phylogenomic analysis revealed clustering (378–496 single nucleotide polymorphism differences) with two L. adecarboxylata strains isolated from human and fish sources in China and Portugal, respectively. Conclusions: L. adecarboxylata is a Gram-negative bacterium of the Enterobacterales order and is considered an emergent opportunistic pathogen. Since L. adecarboxylata has adapted to human and animal hosts, genomic surveillance is highly recommended, in order to identify the emergence and spread of resistant lineages and high-risk clones. In this regard, this study provides genomic data that can help clarify the role of synanthropic animals in the dissemination of clinically relevant L. adecarboxylata within a One Health context.

Background: Acinetobacter baumannii, are involved in hospital- acquired infections and are increasingly developing resistance to fluoroquinolones, such as ciprofloxacin. The most common method of fluoroquinolone resistance is alteration in genes that encode DNA gyrase (gyrA) and topoisomerase IV (parC).Methods: We sought to isolate fluoroquinolone- resistant A. baumannii and search for changes in gyrA (Ser83Leu) and parC (Ser80Leu) loci by polymerase chain reaction- restriction fragment length polymorphism (PCR- RFLP).Results: We found that all 68 A. baumannii isolates that were part of this research were multidrug resistant and harbored gyrA and parC loci. Most isolates had ciprofloxacin minimal inhibitory concentrations of >128 μg/mL (50.8%). Mutations in gyrA were the most prevalent (47.45%), followed by parC mutations (33.9%) and combined mutations in both genes (23.7%).Conclusions: Single mutations in either gyrA (Ser83Leu) or parC (Ser80Leu) genes may be attributed to fluroquinolone resistance in A. baumannii.

Abstract Background Fluoroquinolones have been, and continue to be, routinely used for treatment of many bacterial infections. In recent years, most parts of the world have reported an increasing trend of fluoroquinolone resistant (FQR) Gram-negative bacteria. Methods A cross-sectional study was conducted between March 2017 and July 2018 among children admitted due to fever to referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were used to screen for carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE). ESBL-PE isolates were tested for quinolone resistance by disk diffusion method. Randomly selected fluroquinolone resistant isolates were characterized by using whole genome sequencing. Results A total of 142 ESBL-PE archived isolates were tested for fluoroquinolone resistance. Overall phenotypic resistance to ciprofloxacin, levofloxacin and moxifloxacin was found in 68% (97/142). The highest resistance rate was seen among Citrobacter spp. (100%, 5/5), followed by Klebsiella. pneumoniae (76.1%; 35/46), Escherichia coli (65.6%; 42/64) and Enterobacter spp. (31.9%; 15/47). Whole genome sequencing (WGS) was performed on 42 fluoroquinolone resistant-ESBL producing isolates and revealed that 38/42; or 90.5%, of the isolates carried one or more plasmid mediated quinolone resistance (PMQR) genes. The most frequent PMQR genes were aac(6’)-lb-cr (74%; 31/42), followed by qnrB1 (40%; 17/42), oqx, qnrB6 and qnS1. Chromosomal mutations in gyrA, parC and parE were detected among 19/42 isolates, and all were in E. coli. Most of the E. coli isolates (17/20) had high MIC values of > 32 µg/ml for fluoroquinolones. In these strains, multiple chromosomal mutations were detected, and all except three strains had additional PMQR genes. Sequence types, ST131 and ST617 predominated among E. coli isolates, while ST607 was more common out of 12 sequence types detected among the K. pneumoniae. Fluoroquinolone resistance genes were mostly associated with the IncF plasmids. Conclusion The ESBL-PE isolates showed high rates of phenotypic resistance towards fluoroquinolones likely mediated by both chromosomal mutations and PMQR genes. Chromosomal mutations with or without the presence of PMQR were associated with high MIC values in these bacteria strains. We also found a diversity of PMQR genes, sequence types, virulence genes, and plasmid located antimicrobial resistance (AMR) genes towards other antimicrobial agents.

Background: Fluoroquinolones are some of the most used antimicrobial agents for the treatment of Pseudomonas aeruginosa. This study aimed at exploring the differential activity of ciprofloxacin and levofloxacin on the selection of resistance among P. aeruginosa isolates at our medical center. Methods: 233 P. aeruginosa clinical isolates were included in this study. Antimicrobial susceptibility testing (AST) was done using disk diffusion and broth microdilution assays. Random Amplification of Polymorphic DNA (RAPD) was done to determine the genetic relatedness between the isolates. Induction of resistance against ciprofloxacin and levofloxacin was done on 19 isolates. Fitness cost assay was done on the 38 induced mutants and their parental isolates. Finally, whole genome sequencing was done on 16 induced mutants and their 8 parental isolates. Results: AST results showed that aztreonam had the highest non-susceptibility. RAPD results identified 18 clusters. The 19 P. aeruginosa isolates that were induced against ciprofloxacin and levofloxacin yielded MICs ranging between 16 and 256 μg/mL. Levofloxacin required fewer passages in 10 isolates and the same number of passages in 9 isolates as compared to ciprofloxacin to reach their breakpoints. Fitness cost results showed that 12 and 10 induced mutants against ciprofloxacin and levofloxacin, respectively, had higher fitness cost when compared to their parental isolates. Whole genome sequencing results showed that resistance to ciprofloxacin and levofloxacin in sequenced mutants were mainly associated with alterations in gyrA, gyrB and parC genes. Conclusion: Understanding resistance patterns and risk factors associated with infections is crucial to decrease the emerging threat of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Background We evaluated the relationship between response to efflux pump inhibition in fluoroquinolone-resistant Mycobacterium tuberculosis (Mtb) isolates and differences in gene expression and expression quantitative trait loci (eQTL). Methods We determined ofloxacin minimum inhibitory concentration (MIC) for ofloxacin-resistant and -susceptible Mtb isolates without and with the efflux pump inhibitor verapamil. We performed RNA sequencing (RNA-seq), whole genome sequencing (WGS), and eQTL analysis, focusing on efflux pump, transport, and secretion-associated genes. Results Of 42 ofloxacin-resistant Mtb isolates, 27 had adequate WGS coverage and acceptable RNA-seq quality. Of these 27, 7 had >2-fold reduction in ofloxacin MIC with verapamil; 6 had 2-fold reduction, and 14 had <2-fold reduction. Five genes (including Rv0191) had significantly increased expression in the MIC fold change >2 compared to <2 groups. Among regulated genes, 31 eQTLs (without ofloxacin) and 35 eQTLs (with ofloxacin) had significant allele frequency differences between MIC fold change >2 and <2 groups. Of these, Rv1410c , Rv2459 , and Rv3756c (without ofloxacin) and Rv0191 and Rv3756c (with ofloxacin) have previously been associated with antituberculosis drug resistance. Conclusions In this first reported eQTL analysis in Mtb , Rv0191 had increased gene expression and significance in eQTL analysis, making it a candidate for functional evaluation of efflux-mediated fluoroquinolone resistance in Mtb. [ABSTRACT FROM AUTHOR]

IntroductionFluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug-resistant (MDR) Enterobacterales (Ent) infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with an overall goal to devise treatment and prevention strategies.MethodsA case–control study of children (0–18 years) at three Chicago hospitals was performed. Cases had infections by FQ-susceptible, β-lactamase-producing (bla) Ent harboring a non- or low-level expression of PMFQR genes (PMFQS Ent). Controls had FQR infections due to bla Ent with expressed PMFQR genes (PMFQR Ent). We sought bla genes by PCR or DNA (BD Max Check-Points assay®) and PMFQR genes by PCR. We performed rep-PCR, MLST, and E. coli phylogenetic grouping. Whole genome sequencing was additionally performed on PMFQS Ent positive isolates. Demographics, comorbidities, and device, antibiotic, and healthcare exposures were evaluated. Predictors of infection were assessed.ResultsOf 170 β-lactamase-producing Ent isolates, 85 (50%) were FQS; 23 (27%) had PMFQR genes (PMFQS cases). Eighty-five (50%) were FQR; 53 (62%) had PMFQR genes (PMFQR controls). The median age for children with PMFQS Ent and PMFQR Ent was 4.3 and 6.2 years, respectively (p = NS). Of 23 PMFQS Ent, 56% were Klebsiella spp., and of 53 PMFQR Ent, 76% were E. coli. The most common bla and PMFQR genes detected in PMFQS Ent were blaSHV ESBL (44%) and oqxAB (57%), and the corresponding genes detected in PMFQR Ent were blaCTX-M-1-group ESBL (79%) and aac(6’)-Ib-cr (83%). Whole genome sequencing of PMFQS Ent revealed the additional presence of mcr-9, a transferable polymyxin resistance gene, in 47% of isolates, along with multiple plasmids and mobile genetic elements propagating drug resistance. Multivariable regression analysis showed that children with PMFQS Ent infections were more likely to have hospital onset infection (OR 5.7, 95% CI 1.6–22) and isolates containing multiple bla genes (OR 3.8, 95% CI 1.1–14.5). The presence of invasive devices mediated the effects of healthcare setting in the final model. Differences in demographics, comorbidities, or antibiotic use were not found.ConclusionsParadoxically, PMFQS Ent infections were often hospital onset and PMFQR Ent infections were community onset. PMFQS Ent commonly co-harbored multiple bla and PMFQR genes, and additional silent, yet transferrable antibiotic resistance genes such as mcr-9, affecting therapeutic options and suggesting the need to address infection prevention strategies to control spread. Control of PMFQS Ent infections will require validating community and healthcare-based sources and risk factors associated with acquisition.

Background Levofloxacin prophylaxis (LVXp) is often used for patients with underlying leukemia and severe neutropenia to reduce the risk of fever and bacteremia. This study evaluated trends in viridans group streptococci (VGS) antibiotic susceptibilities over time and clinical outcomes of children with VGS bloodstream infections (BSIs) during institutional adoption of LVXp. Methods VGS blood culture isolates between 1/1/2010 and 12/31/2021 with susceptibility testing reported were included. Available isolates were re-identified to the species level and additional susceptibility testing was performed. Demographic and clinical data were abstracted from medical records. Results A total of 264 VGS BSI isolates were identified in immunocompromised (IC, n = 125) and non-immunocompromised subjects, (non-IC, n = 139). IC subjects had lower rates of VGS isolates susceptible (S) to LVX and higher minimum inhibitory concentration (MICs) to LVX (p = 0.004) and ciprofloxacin (p = 0.0005) compared with non-IC subjects. No other evaluated antibiotic had increased MICs in either group. Fifteen of 19 (74%) LVX not susceptible (NS) isolates occurred in IC subjects, 13 represented breakthrough infections. IC subjects had higher rates of VGS-related shock (p = 0.012), need for pressor support (p = 0.039), and longer duration of hospitalization than non-IC subjects (p < 0.001). Clinical outcomes were comparable between subjects with LVX S and NS VGS BSI isolates. Conclusions VGS with reduced susceptibility to LVX emerged during institutional adoption of LVXp in high-risk children with immunocompromising conditions, but did not result in significant differences in clinical outcomes. Ongoing surveillance and susceptibility testing are critical in weighing the utility of LVXp against emerging antimicrobial resistance in this high-risk population. [ABSTRACT FROM AUTHOR]

Background Emergence of fluoroquinolone resistance in gut pathogens is a cause of concern. Resistant to quinolone is mainly due to the point mutations at the quinolone-resistance determining regions (QRDR). The aim of the study was to develop polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP) to detect QRDR mutations in gyrA and gyrB regions in enteric pathogens. Methodology PCR-RFLP was done for gyrA 83 region using HinfI and for gyrB 447 using AcuI for fluoroquinolone resistant and susceptible gut pathogens. The products were also sequenced to confirm the presence of restriction sites. Results In this study, a PCR-RFLP technique was developed to detect gyrA 83 mutations in Salmonella typhi and Escherichia coli. A first of its kind PCR-RFLP was also developed to detect gyrB 447 mutation using a restriction enzyme AcuI. Restriction digestion of gyrA using Hin fI resulted in three bands for resistant S. typhi isolates due to the presence of mutation at gyrA 83 and four bands were seen for sensitive S. typhi isolates, while two bands for resistant and three bands were seen in sensitive E. coli isolates. Similarly, restriction digestion of gyrB using Acu I resulted in no digestion for resistant S. typhi isolates and two bands for resistant E. coli isolates. This suggest that there is mutation at gyrB 447 region of E. coli , while no mutation was found in S. typhi isolates. Conclusion The PCR-RFLP developed in the present study could successfully detect gyrA 83 and gyrB 447 mutations in fluoroquinolone-resistant S. typhi and E. coli. The technique can be efficiently used in epidemiological studies instead of a cost-intensive sequencing method to detect the status of multiple point mutations in gut pathogens. [ABSTRACT FROM AUTHOR]

Objectives: Acute appendicitis is a common disease that often requires emergency surgery. However, recently, not all cases are treated as an urgent operation, but surgery may be delayed to when medical resources are abundant to perform the operation safely. In such cases, preoperative antibiotics are administered during the waiting period. Though the choice is empiric, an appropriate choice is needed to avoid emergency surgery. Guidelines for the choice of antibiotics recognized as international standards cannot be applied in Asia due to the high rate of extended-spectrum β-lactamase (ESBL) producers or fluoroquinolone-resistant Escherichia coli. The purpose of this study was to determine the optimal antibiotic during the in-hospital waiting period for patients with appendicitis scheduled for surgery. Methods: Bacterial culture results and antibiotic susceptibility were retrospectively examined in 106 cases who underwent surgery for appendicitis. Results: Bacterial cultures were positive in 53 cases (50%). Twenty-six strains of E. coli were identified. Of these, four (15%) were ESBL producers, and seven (27%) were fluoroquinolone resistant. Twenty-two strains of anaerobic bacteria were identified. Carbapenems and tazobactam/piperacillin were effective for all. The rates of susceptibility to clindamycin (CLDM) and cefmetazole (CMZ) were 59% and 82%, respectively. Conclusions: In Japan, from the point of view of reducing carbapenem use, CMZ must be considered a first-choice drug during the in-hospital waiting period for appendectomy.

BackgroundFluoroquinolones are some of the most used antimicrobial agents for the treatment of Pseudomonas aeruginosa. This study aimed at exploring the differential activity of ciprofloxacin and levofloxacin on the selection of resistance among P. aeruginosa isolates at our medical center.Methods233 P. aeruginosa clinical isolates were included in this study. Antimicrobial susceptibility testing (AST) was done using disk diffusion and broth microdilution assays. Random Amplification of Polymorphic DNA (RAPD) was done to determine the genetic relatedness between the isolates. Induction of resistance against ciprofloxacin and levofloxacin was done on 19 isolates. Fitness cost assay was done on the 38 induced mutants and their parental isolates. Finally, whole genome sequencing was done on 16 induced mutants and their 8 parental isolates.ResultsAST results showed that aztreonam had the highest non-susceptibility. RAPD results identified 18 clusters. The 19 P. aeruginosa isolates that were induced against ciprofloxacin and levofloxacin yielded MICs ranging between 16 and 256 μg/mL. Levofloxacin required fewer passages in 10 isolates and the same number of passages in 9 isolates as compared to ciprofloxacin to reach their breakpoints. Fitness cost results showed that 12 and 10 induced mutants against ciprofloxacin and levofloxacin, respectively, had higher fitness cost when compared to their parental isolates. Whole genome sequencing results showed that resistance to ciprofloxacin and levofloxacin in sequenced mutants were mainly associated with alterations in gyrA, gyrB and parC genes.ConclusionUnderstanding resistance patterns and risk factors associated with infections is crucial to decrease the emerging threat of antimicrobial resistance.

Escherichia coli ST131 isolates associated with fluoroquinolone and cephalosporin resistance have increased in the last ten years. This increase has led to the emergence of multidrug-resistant E. coli isolates, resulting in treatment failures for urinary tract infections. The increasing antimicrobial resistance in gram-negative bacteria and the scarcity of new antimicrobials have brought old antimicrobials, such as temocillin, back into consideration. Temocillin has significant advantages and may serve as an alternative to carbapenems in treating serious Enterobacterales infections, such as systemic urinary tract infections. This study aimed to determine the presence of the O25b-ST131 clone in fluoroquinoloneresistant E. coli isolates and assess temocillin resistance. E. coli isolates obtained from urinary tract samples of patients hospitalized in the Faculty of Medicine Hospital of Ondokuz Mayıs University were included in the study. The presence of clone O25b-ST131 in these isolates was investigated using PCR. In addition, temocillin susceptibility in these isolates was determined using the Kirby-Bauer disk diffusion method. According to the PCR results, the prevalence of E. coli O25b-ST131 isolates was 40.8%. The findings of the antimicrobial resistance tests revealed that all isolates had low levels of carbapenem and fosfomycin resistance (2.04% and 3.06%, respectively). The temocillin resistance rate was determined to be 50%. It is known that clone O25b-ST131 is associated with fluoroquinolone and cephalosporin resistance; therefore, a high prevalence of the O25b-ST131 clone was expected in fluoroquinolone-resistant E. coli isolates included in the study. Temocillin is an antimicrobial agent widely used in many European countries, particularly for treating carbapenem-resistant E. coli infections. However, in our study, high rates of temocillin resistance (50%) were observed, despite this agent not being used in our country yet. These high resistance rates could be related to cross-antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Objective: We studied the presence of mutations in the chromosomal quinolone resistance-determining regions (QRDRs) of the fluoroquinolone targets gyrA and parC genes and detected the carbapenem resistance (CR) encoding genes among Acinetobacter baumannii and Escherichia coli isolates from catheter-related bloodstream infections (CRBSIs). Methods: The study included 39 non-duplicate isolates of A. baumannii (14/39, 35.9%) and E. coli (25/39, 64.1%) isolated from 128 confirmed CRBSIs cases. Antimicrobial susceptibility testing was performed, followed by an evaluation of biofilm formation using the tissue culture plate method. The carbapenemase encoding genes were detected by multiplex polymerase chain reaction (PCR). The mutations in QRDRs of gyrA and parC genes were determined by singleplex PCR amplification followed by DNA sequencing and BlastN analysis in the GenBank database. DNA and the translated amino acid sequences were analyzed using the Mega7 bioinformatics tool. Results: Multidrug-resistant (MDR) E. coli and A. baumannii isolates harbored CR encoding genes and combined gyrA and parC genes mutation. The specific substitutions observed in GyrA were Cys173Arg, Cys174Gly, Asp80Val, Tyr178ASP, Tyr84Gly, Glu85Lys, Ser172Leu, and Asp176Asn, while the specific substitutions observed in the ParC amino acid sequence were point mutation 62 Arg, Phe60Leu, Ils66Val, and Gln76Lys. Point mutation 62Arg was detected in two A. baumannii isolates, whereas Ser172Leu mutation was observed in two E. coli isolates. Conclusion: The presence of new single and multiple mutations in QRDR causes the emergence of MDR E. coli and A. baumannii infections in carbapenem-resistant Enterobacteriaceae in Egypt, requiring further investigation in Gram-negative bacteria. [ABSTRACT FROM AUTHOR]

Background: Acinetobacter baumannii, are involved in hospital-acquired infections and are increasingly developing resistance to fluoroquinolones, such as ciprofloxacin. The most common method of fluoroquinolone resistance is alteration in genes that encode DNA gyrase (gyrA) and topoisomerase IV (parC).Methods: We sought to isolate fluoroquinolone-resistant A. baumannii and search for changes in gyrA (Ser83Leu) and parC (Ser80Leu) loci by polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP). Results: We found that all 68 A. baumannii isolates that were part of this research were multidrug resistant and harbored gyrA and parC loci. Most isolates had ciprofloxacin minimal inhibitory concentrations of >128 µg/mL (50.8%). Mutations in gyrA were the most prevalent (47.45%), followed by parC mutations (33.9%) and combined mutations in both genes (23.7%).Conclusions: Single mutations in either gyrA (Ser83Leu) or parC (Ser80Leu) genes may be attributed to fluroquinolone resistance in A. baumannii. [ABSTRACT FROM AUTHOR]

High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods. [ABSTRACT FROM AUTHOR]

Untreated wastewater emanating from healthcare facilities are risk factors for the spread of antimicrobial resistance (AMR) at the human–environment interface. In this study, we investigated the determinants of resistance in three multidrug resistant strains of Proteus mirabilis isolated from untreated wastewater collected from three government owned hospitals in Ibadan, Nigeria. Despite showing low-level resistance to ciprofloxacin, whole genome sequencing revealed the transferable mechanism of quinolone resistance (TMQR) gene qnrD3 carried on Col3M plasmids in all the isolates. Core genome phylogenetic analysis showed the isolates are closely related differing from each other by ≤ 23 single nucleotide polymorphisms (SNP). Further, they shared the closest evolutionary relationship with isolates from China. Similarly, the Col3M plasmids is most closely related to p3M-2A found in P. vulgaris 3 M isolated from the intestine of shrimps in China. This to the best of our knowledge is the first report of Col3M plasmids carrying qnrD3 in environmental bacterial isolates. Our results indicate a possible silent spread of this important plasmid associated with the dissemination of qnrD3 in Nigeria, and further highlights the important role played by untreated wastewater from healthcare facilities in the spread of AMR in low- and middle-income countries. [ABSTRACT FROM AUTHOR]

Abstract Background Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined. Methods In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively. Results In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1–3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P

Abstract Beef is a source of human Campylobacter infections. Antimicrobial treatment is needed when patients are immunocompromised or have other comorbidities. Therefore, we investigated the prevalence and antimicrobial resistance of Campylobacter spp. in beef cattle in Japan. Rectal swab samples were collected from 164 beef cattle at an abattoir between March 2021 and August 2021, and Campylobacter spp. were isolated from 94 (57.3%) cattle. C. jejuni and C. coli were isolated from 68 and 26 cattle, respectively. For Campylobacter jejuni, the resistant rates against ampicillin, tetracycline and ciprofloxacin were 20.6, 75.0 and 64.7%, respectively. For C. coli, the resistant rates against ampicillin, tetracycline and ciprofloxacin were 53.8, 76.9 and 88.5%, respectively. No Campylobacter isolates were resistant to erythromycin. By multilocus sequence typing, C. jejuni and C. coli isolates were classified into 22 and 2 sequence types (STs). The top three STs of C. jejuni were ST806 (12 isolates), ST21 (nine isolates), and ST459 (eight isolates). The most frequent ST of C. coli was ST1068 (23 isolates). The results suggest that Campylobacter spp. are prevalent in the gastrointestinal tract of beef cattle slaughtered at abattoirs. Furthermore, the administration of erythromycin is effective against human campylobacteriosis caused by beef consumption. Monitoring the prevalence and antimicrobial resistance of Campylobacter spp. in beef cattle could be useful for managing the risk of human campylobacteriosis.

The present study was performed to assess the resistance profile to fluoroquinolone and to determine mutations in gyrA and parC genes of Escherichia coli in bovine coliform mastitis. Fluoroquinolones (norfloxacin (NOR), ciprofloxacin (CIP), enrofloxacin (NFX), levofloxacin (LEV), and ofloxacin (OFL) were tested against E. coli isolates, isolated from bovine mastitis (100 milk samples) by disk diffusion method. To determine the extent of gyrA and parC mutations associated with fluoroquinolone resistance in E. coli, two isolates with the highest resistance to each fluoroquinolone were submitted for the amplification and sequencing of the quinolone resistance-determining regions (QRDRs) of gyrA and parC genes. The disk diffusion method indicated that E. coli isolates had the highest intermediate resistance to OFL (16.7%), followed by NFX and NOR (15%), while they had low resistance to CIP and LEV (3.33%). A few silent mutations in gyrA (in codons 91, 100, 111, 131, 132) and in parC (in codons 91, 157, 159) were detected in QRDRs, and mutations in nucleotides 65, 80, and 83 in gyrA, and 195, 209, 212 in parC were detected in the other isolate. These results showed an intermediate rate of resistance to fluoroquinolones in E. coli isolates from raw milk of cows with coliform mastitis

ABSTRACT Mycobacterium avium, a member of the M. avium complex (MAC), is the major pathogen contributing to nontuberculous mycobacteria (NTM) infections worldwide. Fluoroquinolones (FQs) are recommended for the treatment of macrolide-resistant MACs. The association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA of M. avium is not yet clearly understood, as many FQ-resistant clinical M. avium isolates do not have such mutations. This study aimed to elucidate the role of amino acid substitution in the QRDR of M. avium GyrA in the development of FQ resistance. We found four clinical M. avium subsp. hominissuis isolates with Asp-to-Gly change at position 95 (Asp95Gly) and Asp95Tyr mutations in gyrA that were highly resistant to FQs and had 2- to 32-fold-higher MICs than the wild-type (WT) isolates. To clarify the contribution of amino acid substitutions to FQ resistance, we produced recombinant WT GyrA, GyrB, and four GyrA mutant proteins (Ala91Val, Asp95Ala, Asp95Gly, and Asp95Tyr) to elucidate their potential role in FQ resistance, using them to perform FQ-inhibited DNA supercoiling assays. While all the mutant GyrAs contributed to the higher (1.3- to 35.6-fold) FQ 50% inhibitory concentration (IC50) than the WT, Asp95Tyr was the most resistant mutant, with an IC50 15- to 35.6-higher than that of the WT, followed by the Asp95Gly mutant, with an IC50 12.5- to 17.6-fold higher than that of the WT, indicating that these amino acid substitutions significantly reduced the inhibitory activity of FQs. Our results showed that amino acid substitutions in the gyrA of M. avium contribute to FQ resistance. IMPORTANCE The emergence of fluoroquinolone (FQ) resistance has further compounded the control of emerging Mycobacterium avium-associated nontuberculous mycobacteria infections worldwide. For M. avium, the association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA is not yet clearly understood. Here, we report that four clinical M. avium isolates with a mutation in the QRDR of gyrA were highly resistant to FQs. We further clarified the impact of mutations in the QRDR of GyrA proteins by performing in vitro FQ-inhibited DNA supercoiling assays. These results confirmed that, like in Mycobacterium tuberculosis, mutations in the QRDR of gyrA also strongly contribute to FQ resistance in M. avium. Since many FQ-resistant M. avium isolates do have these mutations, the detailed molecular mechanism of FQ resistance in M. avium needs further exploration.