Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract

Exploring staphylococcus in urinary tract infections: A systematic review and meta-analysis on the epidemiology, antibiotic resistance and biofilm formation

This study aimed to determine the epidemiology, biofilm formation and antibiotic resistance of staphylococci collected worldwide in the context of UTIs. This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Forty studies from 23 countries were selected for quantitative review. Electronic databases (PubMed, Scopus, Google Scholar, and Web of Sciences) were searched for articles published between 2010 and 2024 on the epidemiology, biofilm formation, and antibiotic resistance of uropathogenic staphylococci. Strict inclusion and exclusion standards were applied during the review of the articles. Forty articles were included in this systematic review. The prevalence of uropathogenic staphylococci varies from country to country, with the pooled prevalence of S. aureus and coagulase-negative staphylococci (CoNS) being 8.71 % (95 %CI: 6.145-11.69) and 13.17 % (95 %CI: 8.08-19.27) respectively. Among CoNS isolates, S. epidermidis was the most common with 19.3 % (95 %CI: 5.88-38.05). The prevalence of methicillin-resistant S. aureus isolates increased significantly from 23 % in 2010-2015 to 47 % in 2021-2024 (p = 0.03). S. haemolyticus is the most antibiotic-resistant species in CoNS, with 45 % of isolates resistant to methicillin, 33 % to gentamicin, and 29 % to tetracycline. Eighty-eight S. aureus strains were biofilm producers, including 35 % moderate biofilm producers and 48 % strong biofilm producers. The combined frequencies of icaA, clfA and fnbpA were 100, 99, and 89 %, respectively. The development of antibiotic resistance and biofilm formation by staphylococci involved in UTIs explains the need for periodic regional surveillance of these infections, which poses a serious public health problem.

Characteristics and outcomes of urinary tract infections caused by Enterococci: A multicenter retrospective study from two tertiary hospitals in Saudi Arabia

Enterococci are Gram-positive coccus bacteria that are normally present in the gastrointestinal tract and ordinarily function commensally with humans. Very few studies have investigated the characteristics of enterococcal infections. We aimed to characterize patients with urinary tract infections (UTIs) due to Enterococci and their outcomes. This was a retrospective cohort study between June 2012-November 2022. Patients who had clinically and microbiologically confirmed Enterococcal UTI based on a urine culture positive for E. faecalis or E. faecium with a count of ≥105 CFU/mL and having urinary tract symptoms were included. A total of 396 patients were eligible and included. The patients had a median age of 61 years and were mostly females (56.8 %). The most common characteristics were hospitalization in a non-ICU ward, having a urinary catheter, and recent use of antibiotics within the last 3 months (66.4 %, 59.3 %, and 51.8 %, respectively). Infection with E. faecalis was more common than E. faecium (77.3 % vs. 22.7 %). However, the latter exhibited higher rates of antibiotic resistance (P < 0.001 to several antibiotics) and was associated with significantly higher median C-reactive protein level (26.7 vs. 13 mg/dL; P = 0.025), mortality (23 % vs. 10.1 %; P = 0.002), and median length of stay (25 vs. 11.5 days; P < 0.001). We found that most patients with enterococcal UTIs had a history of having a urinary catheter and recent antibiotic use and were mostly females and hospitalized in non-ICU wards. E. faecium-infected patients experienced more severe episodes and poorer outcomes compared to patients infected with E. faecalis; thus, would need more aggressive therapy.

Biological Activity Evaluation of Phenolic Isatin-3-Hydrazones Containing a Quaternary Ammonium Center of Various Structures

A series of new isatin-3-hydrazones bearing different ammonium fragments was synthesized by a simple and easy work-up reaction of Girard's reagents analogs with 1-(3,5-di-tert-butyl-4-hydroxybenzyl)isatin. All derivatives have been shown to have antioxidant properties. In terms of bactericidal activity against gram-positive bacteria, including methicillin-resistant strains of Staphylococcus aureus, the best compounds are 3a, 3e, and 3m, bearing octyl, acetal, and brucine ammonium centers, respectively. In addition, brucine and quinine derivatives 3l, and 3j exhibit platelet antiaggregation activity at the level of acetylsalicylic acid, and this series of isatin derivatives does not adversely affect the hemostasis system as a whole. Thus, all the obtained results can lay the groundwork for future pharmaceutical developments for the creation of effective antibacterial drugs with reduced systemic toxicity due to the presence of antioxidant properties.

Interference-resistant gold nanoparticle assay for detecting Enterococcus in fresh and marine waters

Enterococci are common indicators of fecal contamination and are used to assess the quality of fresh and marine water, sand, soil, and sediment. However, samples collected from these environments contain various cells and other factors that can interfere with the assays used to detect enterococci. We developed a novel assay for the sensitive and specific detection of enterococci that is resistant to interference from other cells and environmental factors. Our interference-resistant assay used 30-nm gold nanoparticles (AuNPs), streptavidin, and a biotinylated Enterococcus antibody. Enterococci inhibited the interaction between streptavidin and biotin and led to the disaggregation of AuNPs. The absence of enterococci led to the aggregation of AuNPs, and this difference was easily detected by spectrophotometry. This interference-resistant AuNP assay was able to detect whole cells of Enterococcus in the range of 10 to 107 CFU/mL within 3 h, had high specificity for enterococci, and was unaffected by the presence of other intestinal bacteria, such as Escherichia coli. Our examination of fresh and marine water samples demonstrated no interference from other cells or environmental factors. The interference-resistant AuNP assay described here has the potential to be used as a rapid, simple, and effective method for monitoring enterococci in diverse environmental samples.

From Awareness to Action: Pioneering Solutions for Women's UTI Challenges in the Era of Precision Medicine

This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.

Synergistic cross-kingdom host cell damage between Candida albicans and Enterococcus faecalis

The fungus Candida albicans and the Gram-positive bacterium Enterococcus faecalis share mucosal niches in the human body. As opportunistic pathogens, both are found to expand population size during dysbiosis, and can cause severe systemic infections in susceptible individuals. Here, we show that the presence of C. albicans results in increased host cell damage by E. faecalis . Furthermore, E. faecalis aggravates oropharyngeal candidiasis in mice. Increased damage is mediated by enterococcal cytolysin, and involves both physical interaction and altered glucose availability. Physical interaction promotes accumulation of bacteria on host cells, facilitating contact of cytolysin with host cells. Glucose depletion by the metabolic activity of the fungus sensitized host cells to cytolysin. This work illustrates how a complex interplay between fungi and bacteria can result in detrimental consequences for the host.

Urinary tract infections and risk of preterm birth: a systematic review and meta-analysis

This systematic review and meta-analysis assessed the association between urinary tract infections (UTIs) during pregnancy and the risk of preterm birth (PTB). We searched multiple databases for relevant observational studies, categorizing them as UTI-based (comparing PTB incidence in women with and without UTIs) or PTB-based (comparing UTI prevalence in women with and without PTB). Using a random-effects model in Stata software version 17.0, we estimated pooled and adjusted odds ratios (ORs) with 95% confidence intervals (CIs), and performed subgroup, sensitivity, and cumulative analyses to explore heterogeneity. In total, 30 studies comprising 32 datasets were included, involving a total of 249,810 cases and 2,626,985 healthy controls. The meta-analysis revealed a significant positive association between UTIs during pregnancy and PTB occurrence (OR, 1.92; 95% CI, 1.62-2.27). A sub-group analysis based on studies, the participants showed significant association in both PTB-based (OR, 2.01; 95% CI, 1.58-2.56) and UTI-based studies (OR, 1.79; 95% CI, 1.42-2.26). However, Egger's test indicated the presence of publication bias (p=0.020), and substantial heterogeneity was observed across the included studies (I2=96.6; p< 0.001). These findings emphasize the critical importance of early detection and effective management of UTIs in pregnant women to reduce the risk of PTB and its associated adverse outcomes. While the results highlight a robust link between UTIs during pregnancy and PTB risk, the potential influence of publication bias and substantial heterogeneity should be considered to interpret these findings. Further research is needed to better understand the underlying mechanisms and to develop targeted interventions for high-risk pregnant women.

A Case of Sepsis in Which Escherichia coli and Fastidiosipila sanguinis Were Isolated and Identified From a Blood Culture

We isolated Fastidiosipila sanguinis for the first time in Asia, alongside Escherichia coli, from blood culture specimens in a case of complicated urinary tract infection with sepsis. In our case, F. sanguinis took 96 hours to form colonies under anaerobic culture and showed sensitivity to ceftriaxone, administered for the urinary tract infection. The pathogenicity and clinical significance of F. sanguinis, as well as its impact on the host when coinfected with other pathogens, require further analysis through the accumulation of cases.

Metabolic interplay between Proteus mirabilis and Enterococcus faecalis facilitates polymicrobial biofilm formation and invasive disease

Polymicrobial biofilms play an important role in the development and pathogenesis of CAUTI. Proteus mirabilis and Enterococcus faecalis are common CAUTI pathogens that persistently co-colonize the catheterized urinary tract and form biofilms with increased biomass and antibiotic resistance. In this study, we uncover the metabolic interplay that drives biofilm enhancement and examine the contribution to CAUTI severity. Through compositional and proteomic biofilm analyses, we determined that the increase in biofilm biomass stems from an increase in the protein fraction of the polymicrobial biofilm matrix. We further observed an enrichment in proteins associated with ornithine and arginine metabolism in polymicrobial biofilms compared to single-species biofilms. We show that L-ornithine secretion by E. faecalis promotes arginine biosynthesis in P. mirabilis, and that disruption of this metabolic interplay abrogates the biofilm enhancement we see in vitro and leads to significant decreases in infection severity and dissemination in a murine CAUTI model.

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome

Bacterial isolates from the human urinary microbiome have been extensively studied for their antibiotic resistance; however, little work has been done on those isolates that are difficult to grow in vitro. This study was designed to qualify a serum-based medium, New York City Broth III (NYCIII), and a broth microdilution method to determine the antibiotic susceptibility of previously underreported or undescribed microbes that have a difficult time growing in standard Mueller-Hinton broth. Here, we demonstrate that NYCIII microbroth dilution can be an effective method for the determination of antibiotic susceptibility of species found in the human urinary microbiome. We show that this method serves well to characterize fastidious and anaerobic urinary microbes that have no Clinical and Laboratory Standards Institute (CLSI) guidelines, including several in the families Aerococcaceae, Lactobacillaceae, or Actinomycetaceae. Previous studies using expanded quantitative urine culture reveal that urine samples from clinical patients are commonly polymicrobial in composition. Thus, we test whether NYCIII can serve as a viable harmonized medium, capable of supporting antibiotic susceptibility testing in a range of fastidious, non-fastidious, and anaerobic urinary microbes. We propose this methodology to be standardized comparable to CLSI standards to allow for resistance testing in uncharacterized urinary bacteria.

IMPORTANCE

Antibiotic susceptibilities of fastidious and anaerobic bacteria of the human urinary microbiome are largely underreported due to difficulty in growing them in the lab environment. The current standard medium, Muller-Hinton broth, has difficulty supporting the growth of many of these species, leaving microbiologists without a standardized method. To address this need, this study offers a methodology to survey susceptibilities in a high-throughput manner of these understudied microbes with a proposed harmonized medium, NYCIII, which is capable of supporting the growth of both fastidious and non-fastidious urinary microbes. Broader standardization of this method can allow for the development of antibiotic-resistant breakpoints of the many uncharacterized urinary microbes.

Adhesion of Klebsiella oxytoca to bladder or lung epithelial cells is promoted by the presence of other opportunistic pathogens

The intestinal and respiratory tracts of healthy individuals serve as habitats for a diverse array of microorganisms, among which Klebsiella oxytoca holds significance as a causative agent in numerous community- and hospital-acquired infections, often manifesting in polymicrobial contexts. In specific circumstances, K. oxytoca, alongside other constituents of the gut microbiota, undergoes translocation to distinct physiological niches. In these new environments, it engages in close interactions with other microbial community members. As this interaction may progress to co-infection where the virulence of involved pathogens may be promoted and enhance disease severity, we investigated how K. oxytoca affects the adhesion of commonly co-isolated bacteria and vice versa during co-incubation of different biotic and abiotic surfaces. Co-incubation was beneficial for the adhesion of at least one of the two co-cultured strains. K. oxytoca enhanced the adhesion of other enterobacteria strains to polystyrene and adhered more efficiently to bladder or lung epithelial cell lines in the presence of most enterobacteria strains and S. aureus. This effect was accompanied by bacterial coaggregation mediated by carbohydrate-protein interactions occurring between bacteria. These interactions occur only in sessile, but not planktonic populations, and depend on the features of the surface. The data are of particular importance for the risk assessment of the urinary and respiratory tract infections caused by K. oxytoca, including those device-associated. In this paper, we present the first report on K. oxytoca ability to acquire increased adhesive capacities on epithelial cells through interactions with common causal agents of urinary and respiratory tract infections.

Alterations in cell arrangements of group B streptococcus due to virulence factor expression can bias estimates of bacterial populations based on colony count measures

Group B streptococcus (GBS) is a chain-forming commensal bacterium and opportunistic pathogen that resides in the gastrointestinal and genitourinary tract of healthy adults. GBS can cause various infections and related complications in pregnant and nonpregnant women, adults, and newborns. Investigations of the mechanisms by which GBS causes disease pathogenesis often utilize colony count assays to estimate bacterial population size in experimental models. In other streptococci, such as group A streptococcus and pneumococcus, variation in the chain length of the bacteria that can occur naturally or due to mutation can affect facets of pathogenesis, such as adherence to or colonization of a host. No studies have reported a relationship between GBS chain length and pathogenicity. Here, we used GBS strain 874391 and several derivative strains displaying longer chain-forming phenotypes (874391pgapC, 874391ΔcovR, 874391Δstp1) to assess the impact of chain length on bacterial population estimates based on the colony-forming unit (c.f.u.) assay. Disruption of GBS chains via bead beating or sonication in conjunction with fluorescence microscopy was used to compare chaining phenotypes pre- and post-disruption to detect long- and short-chain forms, respectively. We used a murine model of GBS colonization of the female reproductive tract to assess whether chaining may affect bacterial colonization dynamics in the host during chronic infection in vivo. Overall, we found that GBS exhibiting long-chain form can significantly affect population size estimates based on the colony count assay. Additionally, we found that the length of chaining of GBS can affect virulence in the reproductive tract colonization model. Collectively, these findings have implications for studies of GBS that utilize colony count assays to measure GBS populations and establish that chain length can affect infection dynamics and disease pathogenesis for this important opportunistic pathogen.

Uncovering Surface Penetration by Enterococci From Urinary Tract Infection Patients

IMPORTANCE

The relationship between Enterococcus faecalis vaginal colonization and urinary tract infections (UTIs) remains uncertain.

OBJECTIVE

We aimed to evaluate the surface invasion capability of E faecalis isolates from patients with and without UTIs as a potential readout of pathogenicity.

STUDY DESIGN

Participants were females from urogynecology clinics, comprising symptomatic UTI and asymptomatic non-UTI patients, categorized by the presence or absence of E faecalis-positive cultures identified via standard urine culture techniques. Vaginal and urine samples from patients were plated on enterococci selective medium, and E faecalis isolates detected in both cohorts were species specific identified using 16S rRNA sequencing. Clinical isolates were inoculated on semisolid media, and both external colonies and underneath colony prints formed by agar-penetrating enterococci were imaged. External growth and invasiveness were quantified by determining colony-forming units of the noninvading and agar-penetrating cells and compared with the E faecalis OG1RF.

RESULTS

We selected E faecalis isolates from urine and vaginal samples of 4 patients with and 4 patients without UTIs. Assays demonstrated that most isolates formed similarly sized external colonies with comparable colony-forming unit. Surface invasion differed across patients and isolation sites compared with OG1RF. The vaginal isolate from UTI patient 1, who had the most recurrences, exhibited significantly greater agar-invading capacity compared with OG1RF.

CONCLUSIONS

Our pilot study indicates that ex vivo invasion assays may unveil virulence traits in E faecalis from UTI patients. Enhanced enterococcal surface penetration could increase urogenital invasion risk. Further research is needed to correlate penetration with disease severity in a larger patient group.

Multispecies bacterial invasion of human host cells

Urinary tract infection (UTI), one of the most common bacterial infections worldwide, is a typical example of an infection that is often polymicrobial in nature. While the overall infection course is known on a macroscale, bacterial behavior is not fully understood at the cellular level and bacterial pathophysiology during multispecies infection is not well characterized. Here, using clinically relevant bacteria, human epithelial bladder cells and human urine, we establish co-infection models combined with high resolution imaging to compare single- and multi-species bladder cell invasion events in three common uropathogens: uropathogenic Escherichia coli (UPEC), Klebsiella pneumoniae and Enterococcus faecalis. While all three species invaded the bladder cells, under flow conditions the Gram-positive E. faecalis was significantly less invasive compared to the Gram-negative UPEC and K. pneumoniae. When introduced simultaneously during an infection experiment, all three bacterial species sometimes invaded the same bladder cell, at differing frequencies suggesting complex interactions between bacterial species and bladder cells. Inside host cells, we observed encasement of E. faecalis colonies specifically by UPEC. During subsequent dispersal from the host cells, only the Gram-negative bacteria underwent infection-related filamentation (IRF). Taken together, our data suggest that bacterial multispecies invasions of single bladder cells are frequent and support earlier studies showing intraspecies cooperation on a biochemical level during UTI.

Novel Antimicrobial Approaches to Combat Bacterial Biofilms Associated with Urinary Tract Infections

Urinary tract infections (UTIs) are prevalent bacterial infections in both community and healthcare settings. They account for approximately 40% of all bacterial infections and require around 15% of all antibiotic prescriptions. Although antibiotics have traditionally been used to treat UTIs for several decades, the significant increase in antibiotic resistance in recent years has made many previously effective treatments ineffective. Biofilm on medical equipment in healthcare settings creates a reservoir of pathogens that can easily be transmitted to patients. Urinary catheter infections are frequently observed in hospitals and are caused by microbes that form a biofilm after a catheter is inserted into the bladder. Managing infections caused by biofilms is challenging due to the emergence of antibiotic resistance. Biofilms enable pathogens to evade the host's innate immune defences, resulting in long-term persistence. The incidence of sepsis caused by UTIs that have spread to the bloodstream is increasing, and drug-resistant infections may be even more prevalent. While the availability of upcoming tests to identify the bacterial cause of infection and its resistance spectrum is critical, it alone will not solve the problem; innovative treatment approaches are also needed. This review analyses the main characteristics of biofilm formation and drug resistance in recurrent uropathogen-induced UTIs. The importance of innovative and alternative therapies for combatting biofilm-caused UTI is emphasised.

Diagnostic and treatment patterns in urinary and genital tract infections: insights from a referral clinic in Beirut, Lebanon

BACKGROUND

Urinary Tract Infections (UTIs) and Genital Tract Infections (GTIs) are common yet serious health concerns. Precise diagnosis is crucial due to the potential severe consequences of misdiagnosis. This study aims to distinguish between UTIs and GTIs, highlighting the importance of accurate differentiation.

MATERIALS AND METHODS

The study encompassed 294 patients, categorized into 4 groups: Group GNI (no infection, N = 57), Group GUI (urinary infection, N = 52), Group GGI (genital infection, N = 139), and Group GGUI (both infections, N = 46). Methods included patient interviews, clinical examinations, and laboratory tests such as urine and vaginal swab cultures.

RESULTS

The investigation revealed no significant differences in age, BMI, residency, or nationality across groups. However, socioeconomic status varied, with Group GNI having the lowest proportion of low socioeconomic status. In obstetrical characteristics, non-pregnancy rates were higher in Groups GUI and GGUI, with GGUI showing a notably higher abortion rate. Symptom analysis indicated lower symptom prevalence in Group GNI, with pain, itching, pruritus, and vaginal discharge being less frequent, suggesting a link between infection presence and symptom severity. Treatment patterns showed higher usage of ciprofloxacin, antifungals, and vaginal tablets in Groups GUI and GGUI. Laboratory findings highlighted significant Leucocyte Esterase presence and variations in WBC and RBC counts, particularly in Group GGUI.

CONCLUSION

The study emphasizes the need for advanced diagnostic techniques, especially those focusing on individual microbial patterns, to enhance UGTI diagnosis. Variations in symptom presentation and treatment across groups underline the necessity for personalized diagnostic and treatment strategies.

Predominance of multidrug-resistant bacteria causing urinary tract infections among symptomatic patients in East Africa: a call for action

Background

In low- and middle-income countries, antibiotics are often prescribed for patients with symptoms of urinary tract infections (UTIs) without microbiological confirmation. Inappropriate antibiotic use can contribute to antimicrobial resistance (AMR) and the selection of MDR bacteria. Data on antibiotic susceptibility of cultured bacteria are important in drafting empirical treatment guidelines and monitoring resistance trends, which can prevent the spread of AMR. In East Africa, antibiotic susceptibility data are sparse. To fill the gap, this study reports common microorganisms and their susceptibility patterns isolated from patients with UTI-like symptoms in Kenya, Tanzania and Uganda. Within each country, patients were recruited from three sites that were sociodemographically distinct and representative of different populations.

Methods

UTI was defined by the presence of >104 cfu/mL of one or two uropathogens in mid-stream urine samples. Identification of microorganisms was done using biochemical methods. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion assay. MDR bacteria were defined as isolates resistant to at least one agent in three or more classes of antimicrobial agents.

Results

Microbiologically confirmed UTI was observed in 2653 (35.0%) of the 7583 patients studied. The predominant bacteria were Escherichia coli (37.0%), Staphylococcus spp. (26.3%), Klebsiella spp. (5.8%) and Enterococcus spp. (5.5%). E. coli contributed 982 of the isolates, with an MDR proportion of 52.2%. Staphylococcus spp. contributed 697 of the isolates, with an MDR rate of 60.3%. The overall proportion of MDR bacteria (n = 1153) was 50.9%.

Conclusions

MDR bacteria are common causes of UTI in patients attending healthcare centres in East African countries, which emphasizes the need for investment in laboratory culture capacity and diagnostic algorithms to improve accuracy of diagnosis that will lead to appropriate antibiotic use to prevent and control AMR.

Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections

IMPORTANCE

Although E. faecalis is a common wound pathogen, its pathogenic mechanisms during wound infection are unexplored. Here, combining a mouse wound infection model with in vivo transposon and RNA sequencing approaches, we identified the E. faecalis purine biosynthetic pathway and galactose/mannose MptABCD phosphotransferase system as essential for E. faecalis acute replication and persistence during wound infection, respectively. The essentiality of purine biosynthesis and the MptABCD PTS is driven by the consumption of purine metabolites by E. faecalis during acute replication and changing carbohydrate availability during the course of wound infection. Overall, our findings reveal the importance of the wound microenvironment in E. faecalis wound pathogenesis and how these metabolic pathways can be targeted to better control wound infections.

Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract

IMPORTANCE

Urinary tract infection (UTI) is a global health issue that imposes a substantial burden on healthcare systems. Women are disproportionately affected by UTI, with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis, a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may be involved in E. faecalis survival in the urinary tract.

Comparison Shows that Multiplex Polymerase Chain Reaction Identifies Infection-associated Urinary Biomarker-positive Urinary Tract Infections That Are Missed by Standard Urine Culture

Background

Multiplex polymerase chain reaction (M-PCR) has increased sensitivity for microbial detection compared with standard urine culture (SUC) in cases diagnosed as urinary tract infections (UTIs), leading to questions whether detected microbes are likely causative of UTIs or are incidental findings.

Objective

To compare infection-associated biomarker levels against M-PCR and SUC results in symptomatic cases with a presumptive diagnosis of a UTI by a urologist.

Design setting and participants

Participants were ≥60 yr old and presented to urology clinics between January and April 2023 with symptoms of UTIs (n = 583). Urine microbial detection was by M-PCR and SUC. Three infection-associated biomarkers (neutrophil gelatinase-associated lipocalin, interleukin-8, and interleukin-1β) were measured by enzyme-linked immunosorbent assay. Symptomatic cases with elevated biomarkers, detection of uropathogens, and a specialist clinical diagnosis of a UTI were considered definitive UTI cases.

Outcome measurements and statistical analysis

Distributions were compared using two-sample Wilcoxon rank sum test, with two-tailed p values of <0.05 considered statistically significant.

Results and limitations

In cases with M-PCR-positive/SUC-negative results (n = 80), all median biomarker levels were significantly higher (p < 0.0001) than in cases with M-PCR-negative/SUC-negative results (n = 107). Two or more biomarkers were positive in 76% of M-PCR-positive/SUC-negative specimens. Limitation was an inability to examine associations between each individual organism and inflammation.

Conclusions

A significant number of M-PCR-positive/SUC-negative cases had elevated levels of infection-related urinary biomarkers, especially when infection was caused by organisms other than Escherichia coli. This is a strong indication that microbes detected by M-PCR, which would be missed by SUC, are associated with UTIs.

Patient summary

We compared infection-associated biomarkers in patients diagnosed with urinary tract infections (UTIs) against the detection of microorganisms by standard urine culture (SUC) and multiplex polymerase chain reaction (M-PCR). We found that most patients with microorganisms detected by M-PCR, which were missed by SUC, had elevated markers of inflammation, indicating that these organisms were likely causative of UTIs.

Characteristics and susceptibility pattern of catheter-associated urinary tract infections (CAUTI) bacteria in Indonesia: A study in a national reference hospital of Sumatra region 2020-2021

Catheter-associated urinary tract infection (CAUTI) is defined as a urinary tract infection associated with catheter placement for more than two consecutive days. Hence, antibiotic resistance in the context of CAUTIs represents a substantial challenge. The aim of this study was to present the characteristics of patients with CAUTI and the susceptibility pattern of CAUTI bacteria in the national reference hospital of the Sumatra region of Indonesia. A cross-sectional study was conducted at H. Adam Malik General Hospital, Medan, Indonesia, from 2020 to 2021, using a total sampling. All CAUTI patients included were on catheterization and diagnosed based on the Centers for Disease Control and Prevention (CDC) guidelines. The patient's urine culture and antibiotic susceptibility test were carried out on the patient's admitted urine sample for further assessment. Identification of bacteria, antibiotic susceptibility test, and the extended-spectrum beta-lactamase (ESBL) test for Escherichia coli and Klebsiella pneumoniae were conducted using the VITEK-2 Compact. A total of 74 CAUTI patients were included in the study, 59.5% were female, 54.1% were 46-65 years old, and a third had cardiovascular disease comorbidities (33.8%). A total of 83 CAUTI-associated bacteria were isolated. The majority were Gram-negative bacteria (74.7%), and the most bacteria isolated was E. coli (31.3%), followed by K. pneumoniae, Enterococcus faecalis, Acinetobacter baumannii, and Enterococcus faecium. The ESBL test was positive mostly in K. pneumoniae (100%) and E. coli (76.9%). CAUTI-associated E. coli was susceptible to tigecycline, meropenem, ertapenem, nitrofurantoin, and gentamicin. The isolated K. pneumoniae was susceptible to tigecycline, meropenem, ertapenem, and amikacin. While E. faecalis showed susceptibility to tigecycline, nitrofurantoin, vancomycin, imipenem, linezolid, ampicillin, piperacillin/tazobactam, amoxicillin/clavulanic acid, ampicillin/sulbactam, and piperacillin.

High frequency of Enterococcus faecalis detected in urinary tract infections in male outpatients - a retrospective, multicenter analysis, Germany 2015 to 2020

BACKGROUND

Urinary tract infections (UTI) in men differ relevantly to women by their pathogens. Gram-positive uropathogens play a relevant role in UTI in men. In this study, we aimed to analyze the epidemiology of Enterococcus faecalis in UTI in male outpatients.

METHODS

We conducted a retrospective observational multicenter study during 2015 to 2020 consisting of urine samples of 99,415 adult male outpatients sent from 6,749 outpatient practices from Germany. Proportions were compared using the z-Test and 95% confidence intervals were calculated using the Clopper-Pearson method.

RESULTS

E. faecalis is the 2nd most frequent bacteria (16%) detected in suspected UTI in male outpatients. Young men are predominantly at risk (17%) for isolation of E. faecalis in suspected UTI. In polymicrobial infections E. faecalis is isolated in 47% of all suspected UTI in men. Recurrency of suspected UTI is significantly more frequent when E. faecalis is isolated compared to Escherichia coli (22% vs 26%; p < .001). Recurrency rates of E. faecalis associated UTI increases by age from 12% (18-29 years) to 28% ([Formula: see text] 70 years); p < .001. Congruently the resistance of E. faecalis against ciprofloxacin increases by age from 22% (18-29 years; 2019) to 37% ([Formula: see text] 70 years; 2019); p < .001.

CONCLUSIONS

E. faecalis is frequently isolated in suspected UTI in male patients. Consequently, Nitrate-sticks results cannot be recommended to exclude UTI in men. The empirical use of ciprofloxacin in young adults can be reasonable. Frequent recurrences in E. faecalis associated suspected UTI emphasizes the importance of microbiological pathogen identification and susceptibility testing in men suffering from UTI.

Antimicrobial susceptibility and clinical characteristics of multidrug-resistant polymicrobial infections in Pakistan, a retrospective study 2019-2021

Background: We determined the prevalence of antimicrobial resistance (AMR) in polymicrobial pathogens in Pakistan. Methods: A total of 70,518 clinical samples were collected aseptically and confirmation of isolates and antibiogram were performed by the VITEK 2 system. Results: Of 70,518 samples, 441 (0.62%) were polymicrobial samples, with 882 (1.2%) polymicrobial pathogens with 689 (78.1%) Gram-negative rods (GNRs), 166 (18.8%) Gram-positive cocci and 27 (3.1%) Candida albicans. Among GNRs, 28.8% were Escherichia coli and 25.9% were Klebsiella pneumoniae. Majority, 15.1% of Pseudomonas aeruginosa and K. pneumoniae were found in combination. 30.1% of isolates were ESBL producers, 9.7% carbapenem-resistant organisms, 35.5% MRSA and 6.0% VRE. 100% of E. coli were resistant to ampicillin and 98% of K. pneumoniae were resistant to piperacillin. Conclusion: A high prevalence of AMR in polymicrobial pathogens was observed.

A test combining multiplex-PCR with pooled antibiotic susceptibility testing has high correlation with expanded urine culture for detection of live bacteria in urine samples of suspected UTI patients

We evaluated whether multiplex polymerase chain reaction (M-PCR) detects viable micro-organisms by comparing micro-organism identification with standard urine culture (SUC) and expanded quantitative urine culture (EQUC). Of the 395 organisms detected by M-PCR, EQUC detected 89.1% (p = 0.10), whereas SUC detected 27.3% (p < 0.0001 vs. M-PCR and p < 0.0001 vs EQUC). M-PCR identified 260 nonfastidious bacteria, EQUC detected 96.5% (p = 0.68), whereas SUC detected 41.5% (p < 0.0001). Common nonfastidious bacteria missed by SUC included Escherichia coli (72.5% detected), Klebsiella pneumoniae (66.7% detected), Enterococcus faecalis (34.6% detected) and Enterococcus faecium (0% detected). M-PCR identified 135 fastidious bacteria and EQUC 101 (74.8%, p = 0.01), whereas SUC failed to detect any (0%, p < 0.0001). Clinical samples evaluated using EQUC and M-PCR yielded very similar findings, indicating that most microbes identified by M-PCR represented viable organisms, and validating M-PCR as a diagnostic tool for UTIs.

Analysis of Cumulative Antibiogram Reports in Search for Optimal Empirical Urinary Tract Infection Treatment at the Central Teaching Hospital of the Medical University of Lodz, Poland: Results of a 3-Year Surveillance

Urinary tract infections are among the most common bacterial infections, accounting for about two-fifths of all healthcare-associated infections. Appropriate antimicrobial therapy is crucial, e.g., to avoid prolonged hospitalization and limit antimicrobial resistance spread. This study was performed to analyze the microbiological profiles of urinary tract infections in the Central Teaching Hospital in Lodz, Poland, and develop local empirical therapy guidelines. This study was a 3-year retrospective surveillance of the cumulative antibiograms from urine cultures. The procedures were based on the current EUCAST and CLSI guidelines. In 2020-2022, a total of 4656 urine cultures were performed, of which 1134 were positive. The most common bacterial isolates were Escherichia coli, followed by Klebsiella spp. and Enterococcus spp. High levels of susceptibility (>90%) have been observed for carbapenems, piperacillin/tazobactam, amikacin, and nitrofurantoin. Development of the appropriate empirical antimicrobial is a challenging task with persistently high levels of resistance to commonly used antimicrobials. Eventually, we separated the uncomplicated and complicated urinary tract infections in local guidelines and recommended nitrofurantoin and amikacin, respectively, in empiric therapy. The clinicians should make a decision based on the presented symptoms and then-with the urine culture result-correct or continue the therapy.

Improving Patient Outcomes While Reducing Empirical Treatment with Multiplex-Polymerase-Chain-Reaction/Pooled-Antibiotic-Susceptibility-Testing Assay for Complicated and Recurrent Urinary Tract Infections

This study compared rates of empirical-therapy use and negative patient outcomes between complicated and recurrent urinary tract infection (r/cUTI) cases diagnosed with a multiplex polymerase chain reaction or pooled antibiotic susceptibility testing (M-PCR/P-AST) vs. standard urine culture (SUC). Subjects were 577 symptomatic adults (n = 207 males and n = 370 females) presenting to urology/urogynecology clinics between 03/30/2022 and 05/24/2023. Treatment and outcomes were recorded by the clinician and patient surveys. The M-PCR/P-AST (n = 252) and SUC (n = 146) arms were compared after patient matching for confounding factors. The chi-square and Fisher's exact tests were used to analyze demographics and clinical outcomes between study arms. Reduced empirical-treatment use (28.7% vs. 66.7%), lower composite negative events (34.5% vs. 46.6%, p = 0.018), and fewer individual negative outcomes of UTI-related medical provider visits and UTI-related visits for hospitalization/an urgent care center/an emergency room (p < 0.05) were observed in the M-PCR/P-AST arm compared with the SUC arm. A reduction in UTI symptom recurrence in patients ≥ 60 years old was observed in the M-PCR/P-AST arm (p < 0.05). Study results indicate that use of the M-PCR/P-AST test reduces empirical antibiotic treatment and negative patient outcomes in r/cUTI cases.

The Essential Role of PCR and PCR Panel Size in Comparison with Urine Culture in Identification of Polymicrobial and Fastidious Organisms in Patients with Complicated Urinary Tract Infections

Complicated urinary tract infections (cUTIs) are difficult to treat, consume substantial resources, and cause increased patient morbidity. Data suggest that cUTI may be caused by polymicrobial and fastidious organisms (PMOs and FOs, respectively); as such, urine culture (UC) may be an unreliable diagnostic tool for detecting cUTIs. We sought to determine the utility of PCR testing for patients presumed to have a cUTI and determine the impact of PCR panel size on organism detection. We reviewed 36,586 specimens from patients with presumptive cUTIs who received both UC and PCR testing. Overall positivity rate for PCR and UC was 52.3% and 33.9%, respectively (p < 0.01). PCR detected more PMO and FO than UC (PMO: 46.2% vs. 3.6%; FO: 31.3% vs. 0.7%, respectively, both p < 0.01). Line-item concordance showed that PCR detected 90.2% of organisms identified by UC whereas UC discovered 31.9% of organisms detected by PCR (p < 0.01). Organism detection increased with expansion in PCR panel size from 5-25 organisms (p < 0.01). Our data show that overall positivity rate and the detection of individual organisms, PMO and FO are significantly with PCR testing and that these advantages are ideally realized with a PCR panel size of 25 or greater.

Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris

Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).

Elevated UTI Biomarkers in Symptomatic Patients with Urine Microbial Densities of 10,000 CFU/mL Indicate a Lower Threshold for Diagnosing UTIs

The literature lacks consensus on the minimum microbial density required for diagnosing urinary tract infections (UTIs). This study categorized the microbial densities of urine specimens from symptomatic UTI patients aged ≥ 60 years and correlated them with detected levels of the immune response biomarkers neutrophil gelatinase-associated lipocalin (NGAL), interleukin-8 (IL-8), and interleukin-1-beta (IL-1β). The objective was to identify the microbial densities associated with significant elevation of these biomarkers in order to determine an optimal threshold for diagnosing symptomatic UTIs. Biobanked midstream voided urine samples were analyzed for microbial identification and quantification using standard urine culture (SUC) and multiplex-polymerase chain reaction (M-PCR) testing, while NGAL, IL-8, and IL-1β levels were measured via enzyme-linked immunosorbent assay (ELISA). NGAL, IL-8, and IL-1β levels were all significantly elevated at microbial densities ≥ 10,000 cells/mL when measured via M-PCR (p < 0.0069) or equivalent colony-forming units (CFUs)/mL via SUC (p < 0.0104) compared to samples with no detectable microbes. With both PCR and SUC, a consensus of two or more elevated biomarkers correlated well with microbial densities > 10,000 cells/mL or CFU/mL, respectively. The association between ≥10,000 cells and CFU per mL with elevated biomarkers in symptomatic patients suggests that this lower threshold may be more suitable than 100,000 CFU/mL for diagnosing UTIs.

Identification of bacteria in mixed infection from urinary tract of patient's samples using Raman analysis of dried droplets

Urinary tract infections (UTI) are among the most frequent nosocomial infections. A fast identification of the pathogen and assignment of Gram type could help to prescribe most suitable treatments. Raman spectroscopy holds high potential for fast and reliable bacterial pathogens identification. While most studies so far have focused on individual pathogens or artificial mixtures, this contribution aims to translate the analysis to primary urine samples from patients with suspected UTIs. For this, we have included 59 primary urine samples out of which 29 were diagnosed as mixed infections. For Raman analysis, we first trained two classification models based on principal component analysis - linear discriminant analysis (PCA-LDA) with more than 3500 Raman spectra of 85 clinical isolates from 23 species in order to (1) identify the Gram type of the bacteria and (2) assign family membership to one of the six most abundant bacterial families in urinary tract infections (Enterobacteriaceae, Morganellaceae, Pseudomonadaceae, Enterococcaceae, Staphylococcaceae and Streptococcaceae). The classification models were applied to artificial mixtures of Gram positive and Gram negative bacteria to correctly predict mixed infections with an accuracy of 75%. Raman scans of dried droplets did not yet yield optimal classification results on family level. When translating the method to primary urine samples, we observed a strong bias towards Gram negative bacteria, on family level towards Morganellaceae, which reduced prediction accuracy. Spectral differences were observed between isolates grown on standard growth medium and bacteria of the same strain when characterized directly from the patient. Thus, improvement of the classification accuracy is expected with a larger data base containing also bacteria measured directly from the urine sample.

Quantitative multiplex polymerase chain reaction in copies ml-1 linearly correlates with standard urine culture in colonies ml-1 for urinary tract infection (UTI) pathogens

Standard urine culture (SUC) is the current standard method for confirmation of a urinary tract infection (UTI). SUC identifies microorganisms in urine samples and semi-quantifies these as colony-forming units (CFUs) ml-1. In contrast, quantitative multiplex polymerase chain reaction (q-MPCR) is a culture-independent assay in which the microbes are quantified by targeting genomic sequences and reported as cells ml-1, calculated from copies ml-1. Using serial dilutions within the 104-105 cells ml-1 range, the usual reporting range of SUC, this study compared the quantification results based on SUC and q-MPCR for four uropathogens with the control hemocytometer counts. The results revealed a linear relationship and a 1:1 correlation between the q-MPCR and SUC results. Additional q-MPCR quantification of 36 uropathogenic non-fastidious and fastidious bacteria and yeast indicated a reproducible linear correlation in a 1:1 manner with the control counts over a range of cell densities (103-106 cells ml-1). The results confirm that the quantifications by q-MPCR in cells ml-1 and by SUC in CFUs ml-1 are comparable and answer to the lingering question of how the results of these two methods correlate. Moreover, q-MPCR provided accurate quantification of various microorganisms over wider cell density ranges without the time required for microbial growth.

Enhancing bacteriophage therapeutics through in situ production and release of heterologous antimicrobial effectors

Bacteriophages operate via pathogen-specific mechanisms of action distinct from conventional, broad-spectrum antibiotics and are emerging as promising alternative antimicrobials. However, phage-mediated killing is often limited by bacterial resistance development. Here, we engineer phages for target-specific effector gene delivery and host-dependent production of colicin-like bacteriocins and cell wall hydrolases. Using urinary tract infection (UTI) as a model, we show how heterologous effector phage therapeutics (HEPTs) suppress resistance and improve uropathogen killing by dual phage- and effector-mediated targeting. Moreover, we designed HEPTs to control polymicrobial uropathogen communities through production of effectors with cross-genus activity. Using phage-based companion diagnostics, we identified potential HEPT responder patients and treated their urine ex vivo. Compared to wildtype phage, a colicin E7-producing HEPT demonstrated superior control of patient E. coli bacteriuria. Arming phages with heterologous effectors paves the way for successful UTI treatment and represents a versatile tool to enhance and adapt phage-based precision antimicrobials.

Emergence of microbial infections in some hospitals of Cairo, Egypt: studying their corresponding antimicrobial resistance profiles

BACKGROUND

Antimicrobial resistance is one of the ten major public health threats facing humanity, especially in developing countries. Identification of the pathogens responsible for different microbial infections and antimicrobial resistance patterns are important to help clinicians to choose the correct empirical drugs and provide optimal patient care.

METHODS

During the period from November 2020 to January 2021, one hundred microbial isolates were collected randomly from different specimens from some hospitals in Cairo, Egypt. Sputum and chest specimens were from COVID-19 patients. Antimicrobial susceptibility testing was performed according to CLSI guidelines.

RESULTS

Most microbial infections were more common in males and in elderly people over 45 years of age. They were caused by Gram-negative, Gram-positive bacteria, and yeast isolates that represented 69%, 15%, and 16%, respectively. Uropathogenic Escherichia coli (35%) were the most prevalent microbial isolates and showed high resistance rates towards penicillin, ampicillin, and cefixime, followed by Klebsiella spp. (13%) and Candida spp. (16%). Of all microbial isolates, Acinetobacter spp., Serratia spp., Hafnia alvei, and Klebsiella ozaenae were extremely multidrug-resistant (MDR) and have resisted all antibiotic classes used, except for glycylcycline, in varying degrees. Acinetobacter spp., Serratia spp., and Candida spp. were secondary microbial infections in COVID-19 patients, while H. alvei was a bloodstream infection isolate and K. ozaenae was recorded in most infections. Moreover, about half of Staphylococcus aureus strains were MRSA isolates and reported low rates of resistance to glycylcycline and linezolid. In comparison, Candida spp. showed high resistance rates between 77 and 100% to azole drugs and terbinafine, while no resistance rate towards nystatin was reported. Indeed, glycylcycline, linezolid, and nystatin were considered the drugs of choice for the treatment of MDR infections.

CONCLUSION

The prevalence of antimicrobial resistance in some Egyptian hospitals was high among Gram-negative, Gram-positive bacteria, and candida spp. The high resistance pattern -especially in secondary microbial infections in COVID-19 patients- to most antibiotics used is a matter of great concern, portends an inevitable catastrophe, and requires continuous monitoring to avoid the evolution of new generations.

Functional and genetic adaptations contributing to Enterococcus faecalis persistence in the female urinary tract

Enterococcus faecalis is the leading Gram-positive bacterial species implicated in urinary tract infection (UTI). An opportunistic pathogen, E. faecalis is a commensal of the human gastrointestinal tract (GIT) and its presence in the GIT is a predisposing factor for UTI. The mechanisms by which E. faecalis colonizes and survives in the urinary tract (UT) are poorly understood, especially in uncomplicated or recurrent UTI. The UT is distinct from the GIT and is characterized by a sparse nutrient landscape and unique environmental stressors. In this study, we isolated and sequenced a collection of 37 clinical E. faecalis strains from the urine of primarily postmenopausal women. We generated 33 closed genome assemblies and four highly contiguous draft assemblies and conducted a comparative genomics to identify genetic features enriched in urinary E. faecalis with respect to E. faecalis isolated from the human GIT and blood. Phylogenetic analysis revealed high diversity among urinary strains and a closer relatedness between urine and gut isolates than blood isolates. Plasmid replicon (rep) typing further underscored possible UT-GIT interconnection identifying nine shared rep types between urine and gut E. faecalis . Both genotypic and phenotypic analysis of antimicrobial resistance among urinary E. faecalis revealed infrequent resistance to front-line UTI antibiotics nitrofurantoin and fluoroquinolones and no vancomycin resistance. Finally, we identified 19 candidate genes enriched among urinary strains that may play a role in adaptation to the UT. These genes are involved in the core processes of sugar transport, cobalamin import, glucose metabolism, and post-transcriptional regulation of gene expression.

IMPORTANCE

Urinary tract infection (UTI) is a global health issue that imposes substantial burden on healthcare systems. Women are disproportionately affected by UTI with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis , a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may mediate urinary E. faecalis adaptation to the female urinary tract.

Differences in Virulence Factors and Antimicrobial Susceptibility of Uropathogenic Enterococcus spp. Strains in a Rural Area of Uganda and a Spanish Secondary Hospital

Enterococcus faecalis and Enterococcus faecium have become two of the most important agents of nosocomial diseases due to their constantly growing resistance. Enterococcal infections are associated with biofilms, which are intrinsically sensitive to antimicrobials. The main goal of this study was to compare and relate their capacity to form biofilm and their antimicrobial sensitivity, as well as their virulence factors and their implicated genes, of strains isolated from patients with urinary tract infection (UTI) in a rural hospital in Uganda and a secondary hospital in Spain. A prospective study was conducted with 104 strains of E. faecalis and E. faecium isolated from patients with suspected UTI and who presented leukocyturia at the Saint Joseph Kitgum hospital (Uganda) and at the Hospital Universitario Principe de Asturias (Spain). All microorganisms were identified in Spain by MALDI-TOF mass spectrometry. Antimicrobial susceptibility studies were carried out using the Vitek^® 2 system (Biomériux, France). The biofilm formation capacity was studied by photospectrometry. Phenotypic and genotypic virulence factors were studied in all cases by PCR or expression techniques. In Uganda, we found a higher incidence of E. faecium (65.3%, n = 32), contrary to the situation found in Spain where most of the bacteria found belonged to E. faecalis (92.7%, n = 51). All E. faecalis strains were found to have very low levels of resistance to ampicillin, imipenem, and nitrofurantoin. However, E. faecium exhibited more than 25% resistance to these antibiotics. Although the esp gene has been shown in the results obtained to be an important initial agent in biofilm formation, we have also demonstrated in this study the intervention of other genes when esp is not present, such as the ace1 gene. No statistically significant relationships were found between the presence of agg and gelE genes and increased biofilm formation. The significant difference between the incidence of E. faecalis and E. faecium and biofilm formation, between samples from Spain and Uganda, shows us very different profiles between countries.

Antibiotic Resistance Profiling of Pathogenic Staphylococcus Species from Urinary Tract Infection Patients in Benin

Staphylococci can cause urinary tract infections (UTIs). These UTIs are among the significant causes of antibiotic resistance and the spread of antibiotic-resistant diseases. The current study is aimed at establishing a resistance profile and determining the pathogenicity of Staphylococcus strains isolated from UTI samples collected in Benin. For this purpose, urine samples (one hundred and seventy) that were collected from clinics and hospitals showed UTI in patients admitted/visited in Benin. The biochemical assay method was used to identify Staphylococcus spp., and the disk diffusion method tested the antimicrobial susceptibility. The biofilm formation ability of the isolates of Staphylococcus spp. was investigated by the colorimetric method. The presence of mecA, edinB, edinC, cna, bbp, and ebp genes was examined by multiplex polymerase chain reaction (PCR). The results showed that Staphylococcus species were identified in 15.29% of all infected individuals and that 58% of these strains formed biofilms. Most Staphylococcus strains (80.76%) were isolated in female samples, and the age group below 30 years appeared to be the most affected, with a rate of 50%. All Staphylococcus strains isolated were 100% resistant to penicillin and oxacillin. The lowest resistance rates were seen with ciprofloxacin (30.8%), gentamicin, and amikacin (26.90%). Amikacin was the best antibiotic against Staphylococcus strains isolated from UTIs. The isolates carried mecA (42.31%), bbp (19.23%), and ebp (26.92%) genes in varying proportions. This study provides new information on the risks posed to the population by the overuse of antibiotics. In addition, it will play an essential role in restoring people's public health and controlling the spread of antibiotic resistance in urinary tract infections in Benin.

Profiling of antibiotic resistance among uropathogens isolated from patients attending Kericho County Referral Hospital

Introduction

urinary tract infection (UTI) comes second after respiratory infections in most communities and hospital settings, affecting people of all ages. Frequent use of antibiotics to manage UTI has resulted in development of resistance, calling upon policymakers to fast-track and enforce policies that guide the use of antibiotics in the country. This study intended to determine the current antibiotic resistance to uropathogens among patients attending Kericho County Referral Hospital.

Methods

three hundred urine samples from eligible participants were cultured and bacteria colonies identified using biochemical tests. Antibiotic sensitivity was done using Kirby Bauer disk diffusion method on Mueller Hinton Agar. Results: the aetiological agents of UTI were Staphylococcus aureus, Enterococci faecalis, E. coli, Proteus spp and Klebsiella pneumonia. Antibiotic resistance was observed among these uropathogens to commonly used antibiotics namely; ampicillin (84.3%), azithromycin (71.9%) and augmentin (69.8%). However, there were some bacteria that were susceptible to all or some commonly used antibiotics. There was moderate resistance to norfloxacin (43%) except in Staphylococcus aureus which showed 64% resistance. The isolates showed less resistance to cefoxitine (13.2%), gentamycin (11.6%) and ciprofloxacin (10%). While most bacteria showed multiple resistance to 3 drugs, some showed resistance to at most 5 drugs tested in the study. Conclusion: this study found Staphylococcus aureus to be the predominant aetiological agent of UTI. Cefoxitine, gentamycin and ciprofloxacin are good therapeutic choices for confirmed recurrent UTI when culture results are unavailable. There is need to have regular screening of aetiological agents of UTI and their resistance to antimicrobials.

Multidrug Resistance Urinary Tract Infection in Chronic Kidney Disease Patients: An Observational Study

OBJECTIVE

To determine the presence of multidrug-resistant (MDR) urinary tract infections (UTI) and the MDR pattern of the bacterial isolates causing MDR UTI in chronic kidney disease (CKD) patients.

METHODS

This cross-sectional study was conducted among 326 diagnosed CKD patients in the Department of Nephrology at Bangabandhu Sheikh Mujib Medical University (BSMMU). Purposive sampling technique was used, and data were collected from the respondents using a semi-structured questionnaire. From duly collected urine samples, identification of organisms and antibiotic susceptibility tests were done, maintaining proper procedure in the microbiology laboratory.

RESULTS

The study population was predominantly female (60.1%). The outpatient department provided the majority of the respondents (75.2%). A history of UTI within the last six months was present among 74.2% of the respondents, and 59.2% had a history of taking antibiotics. Bacterial isolates were predominantly gram-negative (79.4%). Escherichia coli was the most prevalent bacterial isolate, present in 55.5% of the study population. Among the respondents, 64.7% were found to have MDR UTI, and among them, 81.5% were gram-negative, and 18.5% were gram-positive isolates. Among all the antibiotics tested, Colistin Sulphate, Polymyxin B, Cefoxitin, Vancomycin, and Linezolid had the highest (100%) sensitivity, followed by Meropenem, with 94.9% sensitivity. Among the gram-negative isolates, Acinetobacter and Enterobacter were most resistant to aminoglycoside, at 70% and 91.7%, respectively. E. coli, Klebsiella, Proteus, and Pseudomonas were most resistant to quinolone at 76.8%, 76.9%, 83.3%, and 66.7%, respectively. Among the gram-positive isolates, Enterococci and Staphylococcus aureus were most resistant to aminoglycoside, 81.5% and 88.9%, respectively. Streptococcus was found to be most resistant to cephalosporin (75.0%). There was a statistically significant (p < 0.05) relationship between MDR UTI, history of UTI, and previous antibiotic intake, and diabetic CKD.

CONCLUSIONS

The prevalence of MDR UTI among CKD patients is considerably high. When treating UTI, choosing an appropriate antibiotic by urine culture and implementing a guideline on the rational use of antibiotics are essential to managing and preventing the development of MDR UTI.

Is it meaningful to apply midstream urine culture to urine specimens with negative Gram stain results?

INTRODUCTION

Gram staining is a convenient method for bacterial estimation. Urine culture is typically used to diagnose urinary tract infections. Therefore, urine culture is also performed on Gram stain-negative urine specimens. However, the frequency of uropathogen identification in these samples remains unclear.

METHODS

From 2016 to 2019, we retrospectively compared the results of Gram staining and urine culture tests on midstream urine specimens submitted for the diagnosis of urinary tract infections to confirm the significance of urine culture on Gram stain-negative specimens. Analysis was performed according to the patients' sex and age, and the frequency of uropathogen identification in the culture was examined.

RESULTS

A total of 1763 urine specimens (women, 931; men, 832) were collected. Of these, 448 (25.4%) were not positive on Gram staining but were positive on culture. In specimens without bacteria on Gram staining, the frequencies of specimens with uropathogens detected on culture were 20.8% (22/160) in women aged <50 years, 21.4% (71/332) in women aged ≥50 years, 2.0% (2/97) in men aged <50 years, and 7.8% (39/499) in men aged ≥50 years.

CONCLUSIONS

In men aged <50 years, the frequency of uropathogenic bacteria identification by urine culture was low in Gram stain-negative specimens. Therefore, urine cultures may be excluded from this group. In contrast, in women, a small number of Gram stain-negative specimens showed significant culture results for the diagnosis of urinary tract infection. Therefore, urine culture should not be omitted in women without careful consideration.

Urinary Tract Infections: The Current Scenario and Future Prospects

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, occurring in both community and healthcare settings. Although the clinical symptoms of UTIs are heterogeneous and range from uncomplicated (uUTIs) to complicated (cUTIs), most UTIs are usually treated empirically. Bacteria are the main causative agents of these infections, although more rarely, other microorganisms, such as fungi and some viruses, have been reported to be responsible for UTIs. Uropathogenic Escherichia coli (UPEC) is the most common causative agent for both uUTIs and cUTIs, followed by other pathogenic microorganisms, such as Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis, and Staphylococcus spp. In addition, the incidence of UTIs caused by multidrug resistance (MDR) is increasing, resulting in a significant increase in the spread of antibiotic resistance and the economic burden of these infections. Here, we discuss the various factors associated with UTIs, including the mechanisms of pathogenicity related to the bacteria that cause UTIs and the emergence of increasing resistance in UTI pathogens.

Presence and Relevance of Emerging Microorganisms in Clinical Genitourinary Samples

Microorganisms responsible for genitourinary infections increasingly include species other than conventional etiological agents that are of clinical and pathogenic relevance and therapeutic interest. This cross-sectional descriptive study selected samples from clinical genitourinary episodes between January 2016 and December 2019 in which emerging microbiological agents were detected. The patients’ epidemiological characteristics, clinical presentation, antibiotic treatment, and outcome were studied to identify their pathogenic role. The emerging microorganisms most frequently detected in urinary tract infections were Streptococcus bovis (58.5%) and Gardnerella spp. (23.6%) in females and S. bovis (32.3%), Aerococcus urinae (18.6%), and Corynebacterium spp. (16.9%) in males, while the most frequently detected in genital infections were S. viridans (36.4%) in females and C. glucuronolyticum (32.2%) and Gardnerella spp. (35.6%) in males. All cases in female children were produced by S. bovis. Symptomatic episodes were more frequent with Aerococcus spp. and S. bovis and the presence of leukocytosis more frequent with Aerococcus spp. Quinolones and doxycycline were most often prescribed antibiotics for genital infections and quinolones and amoxicillin-clavulanic acid for urinary infections. Urinary infection by Aerococcus spp. was more frequent in males of advanced age, Corynebacterium spp. was more frequent in permanent vesical catheter carriers, and episodes of asymptomatic bacteriuria by Gardnerella spp. were more frequent in patients with kidney transplant and chronic consumers of corticosteroid therapy. Lactobacillus spp. should be considered in urinary infections of patients of advanced age and with a previous antibiotic load. Genital infection by Gardnerella spp. was significantly associated with a history of risky sexual relations.

Prevalence, Resistance Patterns and Biofilm Production Ability of Bacterial Uropathogens from Cases of Community-Acquired Urinary Tract Infections in South Italy

Community-acquired urinary tract infections represent the most common infectious diseases in the community setting. Knowing the antibiotic resistance patterns of uropathogens is crucial for establishing empirical treatment. The aim of the current study is to determine the incidence of the causative agents of UTIs and their resistance profiles. Patients of all ages and both sexes were enrolled in the study, and admitted to San Ciro Diagnostic Center in Naples between January 2019 and Jun 2020. Bacterial identification and antibiotic susceptibility testing were carried out using Vitek 2 system. Among the 2741 urine samples, 1702 (62.1%) and 1309 (37.9%) were negative and positive for bacterial growth, respectively. Of 1309 patients with infection, 760 (73.1%) were females and 279 (26.9%) were males. The greatest number of positive cases were found in the in the elderly (>61 years). Regarding uropathogens, 1000 (96.2%) were Gram-negative while 39 (3.8%) were Gram-positive strains. The three most isolated pathogenic strains were Escherichia coli (72.2%), Klebsiella pneumoniae (12.4%), and Proteus mirabilis (9.0%). Strong biofilm formation ability was observed in about 30% of the tested isolates. The low resistance rates recorded against nitrofurantoin, fosfomycin, piperacillin-tazobactam, and gentamicin could suggest them as the most appropriate therapies for CA-UTIs.

Microbiota Ecosystem in Recurrent Cystitis and the Immunological Microenvironment of Urothelium

Urinary tract infections (UTIs) represent one of the most frequent low genital tract diseases in the female population. When UTIs occur with a frequency of at least three times per year or two times in the last six month, we speak of recurrent UTI (rUTI) and up to 70% of women will have rUTI within 1 year. It was previously thought that antibiotic resistance was principally responsible for the recurrence of UTIs, but nowadays new diagnostic technologies have shown the role of microbiota in the pathophysiology of these diseases. Much research has been conducted on the role of gut microbiome in the development of rUTI, while little is known yet about vaginal and urinary microbiome and the possible immunological and microscopical mechanisms through which they trigger symptoms. New discoveries and clinical perspectives are arising, and they all agree that a personalized, multi-modal approach, treating vaginal and urinary dysbiosis, may reduce rUTIs more successfully.

Nanotechnology Involved in Treating Urinary Tract Infections: An Overview

Considered as the most frequent contaminations that do not require hospitalization, urinary tract infections (UTIs) are largely known to cause significant personal burdens on patients. Although UTIs overall are highly preventable health issues, the recourse to antibiotics as drug treatments for these infections is a worryingly spread approach that should be addressed and gradually overcome in a contemporary, modernized healthcare system. With a virtually alarming global rise of antibiotic resistance overall, nanotechnologies may prove to be the much-needed 'lifebuoy' that will eventually suppress this prejudicial phenomenon. This review aims to present the most promising, currently known nano-solutions, with glimpses on clinical and epidemiological aspects of the UTIs, prospective diagnostic instruments, and non-antibiotic treatments, all of these engulfed in a comprehensive overview.

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study

BACKGROUND

There is a growing body of evidence on the potential involvement of coagulase-negative Staphylococci (CoNS) in causing urinary tract infections (UTIs). The aim of this study was to delineate virulence potential, antimicrobial resistance genes, and sequence types of CoNS isolated from patients with UTI symptoms and pyuria in Tanzania.

METHODS

CoNS from patients with UTI symptoms and more than 125 leucocytes/μL were retrieved, subcultured, and whole-genome sequenced.

RESULTS

Out of 65 CoNS isolates, 8 species of CoNS were identified; Staphylococcus haemolyticus, n = 27 (41.5%), and Staphylococcus epidermidis, n = 24 (36.9%), were predominant. The majority of S. haemolyticus were sequence type (ST) 30, with 8 new ST138-145 reported, while the majority of S. epidermidis were typed as ST490 with 7 new ST1184-1190 reported. Sixty isolates (92.3%) had either one or multiple antimicrobial resistance genes. The most frequently detected resistance genes were 53 (21%) dfrG, 32 (12.9%) blaZ, and 26 (10.5%) mecA genes conferring resistance to trimethoprim, penicillin, and methicillin, respectively. Out of 65 isolates, 59 (90.8%) had virulence genes associated with UTI, with a predominance of the icaC 47 (46.5%) and icaA 14 (13.9%) genes. Conclusion:S. haemolyticus and S. epidermidis harboring icaC, dfrG, blaZ, and mecA genes were the predominant CoNS causing UTI in Tanzania. Laboratories should carefully interpret the significant bacteriuria due to CoNS in relation to UTI symptoms and pyuria before labeling them as contaminants. Follow-up studies to document the outcome of the treated patients is needed to add more evidence that CoNS are UTI pathogens.

A Diagnostic Test Combining Molecular Testing with Phenotypic Pooled Antibiotic Susceptibility Improved the Clinical Outcomes of Patients with Non-E. coli or Polymicrobial Complicated Urinary Tract Infections

Purpose

Complicated UTIs (cUTIs) cause significant morbidity and healthcare resource utilization and cost. Standard urine culture has limitations in detecting polymicrobial and non-E. coli infections, resulting in the under-diagnosis and under-treatment of cUTIs. In this study, patient-reported outcomes were compared between treated and untreated patients when an advanced diagnostic test combining multiplex-polymerase chain reaction (M-PCR) with a pooled antibiotic susceptibility method (P-AST) was incorporated into the patients' clinical management.

Methods

Patients who had symptoms typical of cUTI and positive M-PCR/P-AST test results were recruited from urology clinics. Symptom reduction and clinical cure rates were measured from day 0 through day 14 using the American English Acute Cystitis Symptom Score (ACSS) Questionnaire. Clinical cure was defined based on the sum of the scores of four US Food and Drug Administration (FDA) symptoms and the absence of visible blood in the urine.

Results

Of 264 patients with suspected cUTI, 146 (55.4%) had exclusively non-E. coli infections (115 treated and 31 untreated) and 190 (72%) had polymicrobial infections (162 treated and 28 untreated). Treated patients exhibited greater symptom reduction compared to untreated ones on day 14 for those with exclusively non-E. coli organisms (3.18 vs 1.64, p = 0.006) and polymicrobial infections (3.52 vs 1.41, p = 0.002), respectively. A higher percentage of treated patients than of untreated patients achieved clinical cure for polymicrobial infections on day 14 (58.7% vs 36.4%, p = 0.049).

Conclusion

Patients with cUTIs treated based on the M-PCR/P-AST diagnostic test had significantly improved symptom reduction and clinical cure rates compared to untreated patients among those with non-E. coli or polymicrobial infections.

MODERN TRENDS OF CHANGES IN THE MICROBIOTA OF UROGENITAL SYSTEM IN PATIENTS WITH UROLITHIASIS

OBJECTIVE

Aim: Analysis of trends in the microbial communities of the genitourinary system in patients with urolithiasis.

PATIENTS AND METHODS

Materials and Methods: 165 urine samples from patients with urolithiasis was examined. The quantitative isolation of microflora was carried out using the bacteriological method. Microorganisms were identified using API biochemical test systems (bioMerieux, France). The percentage of the various types of microorganisms was determined. The reliability of differences in the frequency of various types of microorganisms isolation in a monoculture and the composition of microbial associations was determined by two-field tables with Fisher's Exact criterion. The GraphPad Prism 7 software was used.

RESULTS

Results: 198 bacterial cultures of various types were isolated. In one case, a Candida culture was isolated. E. faecalis was the most frequently isolated culture (29.1% of the isolated strains number); E. coli (18.1% of the total number of isolated cultures; K. pneumoniae (11.1%). There were no significant differences in the rate of E. faecalis compared to E. coli. K. pneumonia was isolated significantly less frequently than E. faecalis. These types of microorganisms were also leaders in the formation of bacterial mixes. In addition, these species are involved in the urease activity of bacteria (directly or indirectly), which contributes to the formation of stones in the genitourinary system.

CONCLUSION

Conclusions: E. faecalis is the species most often isolated from patients with purulent-inflammatory processes in patients with urolithiasis, both in the case of mono-infection and as part of mixed bacterial cultures.

Sitafloxacin pharmacokinetics/pharmacodynamics against multidrug-resistant bacteria in a dynamic urinary tract infection in vitro model

OBJECTIVES

Sitafloxacin is one of the newer generation fluoroquinolones with highly active against multidrug-resistant (MDR) bacteria. Our objectives were to identify the sitafloxacin pharmacokinetic/pharmacodynamic (PK/PD) index and breakpoints against MDR isolate in the urinary tract infection model.

METHODS

Forty-eight MDR isolates underwent sitafloxacin and levofloxacin microdilution susceptibility testing. A 24 h in vitro model was established that simulated the healthy subjects urodynamics of sitafloxacin fumarate injection. Ten MDR isolates (four carbapenem-resistant Escherichia coli, three carbapenem-resistant P. aeruginosa and three vancomycin-resistant E. faecium) were selected. The drug efficacy was quantified by the change in log colony counts within 24 h. A sigmoid Emax model was fitted to the killing effect data. Monte Carlo simulations were performed to assess target attainment for the sitafloxacin fumarate doses of 100 and 200 mg q24h.

RESULTS

Analysis indicated that the MICs of sitafloxacin were all significantly lower than that of levofloxacin (P < 0.01). The UAUC0-24h/MIC targets required to achieve stasis, 1-log10 killing and 2-log10 killing were 63.60, 79.49 and 99.45 (carbapenem-resistant E. coli), 60.85, 90.31 and 128.95 (carbapenem-resistant P. aeruginosa), 65.91, 77.81 and 103.11 (vancomycin-resistant E. faecium). Monte Carlo simulation showed the infusion of sitafloxacin fumarate 100 mg q24h was able to achieve 90% probability of target attainment against bacteria with MIC of 8 mg/L for the common complicated urinary tract infections.

CONCLUSIONS

Sitafloxacin fumarate injection is an alternative therapeutic agent for the treatment of UTIs caused by MDR isolates.

Intracellular bacterial communities in patient with recurrent urinary tract infection caused by Staphylococcus spp and Streptococcus agalactiae: a case report and literature review

Background

 Urinary tract infections (UTI) are among the most frequent pathologies worldwide. Uropathogenic Escherichia coli (UPEC) is the leading etiological agent; however, depending on the patient's characteristics, the etiology may include some atypical pathogens. Some pathogenic bacteria can internalize in the urothelial and phagocytic cells complicating treatment and timely diagnosis.

Case presentation

We present a clinical case of a married female patient with urological alteration, constant catheterization, and urethral dilation with recurrent UTI for ten years, with five episodes per year and reports of negative urine culture. The microscopic analysis revealed intracellular bacterial communities (IBC) and pyocytes with active bacteria. A protocol was designed for the release of intracellular bacteria in urine samples; without the proposed treatment, the urine culture was negative. However, upon releasing the internalized bacteria, we obtained a polymicrobial urine culture. We isolated and identified Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus simulans, and Streptococcus agalactiae. All microorganisms were sensitive to nitrofurans and sulfas. The patient is under treatment with nitrofurantoin and continuous follow-up by our workgroup.

Conclusions

 It is essential to look for IBC and pyocytes with active bacteria in patients with recurrent UTIs to avoid false-negative urine culture results and provide timely treatment. Polymicrobial culture must be considered depending on the patient and clinical history.