Comparative Epidemiology and Resistance Trends of Common Urinary Pathogens in a Tertiary-Care Hospital: A 10-Year Surveillance Study

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.

Molecular Mechanisms and Epidemiology of Carbapenem-Resistant Escherichia coli Isolated from Chinese Patients During 2002-2017

Background

The emergence and spread of carbapenem-resistant Escherichia coli (E. coli) pose a serious threat to human health worldwide. This study aimed to investigate the molecular mechanisms underlying carbapenem resistance and their prevalence among E. coli in China.

Methods

A collection of 5796 E. coli clinical isolates were collected from the First Affiliated Hospital of Wenzhou Medical University from 2002 to 2017. Sensitivity to antibiotics was determined using the agar dilution method. The detection of carbapenemases production and the prevalence of resistance-associated genes were investigated through modified carbapenem inactivation method (mCIM), PCR and sequencing. The mutations in outer membrane porins genes (ompC and ompF) were also analyzed by PCR and sequencing assays. The effect of efflux pump mechanism on carbapenem resistance was also tested. E. coli were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

Results

A total of 58 strains (1.0%) of carbapenem-resistant E. coli were identified. The strains carrying bla_KPC-2 and bla_NDM accounted for 22.4% (13/58) and 51.7% (30/58), respectively. Among bla_NDM- positive strains, 27 bla_NDM genes were assigned to bla_NDM-5, while the remaining three strains were bla_NDM-1, whereas bla_VIM, bla_IMP, bla_OXA-48, and bla_SHV were not found. The CTX-M-type β-lactamase genes accounted for 96.6% (56/58). In addition, bla_TEM-1 genes were identified in 58.6% of tested strains. In carbapenem-resistant isolates, mutations in OmpC (the majority of mutated sites were D192G and Q104_F141del, accounting for 54.5%) and OmpF (large deletions S75_V127del, W83_D135del and Q88_D135del) were detected. Of note, the antibiotic resistance was not associated with overexpression of efflux pump. Moreover, MLST categorized the 58 carbapenem-resistant isolates into 19 different sequence types. PFGE analysis revealed that homology among the carbapenem-resistant isolates was low and sporadic.

Conclusion

The bla_NDM was the principal resistance mechanism of carbapenem-resistant E. coli in the hospital. bla_NDM-5 is becoming a new threat to public health and the alteration of outer membrane porins might help further increase the MIC of carbapenem.

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.

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

Introduction

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

Purpose

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

Patients and Methods

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

Results

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

Conclusion

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

Prevalence of Escherichia Coli and Its Antimicrobial Susceptibility Profiles among Patients with UTI at Mulago Hospital, Kampala, Uganda

Background

Urinary tract infections (UTIs) remain the most common infections diagnosed in in- and outpatients as well as hospitalized patients. Current knowledge on antimicrobial susceptibility pattern for uropathogens is essential to effectively manage UTIs. This study aimed at determining the prevalence of E. coli and its antimicrobial susceptibility profiles among patients presenting with signs and symptoms of UTI in Mulago Hospital in Uganda.

Methods

Midstream urine samples were collected from 100 patients presenting with signs and symptoms of UTI at the outpatient department of Mulago Hospital. The samples were cultured, and isolates of E. coli and its antimicrobial susceptibility profiles among patients presenting with signs and symptoms of UTI in Mulago Hospital in Uganda.

Results

Out of 100 patients studied, E. coli and its antimicrobial susceptibility profiles among patients presenting with signs and symptoms of UTI in Mulago Hospital in Uganda. Escherichia coli isolates were highly susceptible to cefotaxime/clavulanic acid (100%) and nitrofurantoin (70%) but showed high resistance to cefuroxime (100%), ceftazidime (100%), nalidixic acid (90%), and ciprofloxacin (90%).

Conclusion

Escherichia coli, the predominant uropathogen, showed significant multidrug resistance to antibiotics commonly prescribed for the management of UTIs. These findings should form a basis for preliminary decision making on the appropriate line of treatment for UTIs.Escherichia coli isolates were highly susceptible to cefotaxime/clavulanic acid (100%) and nitrofurantoin (70%) but showed high resistance to cefuroxime (100%), ceftazidime (100%), nalidixic acid (90%), and ciprofloxacin (90%).

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.

Trans-Kingdom Conjugation within Solid Media from Escherichia coli to Saccharomyces cerevisiae

Conjugation is a bacterial mechanism for DNA transfer from a donor cell to a wide range of recipients, including both prokaryotic and eukaryotic cells. In contrast to conventional DNA delivery techniques, such as electroporation and chemical transformation, conjugation eliminates the need for DNA extraction, thereby preventing DNA damage during isolation. While most established conjugation protocols allow for DNA transfer in liquid media or on a solid surface, we developed a procedure for conjugation within solid media. Such a protocol may expand conjugation as a tool for DNA transfer to species that require semi-solid or solid media for growth. Conjugation within solid media could also provide a more stable microenvironment in which the conjugative pilus can establish and maintain contact with recipient cells for the successful delivery of plasmid DNA. Furthermore, transfer in solid media may enhance the ability to transfer plasmids and chromosomes greater than 100 kbp. Using our optimized method, plasmids of varying sizes were tested for transfer from Escherichia coli to Saccharomyces cerevisiae. We demonstrated that there was no significant change in conjugation frequency when plasmid size increased from 56.5 to 138.6 kbp in length. Finally, we established an efficient PCR-based synthesis protocol to generate custom conjugative plasmids.

Resistance Levels and Epidemiology of Non-Fermenting Gram-Negative Bacteria in Urinary Tract Infections of Inpatients and Outpatients (RENFUTI): A 10-Year Epidemiological Snapshot

Background: Urinary tract infections (UTIs) are one of the most common infections in the human medicine, both among outpatients and inpatients. There is an increasing appreciation for the pathogenic role of non-fermenting Gram-negative bacteria (NFGNBs) in UTIs, particularly in the presence of underlying illnesses. Methods: The study was carried out using data regarding a 10-year period (2008-2017). The antimicrobial susceptibility testing was performed using the disk diffusion method, E-tests, and broth microdilution. Results: NFGNB represented 3.46% ± 0.93% for the outpatients, while 6.43% ± 0.81% of all positive urine samples for the inpatients (p < 0.001). In both groups, Pseudomonas spp. (78.7% compared to 85.1%) and Acinetobacter spp. (19.6% compared to 10.9%), were the most prevalent. The Acinetobacter resistance levels were significantly higher in inpatients isolates (p values ranging between 0.046 and <0.001), while the differences in the resistance levels of Pseudomonas was not as pronounced. The β-lactam-resistance levels were between 15-25% and 12-28% for the Acinetobacter and Pseudomonas spp., respectively. 4.71% of Acinetobacter and 1.67% of Pseudomonas were extensively drug resistant (XDR); no colistin-resistant isolates were recovered. Conclusions: Increasing resistance levels of the Acinetobacter spp. from 2013 onward, but not in the case of the Pseudomonas spp. Although rare, the drug resistant NFGNB in UTIs present a concerning therapeutic challenge to clinicians with few therapeutic options left.