Antimicrobial Agents and Urinary Tract Infections

Epidemiology and risk factors for staphylococcal urinary tract infections in the Moroccan Casablanca area

PURPOSE

This study aimed to ascertain the prevalence and risk factors for developing staphylococcal urinary tract infections (UTIs) in the Casablanca area of Morocco.

METHODS

In Casablanca, Morocco, a retrospective evaluation of 772 UTIs patients was conducted between January 2020 and December 2022. The research included two groups of patients: those with staphylococcal UTIs and those without. Sex, age, chronic illnesses, antibiotic exposure, urinary catheterization, urological surgery, and UTIs history were the risk variables assessed. We employed a logistic regression model to identify the characteristics that were predictive of staphylococcal UTIs.

RESULTS

Eight staphylococcal species were responsible for 16.84% of UTIs in 772 non-repeating individuals. Patients infected with S. saprophyticus (35.38%) were the most common, followed by those infected with S. epidermidis (24.61%), S. aureus (13.85%), and S. hemolyticus (10.78%). Multivariate logistic regression analysis revealed that male sex (95% CI: 0.261-0.563), immunosuppression and immunosuppressive treatments (95% CI: 0.0068-0.64), chronic diseases (95% CI: 0.407-0.965), previous UTIs (95% CI: 0.031-0.228), frequency of urination more than 8 times a day (95% CI:1.04-3.29), frequency of urination once or twice a day (95% CI: 1.05-2.39), and urinary catheterization (95% CI: 0.02-0.22) were the most likely predictors of staphylococcal UTIs. In addition, a larger proportion of patients with staphylococcal UTIs were made aware of the risk factors associated with staphylococcal UTIs (52.31%, χ2 = 4.82, = 0.014).

CONCLUSIONS

This is the first global study to evaluate the predictive factors for acquiring UTIs caused by staphylococci. Monitoring these factors will enable medical authorities to devise effective strategies for managing UTIs and combating antibiotic resistance.

Whole-Genome Sequencing of an Escherichia coli ST69 Strain Harboring blaCTX-M-27 on a Hybrid Plasmid

Objective

Escherichia coli is a common Gram-negative human pathogen. The emergence of E. coli with multiple-antibiotic-resistant phenotypes has become a serious health concern. This study reports the whole-genome sequences of third-generation cephalosporin-resistant (3GC-R) and multidrug-resistant (MDR) E. coli EC6868 and explores the acquired antibiotic-resistance genes (ARGs) as well as their genetic contexts.

Methods

E. coli EC6868 was isolated from a vaginal secretion sample of a pregnant patient in China. The antimicrobial susceptibility was assessed, and whole-genome sequencing was conducted. The acquired ARGs, insertion sequence (IS) elements, and integrons within the genome of E. coli EC6868 were identified, and the genetic contexts associated with the ARGs were analyzed systematically.

Results

E. coli EC6868 was determined to belong to ST69 and harbored a 144.9-kb IncF plasmid (pEC6868-1) with three replicons (Col156, IncFIBAP001918, and IncFII). The ESBL gene blaCTX-M-27 was located on the structure "∆ISEcp1-blaCTX-M-27-IS903B", which was widely present in the species of Enterobacteriales. Other ARGs carried by plasmid pEC6868-1 were mainly located on the 18.9-kb IS26-composite transposon (five copies of intact IS26 and one copy of truncated IS26) composing of IS26-mphA-mrx(A)-mphR(A)-IS6100, ∆TnAs3-eamA-tet(A)-tetR(A)-aph(6)-Id-aph(3")-Ib-sul2-IS26, and a class 1 integron, which was widely present on IncF plasmids of E. coli, mainly distributed in ST131, ST38, and ST405. Notably, pEC6868 in our study was the first report on a plasmid harboring the 18.9-kb structure in E. coli ST69 in China.

Conclusion

The 3GC-R E. coli ST69 strain with an MDR IncF plasmid carrying blaCTX-M-27 and other ARGs, conferring resistance to aminoglycosides, macrolides, sulfonamides, tetracycline, and trimethoprim, was identified in a hospital in China. Mobile genetic elements including ISEcp1, IS903B, IS26, Tn3, IS6100 and class 1 integron were found within the MDR region, which could play important roles in the global dissemination of these resistance genes.

Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection

Introduction

Recurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients' quality of life.

Aim

In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed.

Materials and methods

One hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed.

Results

The UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain.

Conclusion

The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.

Modified Zhibai Dihuang pill alleviated urinary tract infection induced by extended-spectrum β-lactamase Escherichia coli in rats by regulating biofilm formation

CONTEXT

Zhibai Dihuang pill (ZD), a traditional Chinese medicine nourishes Yin and reduces internal heat, is believed to have therapeutic effects on urinary tract infections (UTIs).

OBJECTIVE

To explore the effects and mechanism of modified ZD (MZD) on UTI induced by extended-spectrum β-lactamase (ESBLs) Escherichia coli.

MATERIALS AND METHODS

Thirty Sprague-Dawley rats were randomly divided into control, model (0.5 mL 1.5 × 108 CFU/mL ESBLs E. coli), MZD (20 g/kg MZD), LVFX (0.025 g/kg LVFX), and MZD + LVFX groups (20 g/kg MZD + 0.025 g/kg LVFX), n = 6. After 14 days of treatment, serum biochemical indicators, renal function indicators, bladder and renal histopathology, and urine bacterial counts in rats were determined. Additionally, the effects of MZD on ESBLs E. coli biofilm formation and related gene expression were analyzed.

RESULTS

MZD significantly decreased the count of white blood cells (from 13.12 to 9.13), the proportion of neutrophils (from 43.53 to 23.18), C-reactive protein (from 13.21 to 9.71), serum creatinine (from 35.78 to 30.15), and urea nitrogen (from 12.56 to 10.15), relieved the inflammation and fibrosis of bladder and kidney tissues, and reduced the number of bacteria in urine (from 2174 to 559). In addition, MZD inhibited the formation of ESBLs E. coli biofilms (2.04-fold) and decreased the gene expressions of luxS, pfS and ompA (1.41-1.62-fold).

DISCUSSION AND CONCLUSION

MZD treated ESBLs E. coli-induced UTI inhibited biofilm formation, providing a theoretical basis for the clinical application of MZD. Further study on the clinical effect of MZD may provide a novel therapy option for UTI.

First Emergence of NDM-5 and OqxAB Efflux Pumps Among Multidrug-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Assiut, Egypt

Introduction

New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae poses a high risk, especially among Egyptian pediatric patients who consume carbapenems antibiotics very widely and without adequate diagnostic sources. In addition, presence of efflux pump genes such as OqxAB increases resistance against many groups of antimicrobials which exacerbates the problem faced for human health. This study aimed to determine NDM variants among K. pneumoniae strains isolated from pediatric patients in Egypt, analyze the presence of OqxAB genes, and molecular characterization of blaNDM-5-positive K. pneumoniae.

Methods

Fifty-six K. pneumoniae isolates were recovered from pediatric patients, and tested for carbapenemase by modified carbapenem inactivation methods (mCIM) test. Minimum inhibitory concentrations of meropenem and colistin were determined by meropenem E-test strips and broth microdilution, respectively. PCR was used for the detection of the resistant genes (ESBL gene (blaCTX-M), carbapenemase genes (blaNDM, blaKPC) colistin resistant (mcr1, mcr2)) and genes for efflux pump (oqxA and oqxB). BlaNDM was sequenced. The effect of efflux pump in NDM-5-producing isolates was assessed by measuring MIC of ciprofloxacin and meropenem before and after exposure to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The horizontal gene transfer ability of blaNDM-5 was determined using liquid mating assay and PCR-based replicon typing (PBRT) was done to determine the major plasmid incompatibility group.

Results

Twenty-nine isolates were positive for blaNDM-1, nine isolates were positive for blaNDM-5, and 15 isolates were positive for blaKPC. There is a significant increase of meropenem MIC of NDM-5-positive isolates compared with NDM-1-positive isolates. In addition, 38 isolates were positive for CTX-M, and 15 isolates were positive for mcr1. Both OqxA and OqxB were detected in 26 isolates and 13 isolates were positive for OqxA while 11 isolates were positive for OqxB only. All NDM-5-producing isolates except one isolate could transfer their plasmids by conjugation to their corresponding transconjugants (E. coli J53). Plasmid replicon typing showed that FII was predominant in NDM-5-producing K. pneumoniae. Similar strains were found between the three isolates and similarity was also detected between the two isolates.

Conclusion

The highly resistant K. pneumoniae producing blaNDM-5 type was firstly isolated from pediatric patients. The association of efflux pump genes such as OqxAB is involved in resistance to ciprofloxacin. This highlighted the severity risk of blaNDM-5-positive K. pneumonia as it could transfer blaNDM-5 to other bacteria and has more resistance against carbapenems. This underlines the importance of continuous monitoring of infection control guidelines, and the urgent need for a national antimicrobial stewardship plan in Egyptian hospitals.

Identifying FmlH lectin-binding small molecules for the prevention of Escherichia coli-induced urinary tract infections using hybrid fragment-based design and molecular docking

Nearly 50% of women are affected by urinary tract infections (UTIs) during their lifetimes. The most common agent to cause UTIs is Uropathogenic Escherichia coli (UPEC). UPEC expresses fibers known as chaperone-usher pathway pili with adhesins that specifically bind to receptors as they colonize various host tissues. UPEC uses an F9/Yde/Fml pilus, tipped with FmlH, which interacts with terminal galactoside/galactosaminoside units in glycoproteins in the epithelial cells of the bladder and kidney. The extensive use of traditional antibiotics has led to the rise of various antibiotic-resistant strains of UPEC. An alternative therapeutic approach is to use an anti-adhesion strategy mediated by competitive tight-binding FmlH inhibitors. In the current study, we have applied various computational modeling techniques, including fragment-based e-pharmacophore virtual screening, molecular docking, molecular dynamics simulations and binding free energy calculations for the design of small molecules that exhibit binding to FmlH. Our modeling protocol successfully predicted ligand moieties, such as a thiazole group, which were previously found as components of UPEC adhesin pili inhibitors, thereby validating our designed screening protocol. The screening protocol developed here could be utilized for design of ligands for other homologous protein targets. We also identified several novel galactosaminoside-containing molecules that, according to the computational modeling, are predicted to interact strongly with FmlH and hence we predict will be good FmlH inhibitors. Additionally, we have prepared and supplied a database of ∼190K small molecules obtained from virtual screening, which can serve as an excellent resource for the discovery of novel FmlH inhibitors.

Bacterial Etiology of Urinary Tract Infection and Antibiogram Profile in Children Attending Debre Tabor Comprehensive Specialized Hospital, Northwest Ethiopia

BACKGROUND

Bacterial urinary tract infections are important public health problems in children. This study was conducted to identify the bacterial agents of urinary tract infections and antibiogram patterns in children.

METHODS

A hospital-based cross-sectional study including 220 children was carried out between November 15, 2021, and March 10, 2022. Simple random sampling was used to enroll participants. The sociodemographic and clinically pertinent information was gathered using a semi-structured questionnaire. Every participant in the study who was ≤15 years old gave clean-catch midstream urine. Urine samples were inoculated onto a cystine lactose electrolyte-deficient agar using a calibrated inoculating loop with a 0.001 ml capacity and then incubated aerobically for 24 hours at 37°C. Subculturing for significant bacteriuria was done on MacConkey and blood agar. Gram staining, biochemical assays, and colony characteristics were used for bacterial identification. The disc diffusion method developed by Kirby and Bauer was used for antimicrobial susceptibility testing. SPSS software version 25 was used for data entry and analysis. To find the risk factors, bivariate and multivariate logistic regression analyses were performed. An association was deemed statistically significant if the p value at the 95 percent confidence interval was less than 0.05.

RESULTS

In this study, the majority (50.5%) of the study participants were males. The mean age of the study participants was 6 ± 0.91 years. It was found that 31.8% of children had urinary tract infections. The most prevalent urinary pathogens among the isolates were E. coli (27.1%) and S. aureus (18.6%). Approximately 56% of the participants were infected with multidrug-resistant pathogens. Additionally, compared to children who have never had a urinary tract infection, children with a history of infection had 1.04 (95 percent confidence interval (CI): 0.39, 2.75) times higher risk of infection.

CONCLUSION

This study has shown an alarming increase in the prevalence of pediatric urinary tract infections which warrants further investigation into multidrug-resistant bacterial infection.

Analysis of Antimicrobial Susceptibility in Bacterial Pathogens Associated with Urinary Tract Infections from Beijing Teaching Hospital in China, 2009-2017

Objective

Since a urinary tract infection (UTI) is easy to relapse and difficult to treat, the antibiotic resistance rate has increased year by year in recent years. This study was to analyze the characteristics of the common pathogenic bacteria and the changes of antibiotic resistance in urinary system infection, so as to guide the standard use of antibiotics in a clinical urinary tract infection and control nosocomial infection effectively.

Methods

A total of 5,669 strains of a urinary tract infection in the hospital from January 2009 to December 2017 were retrospectively analyzed. Bacterial identification and the antibiotic sensitivity test (AST) were analyzed by using a VITEK-2 Compact system.

Results

Of the 5669 pathogens, 3,256 (57.44%) of the strains were Gram-negative bacteria (GNB), 1,474 (26%) were Gram-positive bacteria (GPB), and 939 (16.56%) were fungi. Resistant rates of ESBL-producing strains were all significantly different from non-ESBL-producing strains in Escherichia coli (p < 0.05). The resistance rate of ESBL-producing strains to β-lactam antibiotics was all higher than that of non-ESBL-producing strains in Klebsiella pneumoniae (p < 0.05). The detection rate of vancomycin-resistantEnterococcus faecium and Enterococcus faecalis was 37.3% and 3.1%, respectively, and the detection rate of linezolid-resistantEnterococcus faecium and Enterococcus faecalis was 0.68% and 0%, respectively. The drug resistance rate of candida sp. to fluconazole, itraconazole, and voriconazole was 1.7%, 8.5%, and 3.4%, respectively. No amphotericin B-resistant strains were detected in the research.

Conclusions

Among the 5669 strains isolated from urinary tract infection patients, GNB were the main pathogens. Escherichia coli was the major pathogen. The resistance rate of ESBLs-producingEscherichia coli was higher than that of non-ESBLs-producingEscherichia coli in general; meanwhile, β-lactam/β-lactamase inhibitors and carbapenems maintained good antimicrobial activity against Escherichia coli. The resistance rate of non-ESBLs-producingKlebsiella pneumoniae strains was significantly higher than that of ESBLs-producingKlebsiella pneumoniae strains, and drug resistance was more prominent; most of the antibiotic resistance rates were over 50%. The antimicrobial resistance rate of Enterococcus faecium was significantly higher than that of Enterococcus faecalis. There were rare linezolid-resistant strains. The antimicrobial resistance rate of imidazole to fungi was controlled less than 10%.

The Characteristics of Extended-Spectrum β-Lactamases (ESBLs)-Producing Escherichia coli in Bloodstream Infection

Background

Bloodstream infection (BSI) is a common type of infection frequently diagnosed in clinics. The emergence and spread of ESBLs-producing Escherichia coli (E. coli) has emerged as one of the biggest challenges in global community health.

Methods

The production of ESBLs was determined by the composite disk diffusion method. The expression of the various resistance and virulence genes were detected by PCR and sequencing. Multi-locus sequence typing (MLST) and phylogenetic groups were used for the classification. The transfer of resistant plasmids was determined by conjugation assay. The statistical differences were analyzed using Statistical Product and Service Solutions (SPSS) version 23.0.

Results

A total of 60 strains of ESBLs-producing E. coli were collected. The resistance genes that were identified included bla _CTX-M, bla _TEM, bla _SHV, bla _OXA-1 and mcr-1. The most common one was the bla _CTX-M including bla _CTX-M-27 (n = 16), bla _CTX-M-14 (n = 15), bla _CTX-M-15 (n = 11), bla _CTX-M-55 (n = 14) and bla _CTX-M-65 (n = 5). A total of 31 STs were detected, and the most abundant among which was ST131 (n = 16, 26.7%). Most of the E. coli (n = 46, 76.7%) belonged to the groups B2 and D. And some virulence genes were related to the classification of the E. coli. Among them, the detection rates of hek/hra, kpsMII and papGII-III in groups B2 and D were higher than those in groups A and B1. The detection rates of cnf1, iucC and papGII-III in ST131 were higher than those in non-ST131. And the distributions of hek/hra, iroN, iucC, kpsMII and papGII-III were related to the bla _CTX-M subtypes. Finally, most bacterial (n = 32, 53.3%) resistance genes could be transferred between the bacteria by plasmids, especially IncFIB.

Conclusion

ESBLs-producing E. coli in BSI exhibited had high resistance rates and carried a variety of virulence factors (VFs). This is necessary to strengthen the monitoring of ESBLs-producing isolates in the medical environment.

Study on Virulence Genes, Drug Resistance and Molecular Epidemiology of Klebsiella pneumoniae with High Virulence in Inner Mongolia, China

Objective

The purpose of this study was to analyse the clinical, microbiological and molecular epidemiological characteristics of patients with pyogenic liver abscess (PLA) caused by Klebsiella pneumoniae (KPN) in Inner Mongolia, China.

Methods

The KPN isolates from 78 KPN-PLA cases admitted to a tertiary teaching hospital in Baotou, Inner Mongolia, from 2016 to 2019 were studied systematically and described comprehensively. The virulence factors, drug resistance and sequence types of KPN in different samples were identified by a wire-drawing test, polymerase chain reaction, a drug susceptibility test and multi-site sequence typing.

Results

There were more male than female KPN-PLA patients (P<0.05). The mortality rate was 2.5%, and KPN-PLA was significantly associated with diabetes mellitus (P<0.05). Most of the KPN isolates in the puncture fluid of patients with KPN-PLA were hypervirulent KPN (HvKP). The positive rate of the KPN-PLA specimens was higher than that of the blood and urine specimens. The KPN isolates of the urine specimens had higher drug resistance than the other two (P<0.05). The hypermucoviscous KPN, aerobic actin (aero) (+), K1 and K2 serotypes accounted for 80.8%, 89.7%, 56.4% and 26.9%, respectively. In addition to ironB (3.8%), the detection rates of virulence factors rmpA, irp2, entB, iucD, aero, wcaG, iutA, kfu, ybtA, iron, fimH and mrkD were higher (69.2%-100.0%). The positive rate of KPN isolates of the KPN-PLA puncture fluid was higher than that of the blood and urine samples (P<0.05). In addition, ST23 was found to be the dominant ST (32.1%) of KPN-PLA in the Baotou region.

Conclusion

In the KPN-PLA specimens, the KPN isolates were more virulent than those in the blood and urine specimens, and a carbapenem-resistant HvKP strain emerged. This research will help improve the understanding of HvKP and provide useful suggestions for KPN-PLA treatments.

Relationship Between Drug Resistance Characteristics and Biofilm Formation in Klebsiella Pneumoniae Strains

Objective

To conduct epidemiological analysis of Klebsiella pneumoniae (K. pneumoniae) with hypervirulence, and to investigate its drug resistance phenotype, Extended-spectrum β-lactamase (ESBLs) gene, virulence factor, capsular serotype and biofilm formation, so as to provide theoretical basis for further understanding of the drug resistance mechanism of K. pneumoniae with hypervirulence.

Methods

K. Pneumoniae were isolated from clinical samples collected from inpatients. All strains were identified by VITEK2 Compact using fully automatic microbial analyzer, the minimal inhibitory concentration (MIC) of antibiotics was determined by microbroth dilution test. The double disk diffusion method was used to detect the production of ESBLs, modified carbapenem inactivation method (mCIM) was used to detect the production of carbapenemase, and hypermucoviscosity phenotype was detected by wire drawing test. PCR was used to detect ESBLs gene, virulence factor and capsular serotype. Crystal violet staining was used to detect the ability of biofilm formation.

Results

The ESBLs genes detected in this study included strains blaTEM 35 (36.5%), blaSHV 51 (53.1%), and blaCTX-M 49 (51.0%). Most strains carried multiple ESBLs genes, but not all of them produce ESBLs. K1 and K2 accounted for 14.6% and 11.5% respectively. Most (91.7%) strains carried the fimH gene, and the other virulence genes were ybtS (53.1%), entB (46.9%), rmpA (41.7%), aerobactin (32.3%), allS (15.6%), kfu (15.6%). Of all the Klebsiella pneumoniae strains, 33 (34.4%) exhibited ESBLs phenotype, 16 (16.7%) were carbapenemase-producing, and 20 (20.8%) with ESBLs phenotype tested were resistant to all four drugs. The correlation between ESBLs-producing strains and biofilm formation was significantly increased compared to strains without ESBLs phenotype (P=0.035).

Conclusion

Compared to hypervirulent Klebsiella pneumoniae (hvKP), classical Klebsiella pneumoniae (cKP) has a tendency to acquire antibiotic resistance. Our study showed that genes encoding rmpA, K1 or K2, and kfu were highly associated with hvKP.

Carbapenem-Resistant Klebsiella pneumoniae: Virulence Factors, Molecular Epidemiology and Latest Updates in Treatment Options

Klebsiella pneumoniae is a Gram-negative opportunistic pathogen responsible for a variety of community and hospital infections. Infections caused by carbapenem-resistant K. pneumoniae (CRKP) constitute a major threat for public health and are strongly associated with high rates of mortality, especially in immunocompromised and critically ill patients. Adhesive fimbriae, capsule, lipopolysaccharide (LPS), and siderophores or iron carriers constitute the main virulence factors which contribute to the pathogenicity of K. pneumoniae. Colistin and tigecycline constitute some of the last resorts for the treatment of CRKP infections. Carbapenemase production, especially K. pneumoniae carbapenemase (KPC) and metallo-β-lactamase (MBL), constitutes the basic molecular mechanism of CRKP emergence. Knowledge of the mechanism of CRKP appearance is crucial, as it can determine the selection of the most suitable antimicrobial agent among those most recently launched. Plazomicin, eravacycline, cefiderocol, temocillin, ceftolozane-tazobactam, imipenem-cilastatin/relebactam, meropenem-vaborbactam, ceftazidime-avibactam and aztreonam-avibactam constitute potent alternatives for treating CRKP infections. The aim of the current review is to highlight the virulence factors and molecular pathogenesis of CRKP and provide recent updates on the molecular epidemiology and antimicrobial treatment options.

Long Term Characteristics of Clinical Distribution and Resistance Trends of Carbapenem-Resistant and Extended-Spectrum β-Lactamase Klebsiella pneumoniae Infections: 2014-2022

Purpose

Through long-term and large sample size statistical analysis, we revealed the pattern of Klebsiella pneumoniae (KP) infection and drug resistance and provided epidemiological data for the treatment and prevention and control of multidrug-resistant bacterial infection in our hospital.

Patients and Methods

Strains were identified using the BD Phoenix^TM100 system, minimal inhibitory concentration of antibiotics were determined by the broth method, and data were statistically analyzed using WHONET 5.6 and SPSS27.0.

Results

The isolation rate of KP from Enterobacteriaceae (26.2%, 4547/17358) in our hospital showed an increasing annual trend, ranking second only to Escherichia coli. Carbapenem-resistant KP (CRKP) accounted for the highest proportion of carbapenem-resistant Enterobacteriaceae (72.2%, 431/597), showing an upward trend. Infected patients had a male-to-female ratio of approximately 2:1 and were mainly >60 years of age (66.2%), with intensive care units being the most commonly distributed department. Sputum was the most common specimen type (74.0%). Compared with spring and summer, autumn and winter were the main epidemic seasons for KP and extended-spectrum β-lactamase KP (ESBL-KP). The resistance rate of KP to common antibiotics was low, but all showed an increasing trend each year. ESBL-KP was >90% resistant to piperacillin, amoxicillin/clavulanic acid, and cefotaxime and less resistant to other common antibiotics, but showed an increasing trend in resistance to most antibiotics. CRKP resistance to common antibiotics was high, with resistance rates >90%, excluding amikacin (64.1%), gentamicin (87.4%), cotrimoxazole (44.3%), chloramphenicol (13.6%), and tetracycline (30.5%).

Conclusion

KP in our hospital mainly caused pulmonary infection in older men, which occurred frequently in autumn and winter, and the isolation and drug resistance rates showed an increasing trend. Age over 70 years, admission to intensive care unit, and urinary tract infection were found to be the risk factors for CRKP and ESBL-KP-resistance.

Magnitude and Molecular Characterization of Extended-Spectrum β-Lactamase Genes among Klebsiella pneumoniae Isolates in a Large Tertiary Hospital in Ethiopia

Background Extended-spectrum β-lactamases (ESBLs)-producing Klebsiella pneumoniae is reported worldwide increasingly. However, studies on ESBLs are still scarce in Ethiopia. Therefore, the current study aimed to determine the magnitude and resistance patterns of ESBL-producing K. pneumoniae as well as the frequency of ESBL-encoding genes.Methods A cross-sectional study was conducted from September 2018 to February 2019 at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia among a total of 132 non-duplicate K. pneumoniae isolates. Phenotypic detection of ESBL production was done using Combined Disc Test. ESBL-encoding genes of bla_CTX-M, bla_TEM, and bla_SHV were detected through multiplex PCR.Results The magnitude of ESBL production was 102/132 (77.3%). ESBL positive isolates were 100% resistant to ceftriaxone, cefotaxime, and cefuroxime. Co-resistance of ESBL-positive isolates to other non β-lactam antimicrobials was high to trimethoprim-sulfamethoxazole (96.1%) followed by tetracycline (75.5%) and gentamicin (73.5%). However, these isolates showed high susceptibility to amikacin (96.1%) and meropenem (89.2%). From the total ESBL-positive isolates, 82.6%, 73.5%, and 75% carried bla_CTX-M, bla_TEM, and bla_SHV genes, respectively. The majority 78/102 (76.5%) of ESBL-positive isolates harbored all three types of ESBL genes simultaneously.Conclusions The magnitude of ESBL-producing K. pneumoniae isolates was very alarming in the study area. The co-occurrence of bla_CTX-M, bla_TEM, and bla_SHV genes is high, demanding large-scale studies to evaluate the presence of antimicrobial resistance super-clones. ESBL-producing isolates showed high resistance to most of the antimicrobials, needing phenotypic detection of ESBL regularly for better management of patients.

Evidence of Sharing of Carbapenem-Resistant Klebsiella pneumoniae Strains Between Intensive Care Unit Patients and the Environment

Purpose

Carbapenem-resistant Klebsiella pneumoniae (CR-KP) has emerged as an important public health threat. Intestinal colonization with CR-KP increases the risk of infection and death, especially in intensive care unit patients. To clarify the source of colonizing bacteria is very important to prevent the spread of CR-KP, so the purpose of this study was to explore the relationship between the ward environment and intestinal colonization of CR-KP.

Methods

In this study, 353 environmental swabs from ICU (Intensive Care Unit) wards and 241 anal swab samples from ICU patients were collected and screened on MacConkey plates containing 2 μg/mL ertapenem, and the origin and genotype of CR-KP were analyzed by PCR and sequencing. The sequence type of the strains was also obtained by multi-locus sequence type (MLST) analysis, and plasmid conjugation test was used to clarify whether CR-KP can promote the transmission of drug resistance genes through plasmid integration and rearrangement.

Results

A total of 20 CR-KP environmental strains and 7 intestinal strains were obtained, most of which were bla _OXA-48 resistant genotypes. Four different STs were identified by multi-locus sequence type (MLST) analysis, among which the large logarithm was ST485 type, and PFGE clustering showed that the similarity between them was >85%. In the plasmid transcoupling assay, we report that one of the Klebsiella pneumoniae drug-resistant plasmids was successfully transferred to E. coli, indicating that it may promote the spread of drug-resistant genes through plasmid integration and rearrangement.

Conclusion

Our research suggests that the environment may be a potential source of CR-KP and that there is a need for us to adopt more effective disinfection measures.

Carbapenem-Resistant Klebsiella pneumoniae: Diversity, Virulence, and Antimicrobial Resistance

Background

Klebsiella pneumoniae (K. pneumoniae) is one of the most important pathogens in nosocomial infections. It has resistance to most antibiotics, even carbapenem, resulting in restricted therapeutic options.

Purpose

We tried to assess the antimicrobial resistance and virulence fitness of carbapenem-resistant K. pneumoniae (CRKP) in addition to their phenotypic and genotypic diversity.

Materials and Methods

The conventional methods, automated Vitek-32 system, and antimicrobial susceptibility pattern were used to detect CRKP isolates. Virulence and resistance genes profiles were created by using PCR technique. The correlation analysis was done by using R-program.

Results

The antimicrobial resistance profile for all our K. pneumoniae isolates was shocking as the MDR and CRKP were the most prominent phenotypes. Unfortunately, high degrees of heterogeneity among our CRKP isolates were recorded, as 97.5% of them were differentiated into different clusters. We found a negative correlation between the existence of virulence and antimicrobial resistance genes. In contrast to sputum and urine CRPK isolates, the blood isolates showed high antimicrobial resistance and low virulence fitness. Finally, K. pneumoniae creates several outbreaks and crises in Egypt owing to the highly heterogeneity and the wide spread of multidrug-resistant (MDR) and multi-virulent CRKP phenotypes.

Conclusion

Our results are significant and alarming to health organizations throughout the world for the severity and heterogeneity of K. pneumoniae infections. Therefore, the traditional method for treatment of CRKP infections must be renewed. Additionally, the treatment protocols must be well correlated with the site of infections, phenotypes, and genotypes of CRKP strains.

Adherence to European Association of Urology Guidelines and State of the Art of Glycosaminoglycan Therapy for the Management of Urinary Tract Infections: A Narrative Review and Expert Meeting Report

Context

Urinary tract infections (UTIs) have a significant impact on patient's quality of life and society. Antibiotic therapy is the primary approach for the management of UTIs; however, it has major limits in the prevention of recurrent UTIs (rUTIs), also increasing the risk of development of multidrug-resistant micro-organisms.

Objective

The aim of this paper is to discuss the European Association of Urology guidelines for the management of UTIs/rUTIs, the level of adherence to these recommendations, and the available evidence on the use of glycosaminoglycans (GAGs) as a possible alternative treatment to prevent rUTIs.

Evidence acquisition

This narrative review and expert meeting report is based on a literature search concerning the currently available UTI guidelines, the results of a survey administered to 227 urologists, and the opinion of an expert panel in the field of UTIs.

Evidence synthesis

Results obtained from the literature search showed that adherence to guidelines is not optimal. The survey demonstrated that antibiotics remain one of the treatments of UTIs. However, most of the urologists are aware of the problem caused by the resistance to antibiotics and prefer alternative methods for the prophylaxis of UTIs. Considering the alternative methods, the authors concluded that GAG therapy is highly effective in preventing rUTIs.

Conclusions

Adherence to the international guidelines is important to align the clinical practice and avoid the spreading of antibiotic resistance. The survey outlines that the misuse and overuse of antibiotics are major problems; an analysis of clinical evidence confirms that GAG therapy is a valuable therapeutic approach to prevent the recurrence of episodes of UTIs and to limit the onset of antibiotic resistance.

Patient summary

Although antibiotic therapy is primarily used for the management of urinary tract infections (UTIs), misuse and overuse of antibiotics are of concern. Adherence to the international guidelines is important to prevent the spreading of antibiotic resistance. Clinical evidence confirms that the use of glycosaminoglycans is a valuable therapeutic approach to prevent UTI recurrence and limit the onset of antibiotic resistance.

Impact of Carbapenem Peri-Transplant Prophylaxis and Risk of Extended-Spectrum Cephalosporin-Resistant Enterobacterales Early Urinary Tract Infection in Kidney Transplant Recipients: A Propensity Score-Matched Analysis

Background

Urinary tract infection (UTI) is the most common bacterial infection after kidney transplantation (KT), leading to unfavorable clinical and allograft outcomes. Gram-negative uropathogenic bacteria are frequently encountered especially extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales (EB), causing UTI early after KT.

Methods

A retrospective single transplant study was conducted between January 2016 and December 2019. We performed 1:1 nearest-neighbor propensity score matching without replacement using recipient age, recipient sex, induction, transplant year, human leukocyte antigen, cold ischemia time, and panel-reactive antibody before analyses. Cumulative incidence of ESC-R EB early (within 14 days after KT) UTI was estimated by the Kaplan–Meier method. Risk factors for ESC-R EB early UTI were analyzed by a Cox proportional hazards model. Variables measured after transplantation were considered time-dependent covariates.

Results

We included 620 KT recipients (37% women; mean age ± SD, 43 ± 11 years). Overall, 64% and 76% received deceased-donor allograft and induction therapy. Sixty-five (10%) and 555 (90%) received carbapenems and cefuroxime peri-transplant prophylaxis, respectively. Early UTI occurred in 183 (30%) patients, 52% caused by ESC-R EB. Propensity score matching produced 65 well-balanced pairs. During a 14-day follow-up, the cumulative incidence of ESC-R EB early UTI was 5 and 28% in the carbapenems and cefuroxime groups, respectively (log-rank test = 0.003). Peri-transplant carbapenems prophylaxis was a protective factor against ESC-R EB after KT (hazard ratio, 0.19; 95% confidence interval, 0.05–0.64; p = 0.008). Clinical and allograft outcomes did not differ significantly between the groups.

Conclusions

In the setting where ESC-R EB UTI is common among KT recipients, carbapenems peri-transplant prophylaxis could protect against the occurrence of early ESC-R EB UTI after KT. Further prospective studies should focus on this specific infection prevention strategy.

Relationship Between Antibiotic Resistance, Biofilm Formation, and Biofilm-Specific Resistance in Escherichia coli Isolates from Ningbo, China

Purpose

Methods

Results

Conclusion

Antibiotic-resistant pathogenic bacterial isolates from patients attending the outpatient department of university of Cape Coast hospital, Ghana: A retrospective study between 2013-2015

Uropathogenic Escherichia coli (E. coli) is an important urinary tract infection (UTI) that has been associated with both complicated and uncomplicated disease conditions. The global emergence of multiple drug-resistant (MDR) and extended-spectrum β-lactamase (ESBL) is of public health concern as the resistance limits the current treatment options. The objective of this study was to analyze the antibiotic-resistant patterns among the uropathogenic E. coli isolates at the University of Cape Coast (UCC) hospital between 2013 and 2015 as baseline data to understand the current antibiotic resistance situation within UCC and its environs. A retrospective cross-sectional study of bacteria isolates at UCC hospital from January 2013 to December 2015 were analyzed. A standard biochemical and antibiotic susceptibility tests were performed using Kirby-Bauer NCCLs modified disc diffusion technique. The network of interaction between pathogenic isolates and antibiotic resistance was performed using Cytoscape software. Statistical significance was tested using ANOVA and one-sample Wilcoxon test. The overall E. coli prevalence was 15.76% (32/203); females had the highest infection of 17.33% (26/150) compared to male subjects who had 11.32% (6/53) out of all the pathogenic infections. The E. coli prevalence among the age categories were 2/21 (9.52%), 27/154 (17.53%) and 4/21 (19.05%) among ≤20 years, 21-40 years and 41-60 years respectively. The isolated resistant pathogens exhibited different antibiotic resistance patterns. An interaction network of nodes connecting to other nodes indicating positive correlations between the pathogens and antibiotic resistance was established. Escherichia coli, Citrobacter spp, Klebsiella spp among other isolated pathogens formed higher centrality in the network of interaction with antibiotic resistance. The individual E. coli isolates showed a significant difference in the mean ± SD (95% CI) pattern of antibiotic resistance, 2.409±1.205 (1.828-2.990), χ2 = 36.68, p<0.0001. In conclusion, the study reports the interaction of E. coli isolates at UCC hospital and its antibiotic-resistant status between 2013 and 2015. This data forms the baseline information for assessing the current antibiotic status in UCC and its environs.

Antimicrobial resistance among GLASS pathogens in Morocco: an epidemiological scoping review

BACKGROUND

Monitoring of antimicrobial resistance (AMR) is of great importance due to the frequency of strains becoming increasingly resistant to antibiotics. This review, using a public health focused approach, which aims to understand and describe the current status of AMR in Morocco in relation to WHO priority pathogens and treatment guidelines.

METHODS

PubMed, ScienceDirect and Google Scholar Databases and grey literature are searched published articles on antimicrobial drug resistance data for GLASS priority pathogens isolated from Morocco between January 2011 and December 2021. Articles are screened using strict inclusion/exclusion criteria. AMR data is extracted with medians and IQR of resistance rates.

RESULTS

Forty-nine articles are included in the final analysis. The most reported bacterium is Escherichia coli with median resistance rates of 90.9%, 64.0%, and 56.0%, for amoxicillin, amoxicillin-clavulanic acid, and co-trimoxazole, respectively. Colistin had the lowest median resistance with 0.1%. A median resistance of 63.0% is calculated for amoxicillin-clavulanic acid in Klebsiella pneumonia. Imipenem resistance with a median of 74.5% is reported for Acinetobacter baumannii. AMR data for Streptococcus pneumonie does not exceed 50.0% as a median.

CONCLUSIONS

Whilst resistance rates are high for most of GLASS pathogens, there are deficient data to draw vigorous conclusions about the current status AMR in Morocco. The recently join to the GLASS system surveillance will begin to address this data gap.

A Cross-Sectional Study to Evaluate Antimicrobial Susceptibility of Uropathogens from South Punjab, Pakistan

Background

Urinary tract infections (UTIs) are a common infection caused by uropathogenic bacteria. Drug resistance against common antibiotics is a leading cause of treatment failure in UTIs.

Objective

This study was conducted to check the prevalence of antimicrobial susceptibility against uropathogens and identify the best treatment option against UTIs.

Methods

In this cross-sectional study, urine samples (n = 1000) were collected and cultured for pure bacterial growth by using cysteine–lactose–electrolyte-deficient (CLED) media. After physical and biochemical characterization, antibacterial susceptibility was performed by the Kirby–Bauer disk diffusion method.

Results

Uropathogenic bacteria were successfully isolated in 57% (n = 572) of total tested samples (n = 1000). Escherichia coli 51.2% (n = 293/572), Klebsiella species 15.4% (n = 88/572), Enterococcus species 15.4% (n = 88/572), Pseudomonas species 9.4% (n = 54/572), Staphylococcus aureus 3.2% (n = 18/572), coagulase-negative Staphylococci (CoNS) 3.0% (n = 17/572) and Proteus species 2.4% (n = 14/572) were the most prevalent organism in UTIs. Prevalence of Gram-negative rods (GNRs) was 78.5% (n = 449/572) among UTI patients as compared to Gram-positive cocci (GPCs) 21.5% (n = 123/572). Escherichia coli 65.3% (n = 293/449), Klebsiella species 19.6% (n = 88/449), Pseudomonas species 12.0% (54/449) and Proteus species 3.1% (n = 14/449) were the most prevalent GNRs in UTIs, while Enterococcus species 71.5% (n = 88/123), Staphylococcus aureus 14.6% (n = 18/123) and coagulase-negative Staphylococci (CoNS) 13.8% (17/123) were the most prevalent GPCs in UTIs. The majority of isolated uropathogens showed resistance against routinely used antibiotics. However, teicoplanin and linezolid were the most effective drugs against GPCs and piperacillin/tazobactam, meropenem and imipenem were the most effective drugs against GNRs. Nitrofurantoin and fosfomycin were shown to be most effective against both GNRs and GPCs.

Conclusion

In conclusion, Escherichia coli (GNRs) and Enterococcus species (GPCs) are the most prevalent organisms among UTIs patients, which are shown to be antibiotic-resistant to the most commonly used antibiotics. However, nitrofurantoin and fosfomycin are the most effective drugs against uropathogens in UTIs.

How Advanced Is Our Understanding of the Role of Intestinal Barrier Dysfunction in the Pathogenesis of Recurrent Urinary Tract Infections

A comprehensive understanding of urinary tract infections (UTIs), one of the most common human infections, is required as they are complex and poorly understood diseases. Periurethral and vaginal colonization by rectal flora, with the constant presence of pathogens in the urethra, is the initial step of the recurrent UTIs pathway. Current scientific data describe the genetic, etiological, biological, and behavioral risk factors for recurring UTIs, but they do not include the effect of intestinal barrier function on the disease. Although gut microbiota has been proposed as the main source for UTIs, the cross-talk between intestinal barrier dysfunction and the recurrence of UTIs has not yet been supported by scientific data. In this opinion review, based on published data and the results of our clinical studies, I aimed to outline the possible contribution of intestinal barrier dysfunction to the pathogenesis of recurrent UTIs. I believe that the unanswered questions raised by this review can guide further experimental and controlled studies to clarify the mechanisms underlying the role of intestinal barrier dysfunction in the pathogenesis of recurrent UTIs.

Ceftazidime-Avibactam for the Treatment of Multidrug-Resistant Pathogens: A Retrospective, Single Center Study

Background: Ceftazidime/avibactam is a new cephalosporin/beta-lactamase inhibitor combination approved in 2015 by the FDA for the treatment of complicated intra-abdominal and urinary tract infection, hospital-acquired pneumoniae and Gram-negative infections with limited treatment options. Methods: In this retrospective study, we evaluate the efficacy of ceftazidime/avibactam treatment in 81 patients with Gram-negative infection treated in our center from January 2018 to December 2019. The outcome evaluated was 30-days survival or relapse of infection after the first positive blood culture. Results: the majority of patients were 56 male (69%), with median age of 67. Charlson’s Comorbidity Index was >3 in 58 patients. In total, 46% of the patients were admitted into the medical unit, 41% in the ICU, and 14% in the surgical ward. Of the patients, 78% had nosocomial infections, and 22% had healthcare-related infections. The clinical failure rate was 35%: 13 patients died within 30 days from the onset of infection. The outcome was influenced by the clinical condition of the patients: solid organ transplantation (p = 0.003) emerged as an independent predictor of mortality; non-survival patients most frequently had pneumonia (p = 0.009) or mechanical ventilation (p = 0.049). Conclusion: Ceftazidime−avibactam showed high efficacy in infections caused by MDR Gram-negative pathogens with limited therapeutic options.

Dissecting and Evaluating the Therapeutic Targets of Coptis Chinensis Franch in the Treatment of Urinary Tract Infections Induced by Escherichia coli

Coptis chinensis Franch (CCF) is extensively used in the treatment of inflammatory-related diseases. Accumulating studies have previously demonstrated the anti-inflammatory properties of CCF, yet data on its exact targets against urinary tract infections (UTIs) remain largely unknown. Therefore, the present study decodes the potential targets of action of CCF against UTIs by network pharmacology combined with experiment evaluations. Based on the pharmacology network analysis, the current study yielded six core ingredients: quercetin, palmatine (R)-canadine, berlambine, berberine, and berberrubine. The protein–protein interaction network (PPI) was generated by the string database, and then, four targets (IL6, FOS, MYC, and EGFR) were perceived as the major CCF targets using the CytoNCA plug-in. The results of molecular docking showed that the six core constituents of CCF had strong binding affinities toward the four key targets of UTIs after docking into the crystal structure. The enrichment analysis indicated that the possible regulatory mechanisms of CCF against UTIs were based on the modules of inflammation, immune responses, and apoptosis among others. Experimentally, the Escherichia coli (E. coli) strain CFT073 was applied to establish in vivo and in vitro models. In vivo results revealed that the key targets, IL6 and FOS, are significantly upregulated in rat bladder tissues of UTIs, whereas the expression of MYC and EGFR remained steady. Last, in vitro results further confirmed the therapeutic potential of CCF by reducing the expression of IL6 and FOS. In conclusion, IL6 and FOS were generally upregulated in the progression of E. coli–induced UTIs, whereas the CCF intervention exerted a preventive role in host cells stimulated by E. coli, partially due to inhibiting the expression of IL6 and FOS.

Influence of Antimicrobial Resistance on the Course of Symptoms in Female Patients Treated for Uncomplicated Cystitis Caused by Escherichia coli

Background: Resistance to the prescribed antibiotic causes a longer duration of symptoms in patients with urinary tract infection. Yet, a study found that patients infected with trimethoprim-resistant Escherichia coli (E. coli) had a prolonged duration of symptoms even if treated with an antibiotic to which the strain was susceptible. The purpose of this study was to attempt to reproduce this finding in a different cohort. Methods: We analyzed data from two studies from general practice in the Capital Region of Denmark including patients from 2014 to 2016. The primary outcome was the severity of frequency and dysuria. The secondary outcome was the number of days until symptoms had disappeared. Results: We included 180 women treated for uncomplicated cystitis caused by E. coli. We found that 16.11% (n = 29) of the E. coli strains were resistant to all of the three selected antibiotics (ampicillin, sulfamethizole and trimethoprim). There was no significant difference in severity or time until the symptoms had disappeared between women infected with resistant or susceptible E. coli. Conclusions: Strains of E. coli resistant to ampicillin, sulfamethizole and trimethoprim causing uncomplicated cystitis do not result in more severe symptoms or a longer symptom duration if treated with an antibiotic to which they are susceptible.

Urinary Tract Infection in Hemodialysis-Dependent End-Stage Renal Disease Patients

Introduction

The aim of this study was to analyze urinalysis findings and urinary bacterial culture in hemodialysis-dependent end-stage renal disease patients. The research goal was to understand the proportion, risk factors, and the causative organisms of urinary tract infection in hemodialysis-dependent end-stage renal disease patients.

Materials and Methods

Between May 2020 and June 2021, this study included 100 hemodialysis-dependent end-stage renal disease patients (50 male patients and 50 female patients). The urine underwent microscopic examination, pyuria was defined as ≥5 white blood cells per high-power field, and urinary bacterial cultures were conducted for patients with pyuria. Bacteriuria was defined as ≥10⁴ colony-forming units/mL in men and ≥10⁵ colony-forming units/mL in women. Daily urine output was investigated by oral listening. Postvoiding residual urine volume was measured.

Results

Fifty-six percent of male patients and 30% of female patients had normosthenuria, 24% of male patients and 38% of female patients had pyuria, and 20% of male patients and 32% of female patients had a urinary tract infection. A comparison of normosthenuria and urinary tract infection revealed no statistically significant difference in age, time on dialysis, daily urine output, and postvoiding residual urine volume. The proportion of female patients among those with normosthenuria was 34.8%, whereas the proportion of female patients among those with UTI was 61.5%. Urinary bacterial cultures showed that the major causative organisms were Escherichia coli (45%; 18/40 cultures) and extended spectrum beta-lactamase-producing Escherichia coli (17.5%; 7/40 cultures).

Conclusion

The incidence of urinary tract infection was higher in female patients than in male patients. The proportion of resistant bacteria as the causative organisms was high in hemodialysis-dependent end-stage renal disease patients. Urinary bacterial culture should be checked while patients are able to void urine.

Combating antimicrobial resistance with cefiderocol for complicated infections involving the urinary tract

Cefiderocol is a unique siderophore cephalosporin antimicrobial agent that has shown promise in treating complicated urinary tract infections (cUTI). Urinary tract infections are commonly diagnosed infections with risk increasing with age and prevalence more common in women. cUTI poses a risk of recurrence and is more likely to be associated with antibiotic-resistant bacteria. The Food and Drug Administration approved cefiderocol for use as a last-line option in the treatment of cUTI including pyelonephritis. Cefiderocol has activity against all forms of carbapenemases due to its ability to overcome the mechanisms of carbapenemase resistance. Because of this, resistance to cefiderocol is unlikely to occur. Studies show cefiderocol is well tolerated among younger patients and patients greater than 65 years of age, the latter making up most of the study population. Renal dose adjustments are recommended. Dose adjustment in the presence of hepatic impairment is not recommended, as hepatic clearance represents a minor elimination pathway for cefiderocol. The ability of cefiderocol to overcome multiple resistance mechanisms makes it a novel choice in combating multidrug-resistant bacteria in the treatment of cUTI.

Ribosomal Hibernation-Associated Factors in Escherichia coli

Bacteria convert active 70S ribosomes to inactive 100S ribosomes to survive under various stress conditions. This state, in which the ribosome loses its translational activity, is known as ribosomal hibernation. In gammaproteobacteria such as Escherichia coli, ribosome modulation factor and hibernation-promoting factor are involved in forming 100S ribosomes. The expression of ribosome modulation factor is regulated by (p)ppGpp (which is induced by amino acid starvation), cAMP-CRP (which is stimulated by reduced metabolic energy), and transcription factors involved in biofilm formation. This indicates that the formation of 100S ribosomes is an important strategy for bacterial survival under various stress conditions. In recent years, the structures of 100S ribosomes from various bacteria have been reported, enhancing our understanding of the 100S ribosome. Here, we present previous findings on the 100S ribosome and related proteins and describe the stress-response pathways involved in ribosomal hibernation.

Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB PDB) provides a wide range of digital data regarding biology and biomedicine. This huge internet resource involves a wide range of important biological data, obtained from experiments around the globe by different scientists. The Worldwide Protein Data Bank (wwPDB) represents a brilliant collection of 3D structure data associated with important and vital biomolecules including nucleic acids (RNAs and DNAs) and proteins. Moreover, this database accumulates knowledge regarding function and evolution of biomacromolecules which supports different disciplines such as biotechnology. 3D structure, functional characteristics and phylogenetic properties of biomacromolecules give a deep understanding of the biomolecules' characteristics. An important advantage of the wwPDB database is the data updating time, which is done every week. This updating process helps users to have the newest data and information for their projects. The data and information in wwPDB can be a great support to have an accurate imagination and illustrations of the biomacromolecules in biotechnology. As demonstrated by the SARS-CoV-2 pandemic, rapidly reliable and accessible biological data for microbiology, immunology, vaccinology, and drug development are critical to address many healthcare-related challenges that are facing humanity. The aim of this paper is to introduce the readers to wwPDB, and to highlight the importance of this database in biotechnology, with the expectation that the number of scientists interested in the utilization of Protein Data Bank's resources will increase substantially in the coming years.

In Vitro Activities of Ceftazidime-Avibactam and Aztreonam-Avibactam at Different Inoculum Sizes of Extended-Spectrum β-Lactam-Resistant Enterobacterales Blood Isolates

β-lactam–avibactam combinations have been proposed as carbapenem-sparing therapies, but little data exist on their in vitro activities in infections with high bacterial inocula. We investigated the in vitro efficacies and the inoculum effects of ceftazidime–avibactam and aztreonam–avibactam against extended-spectrum β-lactam-resistant Enterobacterales blood isolates. A total of 228 non-repetitive extended-spectrum β-lactam-resistant Escherichia coli and Klebsiella pneumoniae blood isolates were prospectively collected in a tertiary center. In vitro susceptibilities to ceftazidime, aztreonam, meropenem, ceftazidime–avibactam, and aztreonam–avibactam were evaluated by broth microdilution method using standard and high inocula. An inoculum effect was defined as an eightfold or greater increase in MIC when tested with the high inoculum. Of the 228 isolates, 99% were susceptible to ceftazidime–avibactam and 99% had low aztreonam–avibactam MICs (≤8 mg/L). Ceftazidime–avibactam and aztreonam–avibactam exhibited good in vitro activities; MIC₅₀/MIC₉₀ values were 0.5/2 mg/L, 0.125/0.5 mg/L, and ≤0.03/0.25 mg/L, respectively, and aztreonam–avibactam was more active than ceftazidime–avibactam. The frequencies of the inoculum effect with ceftazidime–avibactam and aztreonam–avibactam were lower than with meropenem (14% vs. 38%, p < 0.001 and 30% vs. 38%, p = 0.03, respectively). The β-lactam-avibactam combinations could be useful as carbapenem-sparing strategies, and aztreonam–avibactam has the better in vitro activity but is more subject to the inoculum effect than ceftazidime–avibactam.

Writing a strong scientific paper in medicine and the biomedical sciences: a checklist and recommendations for early career researchers

Scientific writing is an important skill in both academia and clinical practice. The skills for writing a strong scientific paper are necessary for researchers (comprising academic staff and health-care professionals). The process of a scientific research will be completed by reporting the obtained results in the form of a strong scholarly publication. Therefore, an insufficiency in scientific writing skills may lead to consequential rejections. This feature results in undesirable impact for their academic careers, promotions and credits. Although there are different types of papers, the original article is normally the outcome of experimental/epidemiological research. On the one hand, scientific writing is part of the curricula for many medical programs. On the other hand, not every physician may have adequate knowledge on formulating research results for publication adequately. Hence, the present review aimed to introduce the details of creating a strong original article for publication (especially for novice or early career researchers).

Toll-Like Receptors: General Molecular and Structural Biology

Background/Aim

Toll-like receptors (TLRs) are pivotal biomolecules in the immune system. Today, we are all aware of the importance of TLRs in bridging innate and adaptive immune system to each other. The TLRs are activated through binding to damage/danger-associated molecular patterns (DAMPs), microbial/microbe-associated molecular patterns (MAMPs), pathogen-associated molecular patterns (PAMPs), and xenobiotic-associated molecular patterns (XAMPs). The immunogenetic molecules of TLRs have their own functions, structures, coreceptors, and ligands which make them unique. These properties of TLRs give us an opportunity to find out how we can employ this knowledge for ligand-drug discovery strategies to control TLRs functions and contribution, signaling pathways, and indirect activities. Hence, the authors of this paper have a deep observation on the molecular and structural biology of human TLRs (hTLRs).

Methods and Materials

To prepare this paper and fulfill our goals, different search engines (e.g., GOOGLE SCHOLAR), Databases (e.g., MEDLINE), and websites (e.g., SCOPUS) were recruited to search and find effective papers and investigations. To reach this purpose, we tried with papers published in the English language with no limitation in time. The iCite bibliometrics was exploited to check the quality of the collected publications.

Results

Each TLR molecule has its own molecular and structural biology, coreceptor(s), and abilities which make them unique or a complementary portion of the others. These immunogenetic molecules have remarkable roles and are much more important in different sections of immune and nonimmune systems rather than that we understand to date.

Conclusion

TLRs are suitable targets for ligand-drug discovery strategies to establish new therapeutics in the fields of infectious and autoimmune diseases, cancers, and other inflammatory diseases and disorders.

It's Not Easy Being Green: A Narrative Review on the Microbiology, Virulence and Therapeutic Prospects of Multidrug-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is the most frequent cause of infection among non-fermenting Gram-negative bacteria, predominantly affecting immunocompromised patients, but its pathogenic role should not be disregarded in immunocompetent patients. These pathogens present a concerning therapeutic challenge to clinicians, both in community and in hospital settings, due to their increasing prevalence of resistance, and this may lead to prolonged therapy, sequelae, and excess mortality in the affected patient population. The resistance mechanisms of P. aeruginosa may be classified into intrinsic and acquired resistance mechanisms. These mechanisms lead to occurrence of resistant strains against important antibiotics-relevant in the treatment of P. aeruginosa infections-such as β-lactams, quinolones, aminoglycosides, and colistin. The occurrence of a specific resistotype of P. aeruginosa, namely the emergence of carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) strains, has received substantial attention from clinical microbiologists and infection control specialists; nevertheless, the available literature on this topic is still scarce. The aim of this present review paper is to provide a concise summary on the adaptability, virulence, and antibiotic resistance of P. aeruginosa to a readership of basic scientists and clinicians.

Increasing relevance of Gram-positive cocci in urinary tract infections: a 10-year analysis of their prevalence and resistance trends

Urinary tract infections (UTIs) are the third most common types of infection in human medicine worldwide. There is increasing appreciation for the pathogenic role of Gram-positive cocci (GPC) in UTIs, as they have a plethora of virulence factors, maintaining their pathogenicity and high affinity for the epithelial cells of the urinary tract. The study was carried out using microbiological data collected corresponding to the period between 2008 and 2017. Antimicrobial susceptibility testing was performed using the disk diffusion method and E-tests. The age range of patients affected from the outpatient and inpatient groups differed significantly (43 [range 0.7-99] vs. 68 [range 0.4-99] years; p = 0.008). 3962 GPCs were obtained from inpatient and 4358 from outpatient samples, corresponding to 20.5 ± 2.8% (range 17.5-26.8%) and 20.6 ± 2.6% (range 17.8-26.0%) of all positive urine samples (p > 0.05); in both groups, Enterococcus spp. were the most prevalent (outpatients: 79.6%; inpatients: 88.5%). High-level aminoglycoside resistance in enterococci was noted in 31.0-46.6% of cases. A pronounced increase in the number of MRSA was seen in the second half of the study period (0.6-1.9% vs. 9.8-11.6%; p = 0.038). The ratio of VRE isolates was 0.16%, no VISA/VRSA isolates were detected.

Increasing relevance of Gram-positive cocci in urinary tract infections: a 10-year analysis of their prevalence and resistance trends

Urinary tract infections (UTIs) are the third most common types of infection in human medicine worldwide. There is increasing appreciation for the pathogenic role of Gram-positive cocci (GPC) in UTIs, as they have a plethora of virulence factors, maintaining their pathogenicity and high affinity for the epithelial cells of the urinary tract. The study was carried out using microbiological data collected corresponding to the period between 2008 and 2017. Antimicrobial susceptibility testing was performed using the disk diffusion method and E-tests. The age range of patients affected from the outpatient and inpatient groups differed significantly (43 [range 0.7–99] vs. 68 [range 0.4–99] years; p = 0.008). 3962 GPCs were obtained from inpatient and 4358 from outpatient samples, corresponding to 20.5 ± 2.8% (range 17.5–26.8%) and 20.6 ± 2.6% (range 17.8–26.0%) of all positive urine samples (p > 0.05); in both groups, Enterococcus spp. were the most prevalent (outpatients: 79.6%; inpatients: 88.5%). High-level aminoglycoside resistance in enterococci was noted in 31.0–46.6% of cases. A pronounced increase in the number of MRSA was seen in the second half of the study period (0.6–1.9% vs. 9.8–11.6%; p = 0.038). The ratio of VRE isolates was 0.16%, no VISA/VRSA isolates were detected.

FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens

Chaperone-usher fimbrial adhesins are powerful weapons against the uropathogens that allow the establishment of urinary tract infections (UTIs). As the antibiotic therapeutic strategy has become less effective in the treatment of uropathogen-related UTIs, the anti-adhesive molecules active against fimbrial adhesins, key determinants of urovirulence, are attractive alternatives. The best-characterized bacterial adhesin is FimH, produced by uropathogenic Escherichia coli (UPEC). Hence, a number of high-affinity mono- and polyvalent mannose-based FimH antagonists, characterized by different bioavailabilities, have been reported. Given that antagonist affinities are firmly associated with the functional heterogeneities of different FimH variants, several FimH inhibitors have been developed using ligand-drug discovery strategies to generate high-affinity molecules for successful anti-adhesion therapy. As clinical trials have shown d-mannose's efficacy in UTIs prevention, it is supposed that mannosides could be a first-in-class strategy not only for UTIs, but also to combat other Gram-negative bacterial infections. Therefore, the current review discusses valuable and effective FimH anti-adhesive molecules active against UTIs, from design and synthesis to in vitro and in vivo evaluations.

Characterization of Resistance in Gram-Negative Urinary Isolates Using Existing and Novel Indicators of Clinical Relevance: A 10-Year Data Analysis

Classical resistance classifications (multidrug resistance [MDR], extensive drug resistance [XDR], pan-drug resistance [PDR]) are very useful for epidemiological purposes, however, they may not correlate well with clinical outcomes, therefore, several novel classification criteria (e.g., usual drug resistance [UDR], difficult-to-treat resistance [DTR]) were introduced for Gram-negative bacteria in recent years. Microbiological and resistance data was collected for urinary tract infections (UTIs) retrospectively, corresponding to the 2008.01.01–2017.12.31. period. Isolates were classified into various resistance categories (wild type/susceptible, UDR, MDR, XDR, DTR and PDR), in addition, two new indicators (modified DTR; mDTR and mcDTR) and a predictive composite score (pMAR) were introduced. Results: n = 16,240 (76.8%) outpatient and n = 13,386 (69.3%) inpatient UTI isolates were relevant to our analysis. Citrobacter-Enterobacter-Serratia had the highest level of UDR isolates (88.9%), the Proteus-Providencia-Morganella group had the highest mDTR levels. MDR levels were highest in Acinetobacter spp. (9.7%) and Proteus-Providencia-Morganella (9.1%). XDR- and DTR-levels were higher in non-fermenters (XDR: 1.7%–4.7%. DTR: 7.3%–7.9%) than in Enterobacterales isolates (XDR: 0%–0.1%. DTR: 0.02%–1.5%). Conclusions: The introduction of DTR (and its’ modifications detailed in this study) to the bedside and in clinical practice will definitely lead to substantial benefits in the assessment of the significance of bacterial resistance in human therapeutics.

Clinical cases, drug resistance, and virulence genes profiling in Uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) as the most important bacterial agent of urinary tract infections (UTIs) encompasses a wide treasure of virulence genes and factors. In due to this default, the aim of this research was to detect and identify some important virulence genes including cnf1, upaH, hlyA, ibeA, and cdtB in isolated UPEC pathotypes. In this research, clinical samples of urine were collected in Shahr-e-Qods, Tehran, Iran. The UPEC pathotypes were confirmed by standard biochemical tests. The DNAs of isolated bacteria were extracted. The genes of cnf1, upaH, hlyA, ibeA, and cdtB were run for multiplex PCR and gel electrophoresis. Furthermore, the antibiogram was done for the isolated UPEC strains by 11 common antibiotics. In accordance with the results, the virulence genes of cnf1, upaH, hlyA, ibeA, and cdtB were respectively recognized in 100%, 51.2%, 38.4%, 9.3%, and 0% of isolated UPEC pathotypes. In consequence, the final virulence gene profiling of the isolated UPEC strains was patterned as cnf1, cnf1-upaH, cnf1-upaH-hlyA, and cnf1-upaH-hlyA-ibeA. The chi-square tests showed no significant correlations between virulence gene profile and UTIs, between virulence gene profile and antibiotic resistance, and between virulence genes and different types of UTIs. The cnf1 virulence gene contributes in the occurrence of all types of UTIs. In contrast to cnf1, the cdtB gene was absent in the isolated UPEC strains in this investigation. The most ineffective antibiotics were recognized as Penicillin, Tetracycline, and Nalidixic acid, respectively, while Streptomycin, Chloramphenicol, and Ciprofloxacin are the best options for UTIs treatment.

The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options

Urinary tract infections (UTIs) are some of the most common infections in human medicine worldwide, recognized as an important public health concern to healthcare systems around the globe. In addition, urine specimens are one of the most frequently submitted samples for culture to the clinical microbiology laboratory, exceeding the number of most of the other sample types. The epidemiology, species-distribution and susceptibility-patterns of uropathogens vary greatly in a geographical and time-dependent manner and it also strongly correlated with the reported patient population studied. Nevertheless, many studies highlight the fact that the etiological agents in UTIs have changed considerably, both in nosocomial and community settings, with a shift towards "less common" microorganisms having more pronounced roles. There is increasing demand for further research to advance diagnostics and treatment options, and to improve care of the patients. The aim of this review paper was to summarize current developments in the global burden of UTI, the diagnostic aspects of these infectious pathologies, the possible etiological agents and their virulence determinants (with a special focus on the members of the Enterobacterales order), current guidelines and quality indicators in the therapy of UTIs and the emergence of multidrug resistance in urinary pathogens.