Comparative evaluation of Vitek 2 identification and susceptibility testing of urinary tract pathogens directly and isolated from chromogenic media

Direct Urine Resistance Detection Using VITEK 2

Urinary tract infections (UTIs) are the most common infectious diseases in both communities and hospitals. With non-anatomical or functional abnormalities, UTIs are usually self-limiting, though women suffer more reinfections throughout their lives. Certainly, antibiotic treatment leads to a more rapid resolution of symptoms, but also it selects resistant uropathogens and adversely affects the gut and vaginal microbiota. As uropathogens are increasingly becoming resistant to currently available antibiotics, it could be time to explore alternative strategies for managing UTIs. Rapid identification and antimicrobial susceptibility testing (AST) allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and the VITEK 2 system for the direct analysis of urine samples. First, we selected positive urine samples by flow cytometry using UF5000, establishing the cut-off for positive at 150 bacteria/mL. After confirming the identification using MALDI-TOF MS and filtering the urine samples for Escherichia coli, we directly tested the AST N388 card using VITEK 2. We tested a total of 211 E. coli from urine samples. Cefoxitin, ertapenem, imipenem, gentamicin, nalidixic acid, ciprofloxacin, fosfomycin, and nitrofurantoin had no major important errors (MIE), and ampicillin, cefuroxime, and tobramycin showed higher MIEs. Cefepime, imipenem, and tobramycin had no major errors (ME). Fosfomycin was the antibiotic with the most MEs. The antibiotic with the most minor errors (mE) was ceftazidime. The total categorical agreement (CA) was 97.4% with a 95% CI of (96.8–97.9)_95%. The direct AST from the urine samples proposed here was shorter by one day, without significant loss of sensibility regarding the standard diagnosis. Therefore, we hypothesize that this method is more realistic and better suited to human antibiotic concentrations.

Antimicrobial Resistance Patterns and ESBL of Uropathogens Isolated from Adult Females in Najran Region of Saudi Arabia

Background: To explore the prevalence of urinary tract infections (UTIs) among female patients in the Najran region of Saudi Arabia and determine their antimicrobial resistance pattern. Methods: This study was conducted on 136 urine samples collected from outpatient departments (OPDs) of the different government hospitals in the Najran region of Saudi Arabia. Over one year, the results of susceptibility testing reports of outpatient midstream urine samples from three government hospitals were prospectively evaluated. Results: Of 136 urine samples, only 123 (90.45%) were found to show significant growth for UTIs, from which 23 different uropathogens were identified. Escherichia coli (58.5%) was the most commonly isolated organism, followed by Klebsiella pneumoniae (8.1%). The isolated microorganism showed increased resistance patterns from 3.3% to 62.6%, with an overall resistance of 27.19%. Meropenem was the most effective antimicrobial, followed by amikacin and ertapenem (0.47%, 0.91%, and 1.5% resistance, respectively). At the same time, ampicillin and cephazolin were the least (62.6% and 59.5% resistance, respectively) effective. Overall, eleven (8.94%) uropathogens isolates were ESBLs, among which there were eight (6.5%) Escherichia coli, one (0.81%) Klebsiella pneumoniae, one (0.81%) Klebsiella oxytoca, and one (0.81%) Citrobacter amalonaticus. Conclusions: E. coli remains the most commonly isolated causative uropathogens, followed by Klebsiella species. The prevalence of pathogenic E. coli and Klebsiella species underscores the importance of developing cost-effective, precise, and rapid identification systems to minimize public exposure to uropathogens. Antibiotic susceptibility data revealed that most of the isolates were resistant to the majority of the antibiotics. The patients with UTIs in the Najran region of Saudi Arabia are at a high risk of antibiotic resistance, leading to significant problems in outpatient department (OPD) treatment outcomes and raising the alarm for the physician to change their empiric treatment.

An alternative for urine cultures: Direct identification of uropathogens from urine by MALDI-TOF MS

Urinary tract infections are one of the most common bacterial infections and rapid diagnosis of the infection is essential for appropriate antibiotic therapy. The goal of our study was to identify urinary pathogens directly by MALDI-TOF MS and to perform antibiotic susceptibility tests in order to shorten the period spent for culturing.Urine samples submitted for culture to the Clinical Microbiology Laboratory were enrolled in this study. Urine samples were screened for leukocyte and bacteria amount by flow cytometry. Samples with bacterial load of 106-107/mL were tested directly by MALDI-TOF MS and antibiotic susceptibility tests (AST) were performed.In total, 538 positive urine samples were evaluated in our study. MALDI-TOF MS identified the microorganism directly from the urine sample in 91.8% of these samples and the concordance rate of conventional identification and direct detection was 95.8% for Gram-negatives at the genus and species level. Escherichia coli (n:401) was the most frequently isolated microorganism, followed by Klebsiella pneumoniae (n:57). AST results were generated for 111 of these urine samples and the concordance was 90% and 87% for E. coli and K. pneumoniae, respectively.Our results showed that screening of urine samples with flow cytometry to detect positive samples and identification of uropathogens directly by MALDI-TOF MS with an accuracy of over 90% can be a suitable method particularly for Gram-negative bacteria in clinical microbiology laboratories.

Direct identification and susceptibility testing of Gram-negative bacilli from turbid urine samples using VITEK2

INTRODUCTION:

Urinary tract infections (UTIs) are the most common infectious diseases occurring in either the community or healthcare setting. Turnaround time for urine culture is about 24 h, and antimicrobial susceptibility testing (AST) requires another 24 h. Consequently, initial antibiotic therapy is mostly empirical.

MATERIALS AND METHODS:

This study was conducted at Nizam's Institute of Medical Sciences, Hyderabad. Turbid urine samples which showed pus cells and Gram-negative (GN) bacilli of single morphotype were included. The turbidity of the urine was adjusted to 0.5 McFarland and uploaded directly in the VITEK 2 identification (ID) GN and N-280 panel for AST. The specimen was also inoculated on CHROMagar, and the ID and AST of the isolates from the agar plate were repeated on VITEK 2, and the results were compared.

RESULTS:

Out of 844 turbid urines screened, 62 met the inclusion criteria. Escherichia coli was the most common isolate (71.9%). Complete agreement for ID was 80.7%, misidentified were 12.2%, and unidentified were 7%. Complete agreement with AST was 94.3%, very major errors 0.5%, major errors 2.2%, and minor errors 3%.

CONCLUSION:

With a 94.3% agreement for AST and a reduced turnaround time by 24 h, the direct inoculation had a potential clinical benefit for initiating timely and appropriate antibiotic therapy for UTI.

Rapid Antibiotic Susceptibility Testing for Urinary Tract Infections

Antibiotic susceptibility testing is important to guide clinicians in their choice of antibiotic used for treatment of bacterial infections. Current methods are time-consuming and more rapid alternatives are needed. Here, we describe a novel rapid method for antibiotic susceptibility testing which combines phenotypic and genotypic measurements. The use of padlock probes and rolling circle amplification allows for fast and precise determination of antibiotic susceptibilities as well as species identification.

The antimicrobial activity of mecillinam, nitrofurantoin, temocillin and fosfomycin and comparative analysis of resistance patterns in a nationwide collection of ESBL-producing Escherichia coli in Norway 2010-2011

BACKGROUND

The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Norway has been steadily increasing during the last 10-15 years as part of a global pandemic. ESBL producers frequently express co-resistance to other important antimicrobial drug classes, limiting therapeutic options. This has led to regained interest in older antimicrobial agents. The aim of this study was to evaluate the antimicrobial activity of mecillinam, nitrofurantoin, temocillin and fosfomycin, as well as to perform a comparative analysis of resistance patterns in a nationwide collection of ESBL-producing E. coli.

METHODS

A nationwide collection of all 105 clinical isolates of ESBL-producing E. coli from the Norwegian Organisation for Surveillance of Antimicrobial Resistance (NORM) during 2010-2011 was analyzed. Detection and identification of ESBL-encoding genes were performed by PCR and sequencing for confirmation of ESBL variants of blaTEM and blaSHV (2010) or microarray (2011). Minimum inhibitory concentrations (MICs) or MIC correlates were determined using MIC gradient tests or VITEK 2, respectively. Comparative analysis of resistance patterns was performed.

RESULTS

All isolates were susceptible to fosfomycin, temocillin (urinary tract breakpoint) and meropenem. For mecillinam and nitrofurantoin, 6% and 9% of the isolates, respectively, were non-susceptible. A high level of susceptibility was also observed for amikacin (95%). In contrast, the non-susceptibility proportions to ampicillin (100%), cefotaxime (97%), ceftazidime (77%), aztreonam (87%), gentamicin (42%), tobramycin (52%), ciprofloxacin (76%) and trimethoprim-sulfamethoxazole (71%) were higher.

CONCLUSIONS

Overall, the in vitro susceptibility to nitrofurantoin, fosfomycin, mecillinam and temocillin was high, indicating that these drugs are good options for treating uncomplicated urinary tract infections caused by ESBL-producing E. coli.

Does flow cytometry have a role in preliminary differentiation between urinary tract infections sustained by gram positive and gram negative bacteria? An Italian polycentric study

BACKGROUND

Urine culture is the most frequently requested test for a Microbiology Lab. A reliable screening tool would be of paramount importance both to clinicians and laboratorians, provided that it could get fast and accurate negative results in order to rule-out urinary tract infection (UTI).

MATERIALS AND METHODS

We evaluated 1907 consecutive urine samples from outpatients. Culture was performed on chromogenic agar with 1μL loop, using 10(5)CFU/mL as a limit of positive growth. Using Sysmex Uf-1000i analyzer we evaluated bacteria forward scatter (B_FSC) and fluorescent light scatter (B_FLH) in a preliminary discrimination step for UTI caused by Gram+ or Gram- bacteria.

RESULTS

We got 512 positive samples. A mono-microbial infection was observed in 490 samples; two bacterial strains were isolated in 22 samples, so 534 bacterial strains were found: 392 Gram-, 133 Gram+ and 9 yeasts. Comparing Gram+ and Gram- bacteria we observed a statistically significant difference for B_FSC but not for B_FLH. In this application experimental cut-off value for B_FSC was 25ch. Using this cut-off to perform a presumptive identification of UTI sustained by Gram-+ bacteria, we observed a SE 0.68, SP 0.84.

CONCLUSION

Our data although preliminary suggest that B_FSC could be useful in presumptive exclusion of UTI caused by Gram-positive bacteria.

A general method for rapid determination of antibiotic susceptibility and species in bacterial infections

To ensure correct antibiotic treatment and reduce the unnecessary use of antibiotics, there is an urgent need for new rapid methods for species identification and determination of antibiotic susceptibility in infectious pathogenic bacteria. We have developed a general method for the rapid identification of the bacterial species causing an infection and the determination of their antibiotic susceptibility profiles. An initial short cultivation step in the absence and presence of different antibiotics was combined with sensitive species-specific padlock probe detection of the bacterial target DNA to allow a determination of growth (i.e., resistance) and no growth (i.e., susceptibility). A proof-of-concept was established for urinary tract infections in which we applied the method to determine the antibiotic susceptibility profiles of Escherichia coli for two drugs with 100% accuracy in 3.5 h. The short assay time from sample to readout enables fast appropriate treatment with effective drugs and minimizes the need to prescribe broad-spectrum antibiotics due to unknown resistance profiles of the treated infection.

Evaluation of two chromogenic media for the isolation and identification of urinary tract pathogens

Chromogenic media (CM) are available for urine specimens (US) to enable rapid identification of common urinary tract pathogens (UTP). Two CM, chromID™ CPS (CPS4) agar (bioMérieux, St. Laurent, QC) and UriSelect™ 4 (URS4) agar (Bio-Rad, Montreal, QC), were compared to the standard media (SM) for the isolation and identification of UTP. Over a 10-day period, US were inoculated to CPS4, URS4, and SM (BAP and MAC). CM interpretation was done according to the product inserts by one person blinded to the results of SM. SM were read by experienced technologists according to protocol and isolates were identified using BD Phoenix™. The results were grouped into significant (SG), mixed (MG), and no significant growth (NSG). A total of 903 US were studied. SM identified 239 SG, 112 MG, and 552 NSG cultures. The most common pathogens were Escherichia coli (38 %) and Enterococcus spp. (11 %). Comparing CM to SM, the exact agreement was 89.3 and 89.5 % for URS4 and CPS4, respectively. When grouped by clinical significance, agreement with SM was 93.0 and 93.1 % for URS4 and CPS4, respectively. CM were equivalent with respect to processing time. Advantages include decreased need for automated identification of certain species, particularly E. coli. In terms of workflow, CM enables same-day identification for almost 50 % of significant UTP. Overall, both CM compared well to SM and allowed for rapid preliminary identification of many UTP.

Comparative analysis of Staphylococcus aureus and Escherichia coli microcalorimetric growth

BACKGROUND

Microcalorimetric bacterial growth studies have illustrated that thermograms differ significantly with both culture media and strain. The present contribution examines the possibility of discriminating between certain bacterial strains by microcalorimetry and the qualitative and quantitative contribution of the sample volume to the observed thermograms. Growth patterns of samples of Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922) were analyzed. Certain features of the thermograms that may serve to distinguish between these bacterial strains were identified.

RESULTS

The thermograms of the two bacterial strains with sample volumes ranging from 0.3 to 0.7 ml and same initial bacterial concentration were analyzed. Both strains exhibit a roughly 2-peak shape that differs by peak amplitude and position along the time scale. Seven parameters corresponding to the thermogram key points related to time and heat flow values were proposed and statistically analyzed. The most relevant parameters appear to be the time to reach a heat flow of 0.05 mW (1.67 ± 0.46 h in E. coli vs. 2.99 ± 0.53 h in S. aureus, p < 0.0001), the time to reach the first peak (3.84 ± 0.5 h vs. 5.17 ± 0.49 h, p < 0.0001) and the first peak value (0.19 ± 0.02 mW vs. 0.086 ± 0.012 mW, p < 0.0001). The statistical analysis on 4 parameters of volume-normalized heat flow thermograms showed that the time to reach a volume-normalized heat flow of 0.1 mW/ml (1.75 ± 0.37 h in E. coli vs. 2.87 ± 0.65 h in S. aureus, p < 0.005), the time to reach the first volume-normalized peak (3.78 ± 0.47 h vs. 5.12 ± 0.52 h, p < 0.0001) and the first volume-normalized peak value (0.35 ± 0.05 mW/ml vs. 0.181 ± 0.040 mW/ml, p < 0.0001) seem to be the most relevant. Peakfit® decomposition and analysis of the observed thermograms complements the statistical analysis via quantitative arguments, indicating that: (1) the first peak pertains to a faster, "dissolved oxygen" bacterial growth (where the dissolved oxygen in the initial suspension acts as a limiting factor); (2) the second peak indicates a slower "diffused oxygen" growth that involves transport of oxygen contained in the unfilled part of the microcalorimetric cell; (3) a strictly fermentative growth component may slightly contribute to the observed complex thermal signal.

CONCLUSION

The investigated strains of Staphylococcus aureus and Escherichia coli display, under similar experimental conditions, distinct thermal growth patterns. The two strains can be easily differentiated using a selection of the proposed parameters. The presented Peakfit analysis of the complex thermal signal provides the necessary means for establishing the optimal growth conditions of various bacterial strains. These conditions are needed for the standardization of the isothermal microcalorimetry method in view of its further use in qualitative and quantitative estimation of bacterial growth.