Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing.

Increasing global travel and changes in the environment may escalate the frequency of contact with a natural host carrying an infection and, therefore, increase our chances of encountering microorganisms previously unknown to humans. During an emergency, the etiology of infection may be unknown at the time of patient treatment. The existing local or global Antimicrobial Stewardship Programs may not be fully prepared for emerging/re-emerging infectious disease outbreaks, especially if they are caused by an unknown organism, engineered bioterrorist attack, or rapidly evolving superbug. We demonstrate an antimicrobial efficacy profiling method that can be performed in hours directly from clinical urine specimens. The antimicrobial potency was determined by the level of microbial growth inhibition and compared to conventional antimicrobial susceptibility testing results. The oligonucleotide probe pairs on the sensors were designed to target Gram-negative bacteria, specifically Enterobacterales and Pseudomonas aeruginosa. A pilot study of 10 remnant clinical specimens from the Clinical Laboratory Improvement Amendments-certified labs of New York-Presbyterian Queens was conducted, and only one sample was not detected by the probes. The remaining nine samples agreed with reference AST methods (Vitek and broth microdilution), resulting in 100% categorical agreement. In a separate feasibility study, we evaluated a dual-kinetic response approach, in which we inoculated two antibiotic stripwells containing the same antimicrobial concentrations with clinical specimens at the original concentration (1x) and at a 10-fold dilution (0.1x) to cover a broader range of microbiological responses. The combined categorical susceptibility reporting of 12 contrived urine specimens was 100% for ciprofloxacin, gentamicin, and meropenem over a range of microbial loads from 105 to 108 CFU/mL.

Urine Culture in Hospitalized Patients during 2014-2018: An Analysis on Pathogen Distribution and Drug Sensitivity.

OBJECTIVE: We sought to analyze the distribution and antibiotic sensitivity of pathogens in hospitalized patients and to provide a scientific reference for the rational application of antibiotics. METHODS: From January 2014 to December 2018, urine cultures from patients in our hospital were collected and analyzed retrospectively for the presence, distribution, and drug sensitivity of pathogens. RESULTS: A total of 42,854 midstream urine cultures were collected from which 11,891 (27.75%) pathogens were isolated, including 8101 (68.13%) strains of gram-negative bacteria, 2580 (21.69%) strains of gram-positive bacteria, and 1210 (10.18%) strains of fungi. Escherichia coli and Enterococci were the most common species of gram-negative and gram-positive bacteria, respectively. Drug sensitivity varied among different pathogens. Clear drug resistance was observed in bacteria, while fungus exhibited relatively lower resistance. CONCLUSION: Pathogens responsible for urinary tract infections in hospitalized patients are diversiform and display resistance to some antibiotics. Drug resistance monitoring should be enhanced to optimize antimicrobial therapy.

Impact of the Step-by-Step on febrile infants.

OBJECTIVE: To evaluate the impact of introducing the Step-by-Step approach on care quality in young febrile infants. DESIGN: Observational study including infants ≤90 days old with fever without source seen in a paediatric emergency department 5 years before (n=1222) and after (n=1151) its introduction. Quality of care was evaluated in terms of adherence to recommendations, resource use and safety. RESULTS: Adherence: percentages of infants undergoing both urine and blood tests and infants <15 days old receiving full sepsis evaluation increased (84.7% vs 91.0% and 23.9% vs 63.3%, respectively; p<0.01). Resource use: lumbar puncture and admission rates decreased (24.1% vs 18.7% and 43.6% vs 38.3%, respectively; p<0.01), while the rate of antibiotic therapy increased (30.2% vs 43.2%; p<0.01). SAFETY: the invasive bacterial infection rate among infants managed as outpatients was unchanged (0.7% vs 0.3%; p=0.24). CONCLUSION: The introduction of the Step-by-Step increased the quality of care provided to young febrile infants.

Changes in Bacterial Spectrum and Resistance Patterns Over Time in the Urine of Patients with Neurogenic Lower Urinary Tract Dysfunction Due to Spinal Cord Injury.

INTRODUCTION: Urinary tract infections (UTI) are among the most common complications in persons with neurogenic lower urinary tract dysfunction (NLUTD) due to spinal cord injury (SCI). As both asymptomatic bacteriuria and UTI are frequently treated with antibiotics, concerns about multidrug resistance arise. Therefore, we analyzed the bacterial spectrum in the urine and the resistance patterns of the strains over time in patients with NLUTD due to SCI. METHODS: In a systematic chart review, we identified all microbiologic urine test results including resistance patterns of persons with SCI in a tertiary referral hospital at 2 time periods (2010-2011 and 2017-2018). We assessed the frequency of the bacterial strains, the resistance patterns of the 5 most frequent bacteria, and the use of antibiotics for in- as well as for outpatients. RESULTS: From 2010 to 2011, 1,308 (outpatients) and 2,479 (inpatients) bacterial strains were detected in the urinalyses performed; these numbers rose to 3,162 and 6,112 during 2017-2018, respectively. The most frequently detected bacteria during both time periods were Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae/variicola, Streptococcus viridans, Pseudomonas aeruginosa, and coagulase negative Staphylococci. Fluoroquinolones were the most frequently used antibiotics during both time periods. Despite its frequent use, no relevant increase in resistance against fluoroquinolones was detected. The most prominent increase in resistance appeared in E. coli against amocixillin/clavulanic acid in inpatients (from 26.0 to 38.5%). DISCUSSION AND CONCLUSIONS: Although fluoroquinolones were used frequently, we did not observe an increased resistance against these antibiotics over time in the urine of patients with SCI.

Exploring the possibilities of infrared spectroscopy for urine sediment examination and detection of pathogenic bacteria in urinary tract infections.

Objectives In this study, the possibilities of Fourier-transformed infrared spectroscopy (FTIR) for analysis of urine sediments and for detection of bacteria causing urinary tract infections (UTIs) were investigated. Methods Dried urine specimens of control subjects and patients presenting with various nephrological and urological conditions were analysed using mid-infrared spectroscopy (4,000-400 cm-1). Urine samples from patients with a UTI were inoculated on a blood agar plate. After drying of the pure bacterial colonies, FTIR was applied and compared with the results obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Chemometric data analysis was used to classify the different species. Results Due to the typical molecular assignments of lipids, proteins, nucleic acids and carbohydrates, FTIR was able to identify bacteria and showed promising results in the detection of proteins, lipids, white and red blood cells, as well as in the identification of crystals. Principal component analysis (PCA) allowed to differentiate between Gram-negative and Gram-positive species and soft independent modelling of class analogy (SIMCA) revealed promising classification ratios between the different pathogens. Conclusions FTIR can be considered as a supplementary method for urine sediment examination and for detection of pathogenic bacteria in UTI.

An Intact Cell Bioluminescence-Based Assay for the Simple and Rapid Diagnosis of Urinary Tract Infection.

Urinary tract infection (UTI) is one of the most common infections, accounting for a substantial portion of outpatient hospital and clinic visits. Standard diagnosis of UTI by culture and sensitivity can take at least 48 h, and improper diagnosis can lead to an increase in antibiotic resistance following therapy. To address these shortcomings, rapid bioluminescence assays were developed and evaluated for the detection of UTI using intact, viable cells of Photobacterium mandapamensis USTCMS 1132 or previously lyophilized cells of Photobacterium leiognathi ATCC 33981™. Two platform technologies-tube bioluminescence extinction technology urine (TuBETUr) and cellphone-based UTI bioluminescence extinction technology (CUBET)-were developed and standardized using artificial urine to detect four commonly isolated UTI pathogens-namely, Escherichia coli, Proteus mirabilis, Staphylococcus aureus, and Candida albicans. Besides detection, these assays could also provide information regarding pathogen concentration/level, helping guide treatment decisions. These technologies were able to detect microbes associated with UTI at less than 105 CFU/mL, which is usually the lower cut-off limit for a positive UTI diagnosis. Among the 29 positive UTI samples yielding 105-106 CFU/mL pathogen concentrations, a total of 29 urine specimens were correctly detected by TuBETUr as UTI-positive based on an 1119 s detection window. Similarly, the rapid CUBET method was able to discriminate UTIs from normal samples with high confidence (p ≤ 0.0001), using single-pot conditions and cell phone-based monitoring. These technologies could potentially address the need for point-of-care UTI detection while reducing the possibility of antibiotic resistance associated with misdiagnosed cases of urinary tract infections, especially in low-resource environments.

Antimicrobial resistance and recurrent bacterial urinary tract infections in hospitalized patients following kidney transplantation: A single-center experience.

PURPOSE: The burden of urinary tract infections (UTIs) and risk factors for developing infections with multidrug resistant organisms (MDROs) post-kidney transplantation (KT) are poorly understood. METHODS: Single-center retrospective cohort study (January 2015-December 2017) evaluating first and recurrent episodes of bacteriuria and subsequent analysis of episodes caused by MDROs up to 6 months post-KT. Donor and recipient variables were reviewed. RESULTS: A total of 743 adults underwent single KT during the study period, and 106 patients were hospitalized with bacteriuria. 45% were asymptomatic in their first episode. 73.6% had a single episode, and 26.4% had 2 or more episodes. A total of 28 patients had recurrent episodes; 64.3% had an MDRO on the first episode and 78.6% on the second episode. Escherichia coli was the most common organism isolated, 88.5% were resistant to trimethoprim-sulfamethoxazole (TMP-SMX), 9.3% were extended-spectrum beta-lactamase (ESBL) producers, and 38.1% were MDROs. Body mass index ≥30 was significantly associated with the presence of MDROs in both univariate and multivariate analyses (RR 1.37, 95% CI 1.01-1.88; OR 3.26, CI 1.29-8.25). A total of 12 donors had bacteremia or bacteriuria and 6 (50%) with E coli. A total of 10 KT recipients received antibiotic prophylaxis to prevent donor-derived infections. CONCLUSIONS: Our results suggest that a significant proportion of patients develop recurrent bacteriuria post-transplantation; of those, more than half caused by MDROs. There is a possible association between obesity and MDROs in KT recipients that merits further investigation. With the global crisis in antimicrobial resistance, innovative strategies are needed to prevent and treat UTIs in KT patients.

Diagnosis of bacterial urinary tract infection: Utility of urine myeloperoxidase concentration to predict urine culture results in dogs.

Suspected bacterial urinary tract infections (UTI) are a common cause of overuse and misuse of antimicrobials. A bedside diagnostic test that could accurately predict urine culture results would prevent antimicrobial overuse, but accurate biomarkers have not yet been identified in veterinary medicine. The objective of this study was to evaluate urine myeloperoxidase (uMPO) as a rapidly available, accurate marker to predict urine culture results. We hypothesized that uMPO would be higher in dogs with a positive urine culture than in dogs with a negative urine culture, and that uMPO could be used to aid in the accurate diagnosis of significant bacteriuria. Urine samples were collected from a veterinary university clinical pathology lab. uMPO concentration was measured using a commercially available canine myeloperoxidase (MPO) enzyme-linked immunosorbent assay (ELISA). Following validation, samples from 98 dogs that had a urinalysis and urine culture performed as part of their diagnostic investigation were included. Forty-seven dogs had a negative urine culture and fifty-one dogs had a positive urine culture. uMPO levels were significantly higher in samples that had a positive culture (median 2.13 ng/ml; IQR 0.98-7.07) versus samples that had a negative culture (median 1.07 ng/ml; IQR 0.52-1.84)(p < 0.005). Based on receiver-operator characteristic, a cutoff of 0.55 ng/ml was chosen to maximize sensitivity and specificity. Using a cutoff of 0.55 ng/ml, uMPO had a sensitivity of 70% and specificity of 69% to determine the presence of a positive culture. However, the degree of overlap between groups may preclude the use of this test as a surrogate for urine culture in a clinical setting.

Low antimicrobial resistance in general practice patients in Rotterdam, the city with the largest proportion of immigrants in the Netherlands.

Antimicrobial resistance (AMR) is an increasing problem. The prevalence of antimicrobial resistance in general practice patients is expected to be relatively high in Rotterdam, the Dutch city with the largest proportion non-Western immigrants. The aim of this study was to assess the prevalence of antibiotic-resistant uropathogens (Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis) in general practices in Rotterdam, and to find a possible association between the prevalence of antibiotic-resistant E. coli and age, gender, and socioeconomic status (SES). A retrospective analysis was performed of urine samples from general practice patients in 2016. The prevalence of AMR in uropathogens was compared with national resistance data, as was the prevalence of highly and multidrug resistant and extended spectrum ß-lactamase (ESBL) producing E. coli and K. pneumoniae. Univariate logistic regression was used to study associations between antibiotic-resistant E. coli and age, gender, and SES area score. No clinically relevant differences were observed in the prevalence of antibiotic-resistant uropathogens in Rotterdam compared with the national prevalence. For E. coli and K. pneumoniae, the prevalence was 3.6% for ESBL production (both pathogens together), while the prevalence ranged between 4.2%-5.0% for high resistance and between 1.2%-3.3% for multidrug resistance. Ciprofloxacin-resistant E. coli was significantly associated with higher age. Although Rotterdam has a high percentage of non-western immigrants and a low SES, AMR is low among general practice patients. This indicates that adherence to national guidelines in general practice enables maintenance of low AMR, even in high-risk populations.

Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients.

OBJECTIVE: To evaluate whether multiplex PCR-based molecular testing is noninferior to urine culture for detection of bacterial infections in symptomatic patients. METHODS: Retrospective record review of 582 consecutive elderly patients presenting with symptoms of lower urinary tract infection (UTI) was conducted. All patients had traditional urine cultures and PCR molecular testing run in parallel. RESULTS: A total of 582 patients (mean age 77; range 60-95) with symptoms of lower UTI had both urine cultures and diagnostic PCR between March and July 2018. PCR detected uropathogens in 326 patients (56%, 326/582), while urine culture detected pathogens in 217 patients (37%, 217/582). PCR and culture agreed in 74% of cases (431/582): both were positive in 34% of cases (196/582) and both were negative in 40% of cases (235/582). However, PCR and culture disagreed in 26% of cases (151/582): PCR was positive while culture was negative in 22% of cases (130/582), and culture was positive while PCR was negative in 4% of cases (21/582). Polymicrobial infections were reported in 175 patients (30%, 175/582), with PCR reporting 166 and culture reporting 39. Further, polymicrobial infections were identified in 67 patients (12%, 67/582) in which culture results were negative. Agreement between PCR and urine culture for positive cultures was 90%, exceeding the noninferiority threshold of 85% (95% conflict of interest 85.7%-93.6%). CONCLUSION: Multiplex PCR is noninferior to urine culture for detection and identification of bacteria. Further investigation may show that the accuracy and speed of PCR to diagnose UTI can significantly improve patient outcomes.