Diagnostic Microbiology Research Articles

New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa

Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.

Recent advances in microbiological and molecular biological detection techniques of tuberculous meningitis.

Tuberculous meningitis (TBM) is the most common type of central nervous system tuberculosis (TB) and has the highest mortality and disability rate. Early diagnosis is key to improving the prognosis and survival rate of patients. However, laboratory diagnosis of TBM is often difficult due to its paucibacillary nature and sub optimal sensitivity of conventional microbiology and molecular tools which often fails to detect the pathogen. The gold standard for TBM diagnosis is the presence of MTB in the CSF. The recognised methods for the identification of MTB are acid-fast bacilli (AFB) detected under CSF smear microscopy, MTB cultured in CSF, and MTB detected by polymerase chain reaction (PCR). Currently, many studies consider that all diagnostic techniques for TBM are not perfect, and no single technique is considered simple, fast, cheap, and efficient. A definite diagnosis of TBM is still difficult in current clinical practice. In this review, we summarise the current state of microbiological and molecular biological diagnostics for TBM, the latest advances in research, and discuss the advantages of these techniques, as well as the issues and challenges faced in terms of diagnostic effectiveness, laboratory infrastructure, testing costs, and clinical expertise, for clinicians to select appropriate testing methods.

The quality of microbiological diagnostics in Poland based onthe results of external laboratory quality control programmes

<br><b>Introduction:</b> The article describes the results of the 29th edition of the Polish NationalExternal Quality Assessment Scheme in Microbiology POLMICRO created by the Centre ofQuality Control in Microbiology (CQCM).</br><br><b>Aim:</b> The aim of the scheme is the evaluation of the reliability of the results of microbiologicaltests performed by Polish medical laboratories, which includes e.g. identification andassessment of antimicrobial susceptibility of bacterial etiological agents of infections,together with the detection of antimicrobial resistance mechanisms.</br><br><b>Materials and methods:</b> The assessment of external quality control programmes organised byCQCM is based on the analysis of the results of participants of the POLMICRO, POLMICRO/MIKOLOGIA and POLMICRO/SSE programmes in a full annual cycle.</br><br><b>Results:</b> In 2022, 96.00% of POLMICRO participants, as well as 99.22% of laboratories participatingin POLMICRO/SSE and all participants of POLMICRO/MIKOLOGIA, obtained positiveresults.</br><br><b>Conclusions:</b> The results of external quality control programmes conducted by CQCM showthat medical laboratories in Poland have been maintaining a high level of microbiologicaldiagnostics.</br>

Majocchi's granuloma—A multicenter retrospective cohort study

Majocchi's granuloma (MG) is an uncommon deep fungal folliculitis predominantly caused by dermatophytes. Given the rarity of this condition, available data regarding predisposing comorbidities/risk factors, clinical characteristics, offending microbiologic pathogens, diagnostics, pathologic findings, and treatment approaches has been inferred from historical cases. To review our institutional experience with MG. We retrospectively analyzed a multicenter cohort of adult patients diagnosed with MG between 1992 and 2022. We analyzed 147 patients with MG, 105 of which were male with a median age of 55.6years. Immunosuppressant and topical corticosteroid use were common prior to development of MG. Dermatologic lesions and their sites of involvement did not differ based on the immune status of patients. Trichophyton rubrum was the most common causative pathogen of MG, in addition to other dermatophytes. Treatment duration for all prescribed agents was median 31.5days with oral terbinafine being the most frequently utilized agent. Clinical resolution was achieved in 96.6% of cases. Retrospective, nonrandomized study. Although rare and clinically variable in presentation, diagnosis of MG often requires histopathologic confirmation to subsequently direct prolonged treatment with systemic antifungal therapy for mycological cure.

Microbiological Non-Culture-Based Methods for Diagnosing Invasive Pulmonary Aspergillosis in ICU Patients.

The diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care unit (ICU) patients is crucial since most clinical signs are not specific to invasive fungal infections. To detect an IPA, different criteria should be considered. Next to host factors and radiological signs, microbiological criteria should be fulfilled. For microbiological diagnostics, different methods are available. Next to the conventional culture-based approaches like staining and culture, non-culture-based methods can increase sensitivity and improve time-to-result. Besides fungal biomarkers, like galactomannan and (1→3)-β-D-glucan as nonspecific tools, molecular-based methods can also offer detection of resistance determinants. The detection of novel biomarkers or targets is promising. In this review, we evaluate and discuss the value of non-culture-based microbiological methods (galactomannan, (1→3)-β-D-glucan, Aspergillus PCR, new biomarker/targets) for diagnosing IPA in ICU patients.

A case for routine microbial diagnostics: Results from antimicrobial susceptibility testing in post-traumatic wound infections at a Ugandan tertiary care hospital.

The global spread of antimicrobial resistance (AMR) poses an increasing challenge for clinicians in Uganda, where microbiological diagnostics are not routinely available or accessible. The aim of this study was to determine pathogen prevalence and antibiotic resistance patterns in patients with wound infections following trauma at a national referral hospital in Kampala, Uganda. In addition, the suitability of currently used empirical treatment options in this setting was evaluated. This prospective, observational study analysed antimicrobial prescriptions, culture results and antimicrobial sensitivity testing (AST) of wound swabs and blood samples from patients with clinical signs of wound infections on the trauma ward. A total of 124 patients (n = 99, 79.8% male) with a median age of 30 years (IQR 23-39) were enrolled between October 2021 and January 2022. Wound infections were classified as nosocomial in 69% of the cases. Pathogens were isolated from 122 wound swabs, yielding 238 bacterial isolates. The most prevalent pathogens were gram-negative bacteria including Escherichia coli (n = 48, 20.2%) and Acinetobacter spp. (n = 43, 18.1%). Empiric treatment consisted of ceftriaxone and gentamicin which was administered to 67.2% (n = 78) and 62.1% (n = 72) of patients, respectively. High rates of antimicrobial resistance could be demonstrated across gram-negative and gram-positive species towards the most common empiric antibiotics. Following the AST results, over 95% (n = 111) of patients required a change of treatment. Our findings demonstrate that current empiric treatment for wound infections is missing its target in hospitalized patients in Kampala. To address the growing problem of AMR in Uganda, there is a pressing need to enhance diagnostic capacity and implement structured antimicrobial stewardship programs.

P14 Optimization of real-time sequencing for rapid detection of bacterial species and antimicrobial resistance in blood and urine infections

Abstract Objectives To optimize the process to obtain bacterial DNA directly from human urine and blood samples to produce high-quality genomic data using long-read Nanopore sequencer. Methods A total of 22 blood cultures and 24 urine samples positive for Escherichia coli or Klebsiella pneumoniae and corresponding isolates were collected from the microbiology diagnostics laboratory. DNA isolation optimization was performed testing three different sample volumes and seven DNA extraction kits. DNA concentration was quantified with Qubit fluorometer. Nanopore sequencing was performed on a MinION Mk1C device in R9.4.1 flow cells using the Rapid Barcoding Kit. Bacterial species and antimicrobial resistance (AMR) genes were determined with EPI2ME ARMA pipeline. Genomes were assembled with Flye, polished with Medaka and remaining human contigs removed with Krakentools. Bacterial isolates from the same samples were also sequenced using Illumina technology. Illumina and Nanopore assemblies were quality checked with Quast, Kraken was used to identify bacterial species, MLST for multilocus sequence typing and ABRicate with ResFinder database to detect AMR genes. Results A total of 72 DNA extractions from 24 urine and 22 blood samples with different kits were performed to find the optimal extraction protocol for each sample type. DNA from urine samples was isolated from 5 mL, while 1 mL was best for blood cultures. We found that the host depletion step prior to DNA extraction using MolYsis basic 5 Kit (VH-Bio) was essential. DNA from urine samples was extracted with GenElute Bacterial Genomic DNA Kit (Merck) and QIAamp Biostic bacteremia Kit (Qiagen) was best to allow successful bacterial genome sequencing for blood samples. Bacterial isolates from 11 urine and 1 blood sample (out of 54 sequenced) were successfully sequenced. In all 12 cases, the highest percentage of bacterial reads matched with the causative organism found during routine microbiology diagnostics (E. coli). A variety of clinically relevant AMR genes were detected, such as dfrA and bla CTX-M genes, which matched the phenotypic antimicrobial susceptibility testing results. Comparison of genomic assemblies obtained through Nanopore sequencing of 10 urine samples and Illumina sequencing of the corresponding clinical isolates showed a high degree of matching, validating Nanopore sequencing as an alternative option to support diagnosis and treatment choice. Conclusions We have successfully optimized the protocols to extract and sequence pathogenic bacterial DNA directly from blood and urine samples. Short-read sequencing confirmed results acquired by Nanopore sequencer, endorsing long-read sequencing in clinical settings to support timely diagnosis and treatment.

Causes of Death Among Infants and Children in the Child Health and Mortality Prevention Surveillance (CHAMPS) Network.

The number of deaths of children younger than 5 years has been steadily decreasing worldwide, from more than 17 million annual deaths in the 1970s to an estimated 5.3 million in 2019 (with 2.8 million deaths occurring in those aged 1-59 months [53% of all deaths in children aged <5 years]). More detailed characterization of childhood deaths could inform interventions to improve child survival. To describe causes of postneonatal child deaths across 7 mortality surveillance sentinel sites in Africa and Asia. The Child Health and Mortality Prevention Surveillance (CHAMPS) Network conducts childhood mortality surveillance in sub-Saharan Africa and South Asia using innovative postmortem minimally invasive tissue sampling (MITS). In this cross-sectional study, MITS was conducted in deceased children aged 1 to 59 months at 7 sites in sub-Saharan Africa and South Asia from December 3, 2016, to December 3, 2020. Data analysis was conducted between October and November 2021. The expert panel attributed underlying, intermediate, and immediate conditions in the chain of events leading to death, based on histopathologic analysis, microbiological diagnostics, clinical data, and verbal autopsies. In this study, MITS was performed in 632 deceased children (mean [SD] age at death, 1.3 [0.3] years; 342 [54.1%] male). The 6 most common underlying causes of death were malnutrition (104 [16.5%]), HIV (75 [11.9%]), malaria (71 [11.2%]), congenital birth defects (64 [10.1%]), lower respiratory tract infections (LRTIs; 53 [8.4%]), and diarrheal diseases (46 [7.2%]). When considering immediate causes only, sepsis (191 [36.7%]) and LRTI (129 [24.8%]) were the 2 dominant causes. An infection was present in the causal chain in 549 of 632 deaths (86.9%); pathogens most frequently contributing to infectious deaths included Klebsiella pneumoniae (155 of 549 infectious deaths [28.2%]; 127 [81.9%] considered nosocomial), Plasmodium falciparum (122 of 549 [22.2%]), and Streptococcus pneumoniae (109 of 549 [19.9%]). Other organisms, such as cytomegalovirus (57 [10.4%]) and Acinetobacter baumannii (39 [7.1%]; 35 of 39 [89.7%] considered nosocomial), also played important roles. For the top underlying causes of death, the median number of conditions in the chain of events leading to death was 3 for malnutrition, 3 for HIV, 1 for malaria, 3 for congenital birth defects, and 1 for LRTI. Expert panels considered 494 of 632 deaths (78.2%) preventable and 26 of 632 deaths (4.1%) preventable under certain conditions. In this cross-sectional study investigating causes of child mortality in the CHAMPS Network, results indicate that, in these high-mortality settings, infectious diseases continue to cause most deaths in infants and children, often in conjunction with malnutrition. These results also highlight opportunities for action to prevent deaths and reveal common interaction of various causes in the path toward death.

Evaluation of VITEK® 2 AST cards (AST-N376 and AST-N397) for susceptibility testing of challenging Gram negatives

Due to the increasing diffusion of MDR/XDR Gram-negatives it is necessary to offer reliable antibiotic susceptibility testing (AST), which also include new drugs. Here we evaluated the performances of the VITEK®2 AST-N376 and the AST-N397 cards. A collection of 180 clinical Gram-negative bacteria, producing relevant resistance mechanisms, were tested using VITEK 2 and MERLIN, in parallel. Discrepancies between the 2 systems were solved by the reference broth microdilution method. The workflow timing of the VITEK®2 system was also assessed. Overall, the VITEK®2 cards proved to be reliable in determining AST for the molecules evaluated, even if compliance with ISO acceptance criteria for accuracy assessment was not reached for some combinations and showed a short hands-on time for panels preparation. In conclusion, VITEK®2 is a valid system that ensures accurate results for AST of the molecules evaluated in this study and speeds up the workflow in the laboratory of diagnostic microbiology.

Fungal Endocarditis: Pathophysiology, Epidemiology, Clinical Presentation, Diagnosis, and Management.

Fungal endocarditis accounts for 1% to 3% of all infective endocarditis cases, is associated with high morbidity and mortality (>70%), and presents numerous challenges during clinical care. Candida spp. are the most common causes of fungal endocarditis, implicated in over 50% of cases, followed by Aspergillus and Histoplasma spp. Important risk factors for fungal endocarditis include prosthetic valves, prior heart surgery, and injection drug use. The signs and symptoms of fungal endocarditis are nonspecific, and a high degree of clinical suspicion coupled with the judicious use of diagnostic tests is required for diagnosis. In addition to microbiological diagnostics (e.g., blood culture for Candida spp. or galactomannan testing and PCR for Aspergillus spp.), echocardiography remains critical for evaluation of potential infective endocarditis, although radionuclide imaging modalities such as 18F-fluorodeoxyglucose positron emission tomography/computed tomography are increasingly being used. A multimodal treatment approach is necessary: surgery is usually required and should be accompanied by long-term systemic antifungal therapy, such as echinocandin therapy for Candida endocarditis or voriconazole therapy for Aspergillus endocarditis.

Comprehensive evaluation of hematospermia in patients with acute epididymitis compared to patients with isolated hematospermia.

Among the most commonly known causes of hematospermia are infections in the genitourinary tract, but no study exists that has comprehensively investigated hematospermia in patients with acute epididymitis. To assess the impact of hematospermia in patients with acute epididymitis and its association with clinical, microbiological, and semen parameters. Since May 2007, a total of 324 sexually active patients with acute epididymitis were recruited in a prospective cohort study. Patients received a comprehensive medical and sexual history, and clinical, sonographic, laboratory, and microbiological diagnostics. Antibiotic therapy was given according to European Association of Urology guidelines. Semen analysis was offered 14 days after the first presentation and initiation of therapy. Since 2013, a separate control group of 56 patients presenting with isolated hematospermia (=no other urogenital symptoms) was prospectively recruited, and differences between the groups were statistically evaluated. Of 324 patients with acute epididymitis, 50 patients (15%) had self-reported hematospermia. This occurred with a median of 24h before the onset of scrotal symptoms and was associated with significantly elevated prostate-specific antigen levels compared to 274 patients without hematospermia (3.1vs. 1.8ng/ml, p<0.01). The two most common etiological pathogens were Escherichia coli and Chlamydia trachomatis, and the bacterial spectrum was comparable in both epididymitis subgroups (p=0.859). Semen analysis at 14 days still showed hematospermia in 24% of patients associated with massive leukocytospermia. Compared to the hematospermia control group, the two epididymitis subgroups showed significantly increased inflammation markers (pH, leukocytes, and elastase), reduced sperm concentration, and reduced levels of alpha-glucosidase and zinc (always p<0.01). In sexually active patients who develop acute epididymitis, self-reported hematospermia is evident in 15% of patients as early as one day before the onset of scrotal symptoms. Conversely, none of the 56 patients presenting with isolated hematospermia developed epididymitis within the next 4 weeks.

Современные технологии микробиологических исследований в офтальмологии. Часть 2

Purpose. To highlight modern microbiological technologies (mass spectrometry, polymerase chain reaction (PCR), sequencing, laser light scattering) and methods (phenotypic, genetic, analytical methods) for detecting antibiotic sensitivity. Material and methods. To complete this review, a search was carried out for scientific publications of domestic and foreign authors on the resources of PubMed, Medline, eLibrary from 2008 to 2021, devoted to the currently existing methods for determining sensitivity to antibiotics with an emphasis on ophthalmological microbiological diagnostics. Results. Modern technologies make it possible to determine the presence of resistance to specific drugs and additionally reveal its mechanisms, allow direct detection of components of microorganisms responsible for the loss of sensitivity to antibiotics. Conclusion. The modern microbiological technologies presented in the review for determining antibiotic resistance make it possible not only to solve the clinical tasks of treating specific patients in the shortest possible time, but also to carry out epidemiological monitoring to explain the mechanisms leading to the antibiotic resistance in the population at the proteomic and genomic levels. Key words: antibiotic sensitivity, polymerase chain reaction, sequencing, mass spectrometry, antibiotic resistance

Possible Rates of Detection of Neonatal Sepsis Pathogens in the Context of Microbiological Diagnostics in Mothers - Real World Data.

The aim of this study was to identify the rate of detection of neonatal sepsis pathogens in maternal microbiological smears. This is a retrospective study conducted at a Level 1 perinatal center in the context of routine care from 2014 to 2019. For all premature infants and neonates with neonatal sepsis, the neonatal and maternal microbiological findings were examined to see if there was a match. During the study period, a total of 948 premature or newborn infants were identified as having a neonatal infection. Among all of the premature or newborn infants, 209 (22%) met the diagnostic criteria for neonatal sepsis; of these, 157 were premature births and 52 were full-term births. We evaluated the microbiological findings for these 209 mother and child pairs. No pathogens were detected in 27 out of 157 mothers of premature infants (17.1%) and in 31 out of 52 mothers of full-term infants (59.6%). In the premature infant group there were pairs with matching pathogens in 30 out of 130 cases (23.1%, 95% CI: 16.1-31.3), and in the full-term infant group there was a match in 4 out of 21 cases (19%, 95% CI: 5.4-41.9). The number needed to test to have a 90% probability of success for pathogen detection varies between 9 and 11 in the most favorable case and 26 and 32 in the least favorable case, depending on the evaluation method. In cases of neonatal sepsis, the sepsis-causing pathogen was successfully detected through prior analysis of a maternal smear in 7% of full-term infants and in 19% of premature infants. The number needed to test was relatively high in all groups. The value of maternal smears for identifying neonatal sepsis-causing pathogens needs to be critically questioned.

Continuing professional development (CPD) training needs assessment for medical laboratory professionals in Ethiopia

BackgroundContinuing professional development (CPD) is required for health workers in practice to update knowledge and skills regularly to match the changing complexity of healthcare needs. The objective of this study was to identify the training needs of Medical Laboratory professionals in Ethiopia.MethodsA total of 457 medical laboratory professionals from five regions and two city administrations were involved in the study. Data were collected from August 02 to 21, 2021 with structured self-administered online tool with five-point Likert scale. The tool had consent, demography, cross-cutting issues, and main activity area specific to medical laboratory.ResultsMajority of the participants were male (80.1%). Participants from Amhara region 110 (24.1%) were the largest groups in the survey followed by Oromia 105 (23%) and Addis Ababa 101 (22.1%). The study participants comprised 54.7% with a bachelor’s degree, 31.3% with a diploma (associate degree), and 14% with a master’s degree. The participants had varying years of service, ranging from less than one year to over 10 years of experience. Most of the participants work as generalists (24.1%) followed by working in microbiology (17.5%) and parasitology (16%). The majority (96.9%) were working in a public sector or training institutions and the rest were employed in the private sector. Our study showed that the three most important topics selected for training in the cross-cutting health issues were health and emerging technology, computer skills and medico-legal issues. Topics under microbiology, clinical chemistry and molecular diagnostics were selected as the most preferred technical areas for training. Participants have also selected priority topics under research skill and pathophysiology. When the laboratory specific issues were regrouped based on areas of application as technical competence, research skill and pathophysiology, thirteen topics under technical competence, four topics under research skill and three topics under pathophysiology were picked as priority areas.ConclusionIn conclusion, our study identified that CPD programs should focus on topics that address technical competence in microbiology, clinical chemistry and molecular diagnostics. Additionally competencies in research skill and updating knowledge in pathophysiology should also receive due attention in designing trainings.

Seroprevalence of Toxoplasma gondii among general population in Bosnia and Herzegovina: 10-Years single center experience

ObjectivesThe aim of this research was to determine the seroprevalence of Toxoplasma gondii in Bosnia and Herzegovina, with special reference to women of reproductive age in Bosnia and Herzegovina. MethodsThe retrospective cross-sectional study included 3685 participants tested at the Department of Microbiology and Molecular Diagnostics, University Clinical Hospital, Mostar in the period from January 1, 2010 to December 31, 2019. The detection of IgG and IgM antibodies to T. gondii was based on the enzyme immunofluorescence test. ResultsIn this study the total IgG prevalence of T. gondii was 18.7%, while only 1.7% were IgM positive. The IgG prevalence increased according to age of participants from 1.8% in 1–5 age group to 46.8% in participants older than 65 (p < 0.001). Out of total IgG positive participants, 62.8% came from rural areas (p < 0.001). An increased age (OR = 2.233) and rural residence (OR = 1.468) were found as risk factors for toxoplasmosis, whereas gender was not (OR = 1.021). Out of total 1514 women of reproductive age tested, the IgG prevalence of T. gondii was 15.8%, and IgM antibodies was present in 1.6% examined women. ConclusionsThis study showed a seroprevalence of T. gondii in Bosnia and Herzegovina, not only among the general population, but also among women of reproductive age. Results of the study suggest the need for more systematic preventive monitoring of pregnant women and preconception counselling for women of reproductive age.

Detection of polymyxin B resistance in Enterobacterales by broth disk elution method

Background: Antibiotic resistance being the critical issue faced by medical field, especially by Gram negative bacteria. It is a great threat in the case of both hospitals acquired and community acquired infections. They possess various mechanisms for their survival. The widespread resistance in Gram negative bacteria has necessitated evaluation of the use of older antimicrobials such as polymyxins. Polymyxins are disfavoured owing to their potential clinical toxicity, especially nephrotoxicity. Thus, they got abandoned in the sixties. But now they are re- emerged and used as last resort antibiotics. Methods: 274 isolates of Enterobacterales including Klebsiella pneumoniae, Escherichia coli, Citrobacter spp. Enterobacter spp. was collected from various diagnostic microbiology laboratories in Kerala. The polymyxin resistance among Enterobacterales by broth disk elution method recommended by CLSI. Results: In this study prevalence of multi drug resistant is 37% and extensively drug resistant strains is 25%. And the threatening fact is that the colistin also shows resistance among Enterobacterales (9.2%). Conclusions: Though the resistance to Polymyxin B is to the lesser side in the present study, increase in resistance to the agent is being documented globally elsewhere. So, rational use of Polymyxin B is warrantied as we could cherish polymyxin B as a “life - saving drug” to avoid no drug available. Knowledge of antimicrobial resistance and development of new antimicrobial agents and improved treatments are essential in the current situation.

An in vitro study on comparative adherence of oral Candida albicans and non–albicans Candida to human buccal epithelial cells and its antifungal susceptibility pattern

Background: Candida spp. are intra-oral commensals in 40-60% of human subjects and the precise factors involved in the development of Candidiasis are still not clear. The adherence of Candida to epithelial cells is one of the main pathogenic characteristics of the genus. Studies have shown that there are variations in the adherence capabilities of different Candida spp., which may explain why some species colonize mucosal surfaces more frequently than others. The aim of this study was to estimate the adherence properties of Candida spp. to buccal epithelial cells and to determine the antifungal susceptibility. Methods: 87 isolates of Candida spp. from known non-diabetic patients with oral Candidiasis were collected from diagnostic microbiology laboratories in central Kerala. The method of Kimura and Pearsall et al was followed with minor modifications to test the adherence. Results: All the three species exhibited adherence with varying capacity. C. albicans was significantly more adherent to buccal epithelial cells than C. tropicalis and C. krusei. Resistance was not observed among the isolates against fluconazole, voriconazole and clotrimazole. Conclusions: In conclusion Candida spp. isolated from oral candidiasis patients exhibited a higher adherence capacity to normal human buccal epithelial cells considered an essential virulence property. As anticipated C. albicans displayed higher virulence activity than non-Candida albicans species.

Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial

Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial

Deep Learning-Assisted Surface-Enhanced Raman Scattering for Rapid Bacterial Identification.

Bloodstream infection (BSI) is characterized by the presence of viable microorganisms in the bloodstream and may induce systemic immune responses. Early and appropriate antibiotic usage is crucial to effectively treating BSI. However, conventional culture-based microbiological diagnostics are time-consuming and cannot provide timely bacterial identification for subsequent antimicrobial susceptibility test (AST) and clinical decision-making. To address this issue, modern microbiological diagnostics have been developed, such as surface-enhanced Raman scattering (SERS), which is a sensitive, label-free, and quick bacterial detection method measuring specific bacterial metabolites. In this study, we aim to integrate a new deep learning (DL) method, Vision Transformer (ViT), with bacterial SERS spectral analysis to build the SERS-DL model for rapid identification of Gram type, species, and resistant strains. To demonstrate the feasibility of our approach, we used 11,774 SERS spectra obtained directly from eight common bacterial species in clinical blood samples without artificial introduction as the training dataset for the SERS-DL model. Our results showed that ViT achieved excellent identification accuracy of 99.30% for Gram type and 97.56% for species. Moreover, we employed transfer learning by using the Gram-positive species identifier as a pre-trained model to perform the antibiotic-resistant strain task. The identification accuracy of methicillin-resistant and -susceptible Staphylococcus aureus (MRSA and MSSA) can reach 98.5% with only 200-dataset requirement. In summary, our SERS-DL model has great potential to provide a quick clinical reference to determine the bacterial Gram type, species, and even resistant strains, which can guide early antibiotic usage in BSI.

The 2023 Duke-International Society for Cardiovascular Infectious Diseases Criteria for Infective Endocarditis: Updating the Modified Duke Criteria.

The microbiology, epidemiology, diagnostics, and treatment of infective endocarditis (IE) have changed significantly since the Duke Criteria were published in 1994 and modified in 2000. The International Society for Cardiovascular Infectious Diseases (ISCVID) convened a multidisciplinary Working Group to update the diagnostic criteria for IE. The resulting 2023 Duke-ISCVID IE Criteria propose significant changes, including new microbiology diagnostics (enzyme immunoassay for Bartonella species, polymerase chain reaction, amplicon/metagenomic sequencing, in situ hybridization), imaging (positron emission computed tomography with 18F-fluorodeoxyglucose, cardiac computed tomography), and inclusion of intraoperative inspection as a new Major Clinical Criterion. The list of "typical" microorganisms causing IE was expanded and includes pathogens to be considered as typical only in the presence of intracardiac prostheses. The requirements for timing and separate venipunctures for blood cultures were removed. Last, additional predisposing conditions (transcatheter valve implants, endovascular cardiac implantable electronic devices, prior IE) were clarified. These diagnostic criteria should be updated periodically by making the Duke-ISCVID Criteria available online as a "Living Document."