Direct Identification of Urinary Tract Pathogens from Urine Samples, Combining Urine Screening Methods and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

"Urinary tract infection: Conventional testing to developing Technologies"

Urinary tract infections (UTIs) present an escalating global health concern, precipitating increased hospitalizations and antibiotic utilization, thereby fostering the emergence of antimicrobial resistance. Current diagnostic modalities exhibit protracted timelines and substantial financial burdens, necessitating specialized infrastructures. Addressing these impediments mandates the development of a precise diagnostic paradigm to expedite identification and augment antibiotic stewardship. The application of biosensors, recognized for their transformative efficacy, emerges as a promising resolution. Recent strides in biosensor technologies have introduced pioneering methodologies, yielding pertinent biosensors and integrated systems with significant implications for point-of-care applications. This review delves into historical perspectives, furnishing a comprehensive delineation of advancements in UTI diagnostics, disease etiology, and biomarkers, underscoring the potential merits of these innovations for optimizing patient care.

Advances and Progress in Automated Urine Analyzers

The clinical analysis of urine has classically focused on conventional chemical-based urinalysis and urine microscopy. Contemporary advances in both analysis subsets have started to employ new technologies such as automated image analysis, flow cytometry, and mass spectrometry. In addition to new detection technologies, current analyzers have incorporated more advanced imaging, automated sample handing, and machine learning analyses into their workflow. The most advanced semiautomated analyzers can be interfaced with hospital medical record systems, and in the point-of-care setting, smartphones can be used for image analysis. This review will discuss current technological advancements in the field of urinalysis and urine microscopy.

Array-based specific classification of bacterial species via ligands with dimethylamino/amino groups

The early detection of bacterial species plays a crucial role in patient prognosis and the development of effective therapeutic regimens. This study introduces an accessible and promising colorimetric sensor array designed to classify gram-positive (G+) and gram-negative (G-) bacterial species. The classification relies on 6 chemical ligands with dimethylamino/amino groups as sensing elements and silver nanotriangles as colorimetric probes. Using these specific sensor arrays, we successfully differentiated G- and G+ bacterial species and discriminated individual bacterial strains, and the sensors exhibited remarkable reproducibility and high sensitivity. Moreover, the sensor array can identify bacterial mixtures and bacteria at varying concentrations, underscoring its versatility. In summary, this sensor array offers an effective tool for bacterial analysis with promising applications in the field of biomedical diagnostics.

Nanoplasmonic Rapid Antimicrobial-Resistance Point-of-Care Identification Device: RAPIDx

The emergence of antibiotic resistance has become a global health crisis, and everyone must arm themselves with wisdom to effectively combat the "silent tsunami" of infections that are no longer treatable with antibiotics. However, the overuse or inappropriate use of unnecessary antibiotics is still routine for administering them due to the unavailability of rapid, precise, and point-of-care assays. Here, a rapid antimicrobial-resistance point-of-care identification device (RAPIDx) is reported for the accurate and simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype). First, a contamination-free active target enzyme is extracted via the photothermal lysis of preconcentrated bacteria cells on a nanoplasmonic functional layer on-chip. Second, the rapid, precise identification of pathogens is achieved by the photonic rolling circle amplification of DNA on a chip. Third, the simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype) is demonstrated within a sample-to-answer 45 min operation via the RAPIDx. It is believed that the RAPIDx will be a valuable method for solving the bottleneck of employing on-chip nanotechnology for antibiotic-resistant bioassay and other infectious diseases.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and lateral flow immunochromatography for rapid identification of β-lactamase-gene-harboring Enterobacterales in urine specimens: Performance and cost-benefit analyses

In this single-center prospective study, we evaluated the performance to the MALDI-ToF MS based method in conjunction with lateral flow immunochromatographic (LFIC) in urine specimens for rapid diagnosis of bacterial Urinary Tract Infection (UTI) and detection of carbapenemase and/or extended-spectrum β- lactamase (ESBL) enzymes produced by the involved bacteria, compared to standard culture, and antimicrobial susceptibility testing/genotypic resistance markers characterization performed on culture-grown colonies. In addition, a cost-benefit analysis comparing this approach against standard procedures was conducted. A total of 324 urines were included in the study, of which 288 (88.9 %) yielded concordant results by the MALDI-ToF MS and conventional culture (Kappa agreement, 0.82; P<0.001). Direct LFIC testing could be carried out in 249/324 urines. Bacterial species carrying β-lactam genotypic resistance markers were identified in 35 urines (35 CTX-M and 2 OXA-48). Two ESBL-producing Escherichia coli were missed by LFIC (Kappa agreement with standard procedures of 0.96; P<0.001). The cost-benefit analysis indicated that our novel approach resulted in an improvement of clinical outcomes (less need of outpatient care) with a marginal incremental cost (€2.59).

Applications of Artificial Intelligence in Urinalysis: Is the Future Already Here?

BACKGROUND

Artificial intelligence (AI) has emerged as a promising and transformative tool in the field of urinalysis, offering substantial potential for advancements in disease diagnosis and the development of predictive models for monitoring medical treatment responses.

CONTENT

Through an extensive examination of relevant literature, this narrative review illustrates the significance and applicability of AI models across the diverse application area of urinalysis. It encompasses automated urine test strip and sediment analysis, urinary tract infection screening, and the interpretation of complex biochemical signatures in urine, including the utilization of cutting-edge techniques such as mass spectrometry and molecular-based profiles.

SUMMARY

Retrospective studies consistently demonstrate good performance of AI models in urinalysis, showcasing their potential to revolutionize clinical practice. However, to comprehensively evaluate the real clinical value and efficacy of AI models, large-scale prospective studies are essential. Such studies hold the potential to enhance diagnostic accuracy, improve patient outcomes, and optimize medical treatment strategies. By bridging the gap between research and clinical implementation, AI can reshape the landscape of urinalysis, paving the way for more personalized and effective patient care.

Hypervirulent Klebsiella pneumoniae detection methods: a minireview

Hypervirulent Klebsiella pneumoniae (hvKp), characterized by high virulence and epidemic potential, has become a global public health challenge. Therefore, improving the identification of hvKp and enabling earlier and faster detection in the community to support subsequent effective treatment and prevention of hvKp are an urgent issue. To address these issues, a number of assays have emerged, such as String test, Galleria mellonella infection test, PCR, isothermal exponential amplification, and so on. In this paper, we have collected articles on the detection methods of hvKp and conducted a retrospective review based on two aspects: traditional detection technology and biomarker-based detection technology. We summarize the advantages and limitations of these detection methods and discuss the challenges as well as future directions, hoping to provide new insights and references for the rapid detection of hvKp in the future. The aim of this study is to focus on the research papers related to Hypervirulent Klebsiella pneumoniae involving the period from 2012 to 2022. We conducted searches using the keywords "Hypervirulent Klebsiella pneumoniae, biomarkers, detection techniques" on ScienceDirect and Google Scholar. Additionally, we also searched on PubMed, using MeSH terms associated with the keywords (such as Klebsiella pneumoniae, Klebsiella Infections, Virulence, Biomarkers, diagnosis, etc.).

Flow cytometric detection of vancomycin-resistant Enterococcus faecium in urine using fluorescently labelled enterocin K1

A urinary tract infection (UTI) occurs when bacteria enter and multiply in the urinary system. The infection is most often caused by enteric bacteria that normally live in the gut, which include Enterococcus faecium. Without antibiotic treatment, UTIs can progress to life-threatening septic shock. Early diagnosis and identification of the pathogen will reduce antibiotic use and improve patient outcomes. In this work, we develop and optimize a cost-effective and rapid (< 40 min) method for detecting E. faecium in urine. The method uses a fluorescently labelled bacteriocin enterocin K1 (FITC-EntK1) that binds specifically to E. faecium and is then detected using a conventional flow cytometer. Using this detection assay, urine containing E. faecium was identified by an increase in the fluorescent signals by 25-73-fold (median fluorescence intensity) compared to control samples containing Escherichia coli or Staphylococcus aureus. The method presented in this work is a proof of concept showing the potential of bacteriocins to act as specific probes for the detection of specific bacteria, such as pathogens, in biological samples.

Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases

Proteomics is playing an increasingly important role in identifying pathogens, emerging and re-emerging infectious agents, understanding pathogenesis, and diagnosis of diseases. Recently, more advanced and sophisticated proteomics technologies have transformed disease diagnostics and vaccines development. The detection of pathogens is made possible by more accurate and time-constrained technologies, resulting in an early diagnosis. More detailed and comprehensive information regarding the proteome of any noxious agent is made possible by combining mass spectrometry with various gel-based or short-gun proteomics approaches recently. MALDI-ToF has been proved quite useful in identifying and distinguishing bacterial pathogens. Other quantitative approaches are doing their best to investigate bacterial virulent factors, diagnostic markers and vaccine candidates. Proteomics is also helping in the identification of secreted proteins and their virulence-related functions. This review aims to highlight the role of cutting-edge proteomics approaches in better understanding the functional genomics of pathogens. This also underlines the limitations of proteomics in bacterial secretome research.

Update on Current Microbiological Techniques for Pathogen Identification in Infectious Endophthalmitis

Infectious endophthalmitis is a vision-threatening medical emergency that requires prompt clinical diagnosis and the initiation of treatment. However, achieving precision in endophthalmitis management remains challenging. In this review, we provide an updated overview of recent studies that are representative of the current trends in clinical microbiological techniques for infectious endophthalmitis.

Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study

This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.

Rapid identification of bacterial mixtures in urine using MALDI-TOF MS-based algorithm profiling coupled with magnetic enrichment

Urinary tract infections (UTIs) are a severe public health problem caused by mono- or poly-bacteria. Culture-based methods are routinely used for the diagnosis of UTIs in clinical practice, but those are time consuming. Rapid and unambiguous identification of each pathogen in UTIs can have a significant impact on timely diagnoses and precise treatment. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an alternative method for the identification of pathogens in clinical laboratories. However, a certain number of pure bacteria are required for MALDI-TOF MS analysis. Here, we explored a strategy combining magnetic enrichment and MALDI-TOF MS for the rapid identification of pathogenic bacterial mixtures in urine. Fragment crystallizable mannose-binding lectin-modified Fe₃O₄ (Fc-MBL@Fe₃O₄) was used for rapid enrichment and the individual-peak-based similarity model as the analytical tool. Within 30 min, a mixture of the four most prevalent UTI-causing bacteria, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa, was successfully identified using this method. This rapid MALDI-TOF MS-based strategy has potential applications in the clinical identification of UTI pathogens.

LAMP assays for the simple and rapid detection of clinically important urinary pathogens including the detection of resistance to 3rd generation cephalosporins

Background

Timely and accurate identification of uropathogens and determination of their antimicrobial susceptibility is paramount to the management of urinary tract infections (UTIs). The main objective of this study was to develop an assay using LAMP (Loop mediated isothermal amplification) technology for simple, rapid and sensitive detection of the most common bacteria responsible for UTIs, as well as for the detection of the most prevalent genes (encoding cefotaximases from CTX-M group 1) responsible for resistance to 3rd generation of cephalosporins.

Method

We designed primers targeting Proteus mirabilis, while those targeting Escherichia coli, Klebsiella pneumoniae and Enterococcus faecalis and the CTX-M group 1 resistance gene were benchmarked from previous studies. The amplification reaction was carried out in a warm water bath for 60 min at 63 ± 0.5 °C. The amplicons were revealed by staining with Sybr Green I. Specificity and sensitivity were determined using reference DNA extracts spiked in sterile urine samples. The analytical performance of the assays was evaluated directly on pellets of urine samples from patients suspected of UTI and compared with culture.

Results

We found a high specificity (100%) for LAMP assays targeting the selected bacteria (P. mirabilis, E. coli, K. pneumoniae, E. faecalis) and the CTX-M group 1 when using DNA extracts spiked in urine samples. The sensitivities of the assays were around 1.5 10³ Colony Forming Units (CFU) /mL corresponding to the cut-off value used to define bacteriuria or UTIs in patients with symptoms. Out of 161 urine samples tested, using culture as gold standard, we found a sensitivity of the LAMP techniques ranging from 96 to 100% and specificity from 95 to 100%.

Conclusion

We showed that the LAMP assays were simple and fast. The tests showed high sensitivity and specificity using a simple procedure for DNA extraction. In addition, the assays could be performed without the need of an expensive device such as a thermal cycler. These LAMP assays could be useful as an alternative or a complementary tool to culture reducing the time to diagnosis and guiding for more effective treatment of UTIs but also as a powerful diagnostic tool in resource-limited countries where culture is not available in primary health care structures.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06720-5.

A Rapid Antimicrobial Susceptibility Test for Klebsiella pneumoniae Using a Broth Micro-Dilution Combined with MALDI TOF MS

Background

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a novel method that can be used to identify pathogens and has potential applications in the detection of drug-resistant bacteria.

Purpose

To evaluate the ability of a MALDI-TOF MS-based broth micro-dilution method in detecting the minimum inhibitory concentration (MIC) values of Klebsiella pneumoniae to ceftriaxone and imipenem.

Materials and Methods

Sixty strains of K. pneumoniae with different levels of resistance to carbapenems and cephalosporins were randomly collected. The 0.5 McFarland (Mc) concentration of the bacterial suspension was inoculated in cation-adjusted Mueller-Hinton broth (CAMHB) with a final cell turbidity of 5×10⁵ CFU/mL. The broth was incubated with serial concentrations of antibiotics. After centrifuging the bacterial suspensions, the lysed cells were analyzed by MALDI-TOF MS to identify the growth-promoting or inhibitory effects on K. pneumoniae. The molecular mechanisms of resistance were investigated by PCR and DNA sequencing analysis.

Results

The expression of known resistance genes (blaKPC, blaFOX, blaDHA, blaCTX-M and blaTEM) was detected in the 30 carbapenems-resistant strains. The agreement between the MIC values derived from the MALDI-TOF MS analysis and from the broth micro-dilution method was 61.7% for ceftriaxone and 71.7% for imipenem. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance to ceftriaxone and imipenem, the 60 isolates were accurately classified as resistant or susceptible isolates with 100% sensitivity and 100% specificity.

Conclusion

The transmission and infection of multidrug-resistant bacteria could be better managed and treated with the rapid identification of strains and antimicrobial susceptibility. A MALDI-TOF MS-based susceptibility test could be used to identify resistance of K. pneumoniae within a short time-frame. This approach could potentially be used as a supplementary antimicrobial susceptibility test that could be investigated on more bacterial species combined with different antibiotics.

Accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for direct bacterial identification from culture-positive urine samples

Background

Urinary tract infection (UTI) is one of the most frequent reasons for antimicrobial therapy. In typical clinical setting, 18–48 h is needed to identify pathogens by urine culture. A rapid method for pathogenic UTI diagnosis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed in recent years.

Methods

This meta-analysis systematically evaluated the accuracy of MALDI-TOF MS for direct identification of bacteria from culture-positive urine samples. We queried the electronic database of Medline and Web of Science to obtain relevant articles.

Results

Nineteen articles involving 4,579 isolates were included after final selection in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS was 0.82 with 95% confidence interval of 0.79 to 0.86 at the species level. For Gram-negative isolates, the correct identification performance of the species ranged from 0.54 to 0.98, with a cumulative rate of 0.87 (95% CI: 0.83 to 0.91). For Gram-positive isolates, the correct identification rate ranged from 0.32 to 0.80, with a cumulative rate of 0.59 (95% CI: 0.49 to 0.68).

Conclusions

MALDI-TOF MS provides a reliable direct identification of bacteria, particularly in cases of Gram-negative isolates, from clinical urine specimens. Nevertheless, the identification accuracy of this method is moderate for Gram-positive bacteria.

Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants

Urinary tract infections are leading causes of hospital admissions. Accurate and timely diagnosis is important due to increasing morbidity and mortality from antimicrobial resistance. We evaluated a polymerase chain reaction test (Acuitas AMR Gene Panel with the Acuitas Lighthouse Software) for detection of 5 common uropathogens (Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Enterococcus faecalis) and antibiotic resistance genes directly from urine for prediction of phenotypic resistance. Overall percent agreement was 97% for semiquantitative detection of uropathogens versus urine culture using a cut-off of 10⁴ colony forming units per mL urine. Overall accuracy was 91% to 93% for genotypic prediction of common antibiotic resistance harbored by E. coli, K. pneumoniae, and P. mirabilis.

Rapid and sensitive identification of uropathogenic Escherichia coli using a surface-enhanced-Raman-scattering-based biochip

Rapid, selective and sensitive sensing of bacteria remains challenging. We report on a highly sensitive and reproducible surface-enhanced Raman spectroscopy (SERS)-based sensing approach for the detection of uropathogenic Escherichia coli (E. coli) bacteria in urine. The assay is based on the specific capture of the bacteria followed by interaction with cetyltrimethylammonium bromide (CTAB)-stabilised gold nanorods (Au NRS) as SERS markers. High sensitivity up to 10 CFU mL^-1 is achieved by optimizing the capture interface based on hydrogenated amorphous silicon a-Si:H thin films. The integration of CH₃O-PEG750 onto a-Si:H gives the sensing interface an efficient anti-fouling character, while covalent linkage of antibodies directed against the major type-1 fimbrial pilin FimA of the human pathogen E. coli results in the specific trapping of fimbriated E. coli onto the SERS substrate and their spectral fingerprint identification.

Current Status of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology

Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications.

Rapid identification of uropathogens by combining Alfred 60 system with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry technology

Rapid identification of uropathogens is needed to determine appropriate antimicrobial therapy. This study evaluated performance of the Alfred 60 system combined with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) technology for rapid identification of uropathogens. The Alfred 60 system was used to screen urine cultures, followed by identifying the microbial pathogen in positive cultures using MALDI-TOF MS. The Alfred 60 detected positive cultures by measuring the turbidity of urine samples, which were transferred automatically to vials containing liquid medium and incubated for 3.5 h at 35 °C in the Alfred 60 system. Vials that showed growth were removed and centrifuged. The pellet was subjected to MALDI-TOF MS identification. In parallel, positive urine samples were inoculated onto agar plates for identification by conventional culture. The time required to detect positive urine cultures with Alfred 60 and identify the uropathogens with MALDI-TOF MS ranged from 15 min to 3.5 h. Among 146 positive urine samples tested, conventional cultures showed three culture groups: group 1 included 101 samples with growth of a single type of microorganism; group 2 included 34 samples with 2 types of microorganisms; and group 3 included 11 samples with ≥ 3 types of microorganisms. Direct identification by MALDI-TOF MS was concordant with 95% of the samples in group 1, 100% of the principal microorganism in group 2, but could not identify microorganisms in group 3. This combination of methods provides rapid, reliable microbial identification for most positive urine cultures.

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.

Rapid diagnosis of periprosthetic joint infection from synovial fluid in blood culture bottles by direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Background

The aim of this prospective study was to use direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to rapidly diagnose periprosthetic joint infections (PJIs).

Method

Synovial fluid was taken from 77 patients (80 joints, 41 hips and 39 knees) who met the International Consensus Meeting criteria for PJI, and inoculated into blood culture bottles (BCBs) and onto conventional swabs. Positive blood cultures were analyzed using either direct or routine MALDI-TOF MS. Pathogen identification and the time to identification was recorded. Differences between groups were analyzed using the Kruskal-Wallis test and Bonferroni's post-hoc test.

Results

Direct and routine MALDI-TOF MS both detected 64 positive results (80%), compared to 47 (59%) by conventional swabs (p = 0.002). Direct MALDI-TOF MS identified 85.3% of the gram-positive organisms and 92.3% of the gram-negative organisms. No fungi were identified by direct MALDI-TOF MS. In 17 BCBs that were flagged positive, identification by direct MALDI-TOF MS failed. Among the positive results in the direct MALDI-TOF MS group, Staphylococcus aureus accounted for 47%, followed by Staphylococcus epidermidis (17%), Escherichia coli (9%) and Klebsiella pneumoniae (9%). The median time to microorganism identification was significantly shorter with direct MALDI-TOF MS (12.7 h, IQR: 8.9–19.6 h) than with routine MALDI-TOF MS (39.5 h, IQR: 22.8–46.0 h) or swabs (44.4 h, IQR: 27.2–72.6 h) (p < 0.0001). In pairwise comparisons, there were significant differences in the time of microorganism identification between direct MALDI-TOF MS and routine MALDI-TOF MS (p < 0.0001) or swab culture (p < 0.0001). There was no significant difference between routine MALDI-TOF MS and swab culture (p = 0.0268).

Conclusion

Compared with current laboratory practice, direct MALDI-TOF MS shortened the time to microorganism identification and had superior results compared to conventional swabs, except for fungi. Further studies should investigate whether the earlier administration of appropriate antimicrobial agents can improve the treatment outcomes of PJIs.

Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry

Background

Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample.

Methods

In total, 16 urine samples having more than 10⁵ CFU/mL were collected from clinical outpatients. These samples were analysed using standard urine culture methods, followed by 16S rRNA gene sequencing serving as control and here described culture-independent MALDI-TOF/TOF MS method being tested.

Results

Here we present advantages and disadvantages of bottom-up proteomics, using MALDI-TOF/TOF tandem mass spectrometry, for culture-independent identification of uropathogens (e.g. directly from urine samples). The direct approach provided reliable identification of bacteria at the genus level in monobacterial samples. Taxonomic identifications obtained by proteomics were compared both to standard urine culture test used in clinics and genomic test based on 16S rRNA sequencing.

Conclusions

Our findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in order to identify pathogens in polymicrobial urine samples.

Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines

Background

Increasing resistance drives empirical use of less potent and previously reserved antibiotics, including for urinary tract infections (UTIs). Molecular profiling, without culture, might better guide early therapy.

Objectives

To explore the potential of AusDiagnostics multiplex tandem (MT) PCR UTI assays.

Methods

Two MT-PCR assays were developed successively, seeking 8 or 16 resistance genes. Amplification was tracked in real time, with melting temperatures used to confirm product identity. Assays were variously performed on: (i) extracted DNA; (ii) cultured bacteria; (iii) urine spiked with reference strains; and (iv) bacteria harvested from clinical urines. Results were compared with those from sequencing, real-time SybrGreen PCR or phenotypic susceptibility.

Results

Performance was similar irrespective of whether DNA, cultures or urines were used, with >90% sensitivity and specificity with respect to common β-lactamases, dfr genes and aminoglycoside resistance determinants except aadA1/A2/A3, for which carriage correlated poorly with streptomycin resistance. Fluoroquinolone-susceptible and -resistant Escherichia coli (but not other species) were distinguished by the melting temperatures of their gyrA PCR products. The time from urine to results was <3 h.

Conclusions

The MT-PCR assays rapidly identified resistance genes from Gram-negative bacteria in urines as well as from cultivated bacteria. Used directly on urines, this assay has the potential to guide early therapy.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry combined with UF-5000i urine flow cytometry to directly identify pathogens in clinical urine specimens within 1 hour

Background

Urinary tract infection (UTI) is one of the most common hospital-associated infectious. The traditional laboratory diagnosis method for UTI requires at least 24 hours, and it cannot provide the etiology basis for the clinic in time. The aim of our study is to develop a new method for pathogenic diagnosis of UTI by combining matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and UF-5000i from urine samples directly within 1 hour.

Methods

A total of 1,503 urine samples were collected from patients suggesting symptoms of UTI from August 2018 to January 2019. Each of these samples was divided into three aliquots. The first aliquot was used for conventional cleaning mid-stream urine culture; the second one for UF-5000i analysis to screen out the bacterial counts, which were more than 1×10⁵ bacteria/mL. The third one was processed to bacterial purification and directly identified by the MALDI-TOF MS.

Results

In our study, 296 of 1,503 urine specimens were screened out by UF-5000i (bacterial pellets counts ≥10⁵/mL). Compared the conventional culture-dependent method, the results of our methods were consistent in 249 of 263 (94.7%) cases, and they were both single-microorganism. Among 249 credible results, species-level identification (score ≥2.0) was contained 233 (233/249. 93.6%), 16 (16/249, 6.4%) samples scored between 1.7 and 1.99, and 14 (14/249, 5.6%) samples scored <1.7 or no peaks found. When there were 2 different kinds of bacteria in the urine, the result of MALDI-TOF MS was unreliable.

Conclusions

MALDI-TOF MS combined with UF-5000i to identify the pathogenic bacteria in urine directly is a novel and reliable method and saves at least 23 hours relative to the current routine conventional method. Thus its rapid and accurate detection may provide the basis of etiology for clinical diagnosis of UTIs efficiently.

Diagnostic Accuracy of MALDI-TOF Mass Spectrometry for the Direct Identification of Clinical Pathogens from Urine

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.

Uracil-DNA-glycosylase-assisted loop-mediated isothermal amplification for detection of bacteria from urine samples with reduced contamination

Urine specimens are detected by conventional culture method and colonies with more than 10⁴ are identified by MALDI-TOF MS. Meanwhile, we analyze urine samples using FTA cards for simple DNA extraction and UDG-assisted LAMP.

Rapid pathogen identification and antimicrobial susceptibility testing in in vitro endophthalmitis with matrix assisted laser desorption-ionization Time-of-Flight Mass Spectrometry and VITEK 2 without prior culture

PURPOSE

Prompt clinical diagnosis and initiation of treatment are critical in the management of infectious endophthalmitis. Current methods used to identify causative agents of infectious endophthalmitis are mostly inefficient, owing to suboptimal sensitivity, length, and cost. Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) can be used to rapidly identity pathogens without a need for culture. Similarly, automated antimicrobial susceptibility test systems (AST, VITEK 2) provide accurate antimicrobial susceptibility profiles. In this proof-of-concept study, we apply these technologies for the direct identification and characterization of pathogens in vitreous samples, without culture, as an in vitro model of infectious endophthalmitis.

METHODS

Vitreous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of Staphylococcus aureus (S. aureus) and incubated at 37°C. Vitreous endophthalmitis samples were centrifuged and pellets were directly analyzed with MALDI-TOF MS and VITEK 2 without prior culture. S. aureus colonies that were conventionally grown on culture medium were used as control samples. Time-to-identification, minimum concentration of bacteria required for identification, and accuracy of results compared to standard methods were determined.

RESULTS

MALDI-TOF MS achieved accurate pathogen identification from direct analysis of intraocular samples with confidence values of up to 99.9%. Time from sample processing to pathogen identification was <30 minutes. The minimum number of bacteria needed for positive identification was 7.889x106 colony forming units (cfu/μl). Direct analysis of intraocular samples with VITEK 2 gave AST profiles that were up to 94.4% identical to the positive control S. aureus analyzed per standard protocol.

CONCLUSION

Our findings demonstrate that the direct analysis of vitreous samples with MALDI-TOF MS and VITEK 2 without prior culture could serve as new, improved methods for rapid, accurate pathogen identification and targeted treatment design in infectious endophthalmitis. In vivo models and standardized comparisons against other microbiological methods are needed to determine the value of direct analysis of intraocular samples from infectious endophthalmitis with MALDI-TOF MS and VITEK 2.

Identification performance of MALDI-ToF-MS upon mono- and bi-microbial cultures is cell number and culture proportion dependent

Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 10⁸ and 1.10 × 10¹⁰ viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper^® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.

Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults

OBJECTIVES

Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections.

METHODS

We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes.

RESULTS

mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79-92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68-57.24%) for culture and 57.53% (95% CI: 45.43-68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05) CONCLUSIONS: mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.

Evaluation of flow cytometry for the detection of bacteria in biological fluids

OBJECTIVES

Conventional microbiological procedures for the isolation of bacteria from biological fluids consist of culture on solid media and enrichment broth. However, these methods can delay the microbiological identification for up to 4 days. The aim of this study was to evaluate the analytical performance of Sysmex UF500i (Sysmex, Kobe, Japan) as a screening method for the detection of bacteria in different biological fluids in comparison with direct Gram staining and the conventional culture on solid media and enrichment broth.

METHODS

A total of 479 biological fluid samples were included in the study (180 ascitic, 131 amniotic, 56 synovial, 40 cerebrospinal, 36 pleural, 24 peritoneal, 9 bile and 3 pericardial fluids). All samples were processed by conventional culture methods and analyzed by flow cytometry. Direct Gram staining was performed in 339 samples. The amount of growth on culture was recorded for positive samples.

RESULTS

Bacterial and white blood cell count by flow cytometry was significantly higher among culture positive samples and samples with a positive direct Gram stain compared to culture negative samples. Bacterial count directly correlated with the amount of growth on culture (Kruskall-Wallis H χ2(3) = 11.577, p = 0.009). The best specificity (95%) for bacterial count to predict culture positivity was achieved applying a cut-off value of 240 bacteria/μL.

CONCLUSIONS

Bacterial and white blood cell counts obtained with flow cytometry correlate with culture results in biological fluids. Bacterial count can be used as a complementary method along with the direct Gram stain to promptly detect positive samples and perform other diagnostic techniques in order to accelerate the bacterial detection and identification.

16S rRNA gene profiling of bacterial communities mediating production of tsetse attractive phenols in mammalian urine

Several types of odours are involved in the location of host animals by tsetse (Diptera: Glossinidae), a vector of animal African trypanosomiasis. Host animals' ageing urine has been shown to be the source of a phenolic blend attractive to the tsetse. Nevertheless, limited research has been performed on the microbial communities' role in the production of phenols. This study aimed at profiling bacterial communities mediating the production of tsetse attractive phenols in mammalian urine. Urine samples were collected from African buffalo (Syncerus caffer), cattle (Bos taurus) and eland (Taurotragus oryx) at Kongoni Game Valley Ranch and Kenyatta University in Kenya. Urine samples, of each animal species, were pooled and left open to age in ambient conditions. Bacteriological and phenols analyses were then carried out, at 4 days ageing intervals, for 24 days. Phenols analysis revealed nine volatile phenols: 4-cresol, ortho-cresol, 3-cresol, phenol, 3-ethylphenol, 3-propylphenol, 2-methyloxyphenol, 4-ethylphenol and 4-propylphenol. Eight out of 19 bacterial isolates from the ageing urine revealed the potential to mediate production of phenols. 16S rRNA gene characterisation of the isolates closely resembled Enterococcus faecalis KUB3006, Psychrobacter alimentarius PAMC 27887, Streptococcus agalactiae 2603V, Morganella morganii sub.sp. morganii KT, Micrococcus luteus NCTC2665, Planococcus massiliensis strain ES2, Ochrobactrum pituitosum AA2 and Enterococcus faecalis OGIRF. This study established that some of the phenols emitted from mammalian urine, which influence the tsetse's host-seeking behaviour, are well characterised by certain bacteria. These results may allow the development of biotechnological models in vector control that combines the use of these bacteria in the controlled release of semiochemicals.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress

This article summarizes recent advances in the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to new areas of infectious diseases diagnostics. We discuss progress toward routine identification of mycobacteria and filamentous fungi and direct identification of pathogens from clinical specimens. Of greatest interest is the use of MALDI-TOF MS for identifying organisms from positive blood cultures and from clinical specimens such as urine. Last, We highlight some exciting new possibilities for MALDI-TOF MS phenotypic susceptibility testing for bacteria and yeast.

Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol

Usually, 18–48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18–24 h. Rapid identification and AST of the pathogens 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 AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6–24 h for AST; noteworthily, only 6–8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.

MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review

BACKGROUND

Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a widely used technique for the rapid and accurate identification of bacteria, mycobacteria and certain fungal pathogens in the clinical microbiology laboratory. Thus far, only few attempts have been made to apply the technique in clinical parasitology, particularly regarding helminth identification.

METHODS

We systematically reviewed the scientific literature on studies pertaining to MALDI-TOF MS as a diagnostic technique for helminths (cestodes, nematodes and trematodes) of medical and veterinary importance. Readily available electronic databases (i.e. PubMed/MEDLINE, ScienceDirect, Cochrane Library, Web of Science and Google Scholar) were searched from inception to 10 October 2018, without restriction on year of publication or language. The titles and abstracts of studies were screened for eligibility by two independent reviewers. Relevant articles were read in full and included in the systematic review.

RESULTS

A total of 84 peer-reviewed articles were considered for the final analysis. Most papers reported on the application of MALDI-TOF for the study of Caenorhabditis elegans, and the technique was primarily used for identification of specific proteins rather than entire pathogens. Since 2015, a small number of studies documented the successful use of MALDI-TOF MS for species-specific identification of nematodes of human and veterinary importance, such as Trichinella spp. and Dirofilaria spp. However, the quality of available data and the number of examined helminth samples was low.

CONCLUSIONS

Data on the use of MALDI-TOF MS for the diagnosis of helminths are scarce, but recent evidence suggests a potential role for a reliable identification of nematodes. Future research should explore the diagnostic accuracy of MALDI-TOF MS for identification of (i) adult helminths, larvae and eggs shed in faecal samples; and (ii) helminth-related proteins that are detectable in serum or body fluids of infected individuals.

Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization-Time of Flight Spectrum Database

Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae, Staphylococcus aureus, Staphylococcus saprophyticus, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra.

[Economic evaluation of the Alfred 60/AST device implantation for bacterial growth detection with automatic sewing machine]

OBJECTIVE

It is becoming increasingly necessary to automatize screening of urine samples to culture at Microbiology laboratories. Our objective was to estimate the budget threshold from which the Alfred 60/AST device would be profitable for our hospital.

METHODS

Cost minimization study by decision trees, carried out in a General Hospital. The cost of traditional urine culture and urine processing using Alfred-60/AST were compared. Traditional processing involves the culture of all urine specimens received onto blood and MacConkey agar, and identification of every microorganism isolated by Vitek-2 system. The autoanalyzer would only inoculate the positive urines onto a chromogenic media, directly identifying the Escherichia coli isolates.

RESULTS

The variables with the greatest economic impact in the model were the probability of obtaining a positive culture, the prevalence of E. coli in the urine cultures and the cost per sample using Alfred-60/AST. The multivariate sensitivity analysis showed that the model was solid. The bivariate sensitivity analysis showed that the model is suceptible to cost modification, mainly of the automatic device. At a threshold value of 1.40 euros/determination, the automatic processing would decrease the annual costs in 2,879 euros.

CONCLUSIONS

The introduction of the Alfred-60/AST device in our laboratory at 1.40 euros/determination would reduce urine processing workload, saving time and costs.

A multicentre study investigating parameters which influence direct bacterial identification from urine

Rapid diagnosis is one of the best ways to improve patient management and prognosis as well as to combat the development of bacterial resistance. The aim of this study was to study parameters that impact the achievement of reliable identification using a combination of flow cytometry and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF-MS).The study was carried out in nine hospitals in Spain and included 1,050 urine samples with bacterial counts of 5x10⁶ bacteria/ml. MALDI-ToF-MS-based identification was performed according to a previously described protocol. Valid identification by direct MALDI-ToF-MS was obtained in 72.8% of samples, in 80.3% of samples found to be positive by culture, 32.2% of contaminated samples, and 19.7% of negative samples. Among the positives samples with a valid identification the concordance at the species level was 97.2%. The parameters related to success of direct identification were: high bacterial count, the presence of Escherichia coli as a pathogen and rod-bacteria morphology provided by flow cytometry. The parameters related to failure were a high epithelial cell (EC) count, a high white blood cell (WBC) count and urine samples obtained from in-patients. In summary, this multicentre study confirms previously published data on the usefulness and accuracy of direct MALDI-ToF-MS-based identification of bacteria from urine samples. It seems important to evaluate not only the bacterial count, but also other parameters, such as EC and WBC counts, bacterial species and morphology, and the health care setting, to decide whether the sample is suitable for direct identification.

Progress in Automated Urinalysis

New technological advances have paved the way for significant progress in automated urinalysis. Quantitative reading of urinary test strips using reflectometry has become possible, while complementary metal oxide semiconductor (CMOS) technology has enhanced analytical sensitivity and shown promise in microalbuminuria testing. Microscopy-based urine particle analysis has greatly progressed over the past decades, enabling high throughput in clinical laboratories. Urinary flow cytometry is an alternative for automated microscopy, and more thorough analysis of flow cytometric data has enabled rapid differentiation of urinary microorganisms. Integration of dilution parameters (e.g., creatinine, specific gravity, and conductivity) in urine test strip readers and urine particle flow cytometers enables correction for urinary dilution, which improves result interpretation. Automated urinalysis can be used for urinary tract screening and for diagnosing and monitoring a broad variety of nephrological and urological conditions; newer applications show promising results for early detection of urothelial cancer. Concomitantly, the introduction of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has enabled fast identification of urinary pathogens. Automation and workflow simplification have led to mechanical integration of test strip readers and particle analysis in urinalysis. As the information obtained by urinalysis is complex, the introduction of expert systems may further reduce analytical errors and improve the quality of sediment and test strip analysis. With the introduction of laboratory-on-a-chip approaches and the use of microfluidics, new affordable applications for quantitative urinalysis and readout on cell phones may become available. In this review, we present the main recent developments in automated urinalysis and future perspectives.

Diagnosing Emerging Fungal Threats: A One Health Perspective

Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.

Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide

Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.

An improved in-house lysis-filtration protocol for bacterial identification from positive blood culture bottles with high identification rates by MALDI-TOF MS

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is now a well-established method for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial proteins are a prerequisite for successful identification, and a variety of protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We developed a new, in-house lysis-filtration protocol and prospectively evaluated its performance compared to the Sepsityper kit. The in-house protocol consists of three simple steps: lysis by ammonium chloride, aspiration with a syringe fitted with a 0.45-μm membrane, and centrifugation to collect microbes. The novel protocol requires only 20 min. Performance of the in-house protocol was evaluated using a total of 117 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the in-house protocol or the commercial kit, and isolated cells were subjected to direct identification by mass spectrometry fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with score > 1.7 and > 2.0 obtained using the in-house protocol were 99.2% and 85.5%, respectively, whereas those obtained using the Sepsityper Kit were 85.4% and 61.5%, respectively. For Gram-positive cases, the in-house protocol yielded scores >1.7 and > 2.0 at 98.5% and 76.1%, respectively, whereas the commercial kit yielded these scores at 76.1% and 43.3%, respectively. Although these are preliminary results, these values suggest that this easy lysis-filtration protocol deserves assessment in a larger-scale test.

Methods for the detection and identification of pathogenic bacteria: past, present, and future

In order to retard the rate of development of antibacterial resistance, the causative agent must be identified as rapidly as possible, so that directed patient treatment and/or contact precautions can be initiated. This review highlights the challenges associated with the detection and identification of pathogenic bacteria, by providing an introduction to the techniques currently used, as well as newer techniques that are in development. Focusing on the chemical basis for these techniques, the review also provides a comparison of their advantages and disadvantages.

In vitro detection of bacterial contamination in platelet concentrates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a preliminary study

PURPOSE

Platelet concentrates are at risk of transfusion-related sepsis. The microbial detection methods currently available have reached their limits, as they do not completely prevent transfusion-related bacterial contamination.The aim of this study was to develop a new strategy to detect the risk of platelet transfusion-related bacterial contamination using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

METHODOLOGY

In vitro, platelet concentrates were seeded with known concentrations of bacterial strains. Protein mass profiles were acquired by using a Microflex MALDI-TOF instrument. Dedicated 'Platelet' software was used as a spectrum subtraction tool to reveal specific peaks caused by the presence of pathogens in samples.

RESULTS

The MALDI-TOF spectra of platelets were characterized and the reproducibility over time, regardless of the blood donor, was demonstrated with a positive predictive value of 100 %. In addition, the negative predictive value of the total number of specific peaks to predict contamination was 100 %.

CONCLUSION

Detecting bacteria in platelet concentrates using the MALDI-TOF approach and analysing spectra with the Platelet software present the advantage of combining the precocity of results and sufficient sensitivity (10 c.f.u. ml^-1). Further research will be conducted to compare this novel method with the current conventional method in order to validate our results, the objective being to reduce the risk of platelet transfusion-related bacterial contamination.

Improved bacterial identification directly from urine samples with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

BACKGROUND

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) contributes to rapid identification of pathogens in the clinic but has not yet performed especially well for Gram-positive cocci (GPC) causing complicated urinary tract infection (UTI). The goal of this study was to investigate the possible clinical use of MALDI-TOF MS as a rapid method for bacterial identification directly from urine in complicated UTI.

METHODS

MALDI-TOF MS was applied to urine samples gathered from 142 suspected complicated UTI patients in 2015-2017. We modified the standard procedure (Method 1) for sample preparation by adding an initial 10 minutes of ultrasonication followed by centrifugation at 500 g for 1 minutes to remove debris such as epithelial cells and leukocytes from the urine (Method 2).

RESULTS

In 133 urine culture-positive bacteria, the rate of corresponded with urine culture in GPC by MALDI-TOF MS in urine with standard sample preparation (Method 1) was 16.7%, but the modified sample preparation (Method 2) significantly improved that rate to 52.2% (P=.045). Method 2 also improved the identification accuracy for Gram-negative rods (GNR) from 77.1% to 94.2% (P=.022). The modified Method 2 significantly improved the average MALDI score from 1.408±0.153 to 2.166±0.045 (P=.000) for GPC and slightly improved the score from 2.107±0.061 to 2.164±0.037 for GNR.

CONCLUSION

The modified sample preparation for MALDI-TOF MS can improve identification accuracy for complicated UTI causative bacteria. This simple modification offers a rapid and accurate routine diagnosis for UTI, and may possibly be a substitute for urine cultures.

NaOH-HCl neutralized urine preparation for direct testing of uropathogens by Bruker MS

BACKGROUND

We evaluated the analytical performance of a NaOH-HCl neutralization protocol for identifying uropathogens directly from urine samples by a Bruker MS system (Bruker Daltonics, German) and sought to establish a protocol for integrating the method with conventional screening.

METHODS

Among all urine samples requested for Gram staining, UF-1000i, and urine cultures by physicians, we selected samples that were positive by both Gram staining and UF-1000i testing. Urine was prepared by neutralization using 0.01M NaOH-HCl, and the samples were processed by Bruker MS. For the low detection limit, one strain each of Escherichia coli and Enterococcus faecium was inoculated in sterile deionized water and sterile urine specimens at sequential dilutions.

RESULTS

In a total of 1270 urine samples, 125 samples (9.8%) were positive by both Gram staining and UF-1000i. Of 94 samples showing a single morphotype on agar plates, 82 samples had colony counts ≥10⁵  CFU/mL and most uropathogens (95.1%, 78 of 82) had UF-1000i counts ≥10⁶  bacteria/mL. Among them, Bruker MS correctly identified 86.6% (71/82) of all isolates, 89.2% (66/74) of Gram-negative bacteria (GNB), and 62.5% (5/8) of Gram-positive cocci (GPC) with higher average scores for GPC (mean score 2.013) and GNB (mean score 2.110).

CONCLUSIONS

Bruker MS with urine preparation by NaOH-HCl neutralization provides a simple, cost-effective, and accurate method for identifying uropathogens directly from urine. Using Bruker MS when single morphotype Gram staining and the UF-1000i count as ≥10⁶  bacteria/mL may improve the efficiency of bacterial identification in routine practice.

New and developing diagnostic technologies for urinary tract infections

Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.