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Objective: We aimed to evaluate the frequency and associated factors of baseline NS5A resistance-associated substitutions (RASs) in patients coinfected with human immunodeficiency virus (HIV) and h...

Fungi of the genus Fusarium are especially dangerous phytopathogens affecting common wheat (Triticum aestivum L.) among other crops, as they may cause not only crop losses but poisoning of humans and livestock. The review highlights current approaches to identify fungi of the genus Fusarium infecting common wheat. Microbiological techniques for identification of Fusarium species are still among laboratory protocols and recommendations, therefore some of the most popular genus- and species-specific media are mentioned in the review. However, in the modern literature, much more attention is paid to identification of Fusarium fungi with the use of the polymerase chain reaction (PCR). Therefore, conventional PCR assays for identification of representatives of the genus Fusarium in general or only species producing especially dangerous metabolites (nivalenol, deoxynivalenol, 3-acetyldeoxynivalenol, 4-acetylnivalenol, and enniatin) are highlighted in the review. The primer pairs to identify the presence of certain Fusarium species or their combinations in samples are described. For real-time PCR assays, which may be used for more precise quantitative and qualitative genus- and species-specific identification of Fusarium fungi, protocol details, primer and probe sequences are described, as well as recommended dyes are mentioned for the probes. For some primer pairs, additional details regarding their validation and assay sensitivity are mentioned. Thus, the techniques described in the review are precise and comprehensive enough and may be used in combination and separately for genus- and species-specific quantitative or qualitative identification of fungi of the genus Fusarium.

Abstract Diagnosis of bacterial infections until today mostly relies on conventional microbiological methods. The resulting long turnaround times can lead to delayed initiation of adequate antibiotic therapy and prolonged periods of empiric antibiotic therapy (e.g., in intensive care medicine). Therewith, they contribute to the mortality of bacterial infections and the induction of multidrug resistances. The detection of species specific volatile organic compounds (VOCs) emitted by bacteria has been proposed as a possible diagnostic approach with the potential to serve as an innovative point-of-care diagnostic tool with very short turnaround times. A range of spectrometric methods are available which allow the detection and quantification of bacterial VOCs down to a range of part per trillion. This narrative review introduces the application of spectrometric analytical methods for the purpose of detecting VOCs of bacterial origin and their clinical use for diagnosing different infectious conditions over the last decade. Key Points • Detection of VOCs enables bacterial differentiation in various medical conditions. • Spectrometric methods may function as point-of-care diagnostics in near future.

INTRODUCTION: Bacteremia is a major cause of morbidity and mortality in hospitalized patients. Predictors of mortality are critical for the management and survival of hospitalized patients. The objective of this study was to determine the factors related to blood culture positivity and the risk factors for mortality in patients whose blood cultures were collected. METHODS: A prospective 2-cohort study (derivation with 784 patients and validation with 380 patients) based on the Pitt bacteremia score for all patients undergoing blood culture collection. The score was obtained from multivariate analysis. The Kaplan–Meier survival curve of the cohort derivation and the cohort validation groups was calculated, and the difference was assessed using a log-rank test. Mortality-related factors were older age, extended hospitalization, > 10% of immature cells in the leukogram, lower mean blood pressure, elevated heart rate, elevated WBC count, and elevated respiratory rate. These continuous variables were dichotomized according to their significance level, and a cut-off limit was created. RESULTS: The area under the ROC curve (AUC) was 0.789. The score was validated in a group of 380 patients who were prospectively evaluated. CONCLUSION: Prolonged hospitalization, body temperature, and elevated heart rate were related to positive blood cultures. The Pitt score can be used to assess the risk of death; however it can be individualized according to the epidemiology of each hospital.

Purpose of Review This review summarises the epidemiology of Candida auris infection and describes contemporary and emerging diagnostic methods for detection and identification of C. auris. Recent Findings A fifth C. auris clade has been described. Diagnostic accuracy has improved with development of selective/differential media for C. auris. Advances in spectral databases of matrix-associated laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) systems have reduced misidentification. Direct detection of C. auris in clinical specimens using real time PCR is increasingly used, as is whole genome sequencing (WGS) to track nosocomial spread and to study phylogenetic relationships and drug resistance. Summary C. auris is an important transmissible, nosocomial pathogen. The microbiological laboratory diagnostic capacity has extended beyond culture-based methods to include PCR and WGS. Microbiological techniques on the horizon include the use of MALDI-TOF MS for early echinocandin antifungal susceptibility testing (AST) and expansion of the versatile and information-rich WGS methods for outbreak investigation.

This study aimed to evaluate the preoperative and intraoperative factors that may cause systemic inflammatory response syndrome (SIRS) after percutaneous nephrolithotomy (PCNL) and to investigate the effect of the duration between urine culture (UC) and operation on postoperative SIRS. Three hundred and fifty-six patients who had PCNL between January 2015 and June 2019 were retrospectively included in the study. UC was obtained from all patients before the operation and during the puncture at the beginning of the operation. Postoperatively, patients were closely monitored for fever and other signs of SIRS. The post-PCNL SIRS incidence was 7%. In univariable and multivariable analyses, the rate of ipsilateral PCNL history, recurrent urinary tract infection (UTI) history, operation time and the length of hospital stay were significant predictive factors for SIRS. The duration between UC and PCNL was not a statistically significant variable in both univariable and multivariable analysis. Our study concluded that the duration between UC and PCNL is not an influential factor for post-PCNL SIRS. Clarifying this issue may be possible with prospective studies in which the effects of factors such as ipsilateral PCNL history and recurrent urinary tract infection history which has been proven to be risk factors for post-PCNL SIRS are restricted.

Objective To evaluate the diagnostic efficacy of gastric juice-based genotypic methods for Helicobacter pylori detection and antibiotic resistance testing. Methods We used electronic databases including Medline, Embase, Web of Science and the Cochrane Central Register of Controlled Trial for literature survey using keywords such as "gastric juice", "Helicobacter pylori" and their synonyms. The quality of the studies was assessed using QUADAS-2. Summary performance measures (sensitivity, specificity, positive predictive values, negative predictive values, diagnostic odds ratio, and area under the summary receiver operating characteristic curve) and HSROC curves were produced. In addition, fagan plots were applied to illustrate the relationship among the prior test probability, PLR/NLR, and posterior test probability. Results Our study cohort comprised eight studies with 1235 participants (617 participants of H. pylori infection and 618 participants of non-H. pylori infection). Pooled sensitivity and specificity with a corresponding 95% confidence interval (CI) of gastric juice-based genotypic methods reflected values of 94% (95%CI, 86% - 98%) and 98% (95%CI, 85% - 100%), respectively. The global sensitivity and specificity of clarithromycin resistance were 92% (95%CI, 85% - 96%) and 90% (95%CI, 80% - 95%), respectively. Conclusion Gastric juice-based genotypic methods can be used for diagnostic prediction of H. pylori infection as well as clarithromycin resistance testing.

Numerous metagenome-wide association studies (MWAS) for urolithiasis have been published, leading to the discovery of potential interactions between the microbiome and urolithiasis. However, questions remain about the reproducibility, applicability and physiological relevance of these data owing to discrepancies in experimental technique and a lack of standardization in the field. One barrier to interpreting MWAS is that experimental biases can be introduced at every step of the experimental pipeline, including sample collection, preservation, storage, processing, sequencing, data analysis and validation. Thus, the introduction of standardized protocols that maintain the flexibility to achieve study-specific objectives is urgently required. To address this need, the first international consortium for microbiome in urinary stone disease — MICROCOSM — was created and consensus panel members were asked to participate in a consensus meeting to develop standardized protocols for microbiome studies if they had published an MWAS on urolithiasis. Study-specific protocols were revised until a consensus was reached. This consensus group generated standardized protocols, which are publicly available via a secure online server, for each step in the typical clinical microbiome–urolithiasis study pipeline. This standardization creates the benchmark for future studies to facilitate consistent interpretation of results and, collectively, to lead to effective interventions to prevent the onset of urolithiasis, and will also be useful for investigators interested in microbiome research in other urological diseases., Metagenome-wide association studies have led to the discovery of potential interactions between the microbiome and urolithiasis, but a lack of standardization has raised questions about the reproducibility, applicability and physiological relevance of metagenome-wide association study data. This Consensus Statement describes the formation of the first international consortium for microbiome in urinary stone disease — MICROCOSM — and the outcomes of a consensus meeting to develop standardized protocols for microbiome studies and generate a data repository, which are both publicly available via a secure online server.

espanolObjetivo. Nuestro trabajo trata de aportar informacion sobre el impacto del nuevo sistema Sepsis Chip Flow system (SFC) y otras tecnicas de diagnostico microbiologico rapido en la seleccion del tratamiento antibiotico apropiado por el equipo de infectologos dentro de un grupo multidisciplinar PROA. Metodo. Dos infectologos con amplia experiencia clinica llevan a cabo un ejercicio teorico de forma independiente seleccionando los tratamientos de los pacientes diagnosticados de bacteriemia por bacilos gramnegativos. En primer lugar, los infectologos solo tienen acceso a los datos reales de 74 pacientes. Secuencialmente, se les aporta informacion de los resultados de la tincion de Gram, MALDI-TOF y SFC (Vitro). Inicialmente, los infectologos prescriben un tratamiento antibiotico en base a los datos clinicos y mas tarde, van modificando los tratamientos en base a la informacion microbiologica recibida. Resultados. Los datos aportados por la tincion de Gram reducen el numero de pacientes pautados con tratamientos combinados (para el clinico 1, de 23 a 7, y en el clinico 2, de 28 a 12), pero el uso de carbapenemicos permanece constante. En la misma linea, los datos aportados por MALDI-TOF tambien disminuyen el numero de tratamientos antibioticos combinados aunque sigue sin modificarse el numero de tratamientos con carbapenemicos. Por contra, los datos de resistencia antibiotica aportados por SFC reducen el numero de tratamientos con carbapenemicos. Conclusiones. A partir del modelo teorico, la tincion de Gram y los resultados de MALDI-TOF lograron una reduccion en el tratamiento combinado. Sin embargo, el nuevo sistema probado (SFC), debido a los datos de mecanismos de resistencia proporcionados, no solo redujo el tratamiento combinado sino que tambien disminuyo la prescripcion de los carbapenemicos. EnglishObjective. The aim of this study was to assess the impact of the information provided by the new Sepsis Chip Flow system (SFC) and other fast microbiological techniques on the selection of the appropriate antimicrobial treatment by the clinical researchers of an antimicrobial stewardship team. Methods. Two experienced clinical researchers performed the theoretical exercise of independently selecting the treatment for patients diagnosed by bacteremia due to bacilli gram negative (BGN). At first, the clinicians had only available the clinical characteristics of 74 real patients. Sequentially, information regarding the Gram stain, MALDI-TOF, and SFC from Vitro were provided. Initially, the researchers prescribed an antimicrobial therapy based on the clinical data, later these data were complementing with information from microbiological techniques, and the clinicians made their decisions again. Results. The data provided by the Gram stain reduced the number of patients prescribed with combined treatments (for clinician 1, from 23 to 7, and for clinician 2, from 28 to 12), but the use of carbapenems remained constant. In line with this, the data obtained by the MALDI-TOF also decreased the combined treatment, and the use of carbapenems remained unchanged. By contrast, the data on antimicrobial resistance provided by the SFC reduced the carbapenems treatment. Conclusions. From the theoretical model the Gram stain and the MALDI-TOF results achieved a reduction in the combined treatment. However, the new system tested (SFC), due to the resistance mechanism data provided, not only reduced the combined treatment, it also decreased the prescription of the carbapenems.

Objective To validate the use of Seegene Allplex™ Vaginitis assay in the diagnosis of candidiasis, bacterial vaginosis (BV) and trichomoniasis. Design Cross-sectional, prospective study conducted in a single centre. Setting Outpatient clinic of a gynaecology department. Population Consecutive symptomatic and asymptomatic women (18-60 years of age). Methods Comparison of the assay test with the reference standards for the diagnosis of vaginitis (cultures for yeasts, Nugent for BV and nucleic acid amplification test for trichomoniasis). Main outcome measures Performance of the investigational assay, in comparison with the reference standards for the diagnosis of the presence of Candida spp., Trichomonas vaginalis and BV. Secondary objectives are the evaluation of the performance of the test in postmenopausal women and in symptomatic women. Results A diagnosis of vaginitis was established in 14.0%. The global prevalences of BV, Candida spp. and T. vaginalis were 22.3%, 13.2% and 2.4%, respectively. The sensitivity and specificity of the assay test for those three causes of vaginitis were as follows: BV 91.7% and 86.6%; any Candida spp. 91.1% and 95.6%; Candida albicans 88.1% and 98.2%, non-albicans Candida 100% and 97.5%, and T. vaginalis 94.4 and 99.9%. The performance of the test was identical in the subgroup of women that reported vulvovaginal symptoms. The presence of multiple infections did not interfere with the performance of the test. Conclusions The Seegene Allplex™ Vaginitis assay has an excellent performance in the diagnosis of the BV and presence of Candida; the results were good for trichomoniasis, but the study was underpowered for this outcome. Tweetable abstract Seegene Allplex™ Vaginitis is an excellent option for screening and diagnosis of vaginitis.

Antimicrobials are a common cause of drug toxicity. Understanding the relationship between systemic antimicrobial exposure and toxicity is necessary to enable providers to take a proactive approach to prevent undesired drug effects. When an exposure threshold has been defined that predicts drug toxicity, therapeutic drug monitoring (TDM) can be performed to assure drug exposure does not exceed the defined threshold. Although some antimicrobials have well-defined dose-dependent toxicities, many other exposure-toxicity relationships have either not been well-defined or, in some cases, not been evaluated at all. In this review, we examine the relationship between exposures and toxicities for antibiotic, antifungal, and antiviral agents. Furthermore, we classify these relationships into four categories: known association between drug exposure and toxicity such that clinical implementation of a specific exposure threshold associated with toxicity for TDM is supported (category 1), known association between drug exposure and toxicity but the specific exposure threshold associated with toxicity is undefined (category 2), association between drug exposure and toxicity has been suggested but relationship is poorly defined (category 3), and no known association between drug exposure and toxicity (category 4). Further work to define exposure-toxicity thresholds and integrate effective TDM strategies has the potential to minimize many of the observed antimicrobial toxicities.

Globally, it is estimated that there are 2 billion cases of diarrhoeal disease each year, with 525,000 children under the age of 5 years, dying from diarrhoea. This also affects 1 in 5 people in the UK each year. Rapid diagnosis, appropriate treatment and infection control measures are, therefore, particularly important. Currently, Public Health Wales and England Microbiology Division test for five key bacterial gastrointestinal pathogens, i.e. Escherichia coli O157 (VTEC), Shigella dysenteriae, Salmonella spp., Campylobacter spp. and Clostridioides difficile. There is, however, a poor success rate with identification of these pathogens, leaving the patient at risk from untreated infections. This study has developed effective and reliable tools with a high positive outcome for diagnosis of diarrhoeal infection. The study blindly analysed 592 samples, with the most abundant species being Shigella sonnei at 15%, and the top genus Bacteroides at 26%. Campylobacter spp. had an abundance of 4%, Clostridium difficile 3%, and Salmonella spp. 0.2%. There were also significant differences in abundance at genus level, between the Flemish Gut project and diarrhoea samples, with respect to Shigella (0.2%) and Campylobacter (0.1%). The project introduced a novel Shigella spp. (Escherichia) threshold of 5.32% to determine (Escherichia) a healthy or unhealthy community. A DMBiome model was developed to integrate the 5.32% threshold of Shigella spp., the Public Health laboratory tested pathogens, and two emerging enteropathogens. The overall positive outcome was that 89% of all samples were diagnosed with diarrhoea infections, leaving 11% unknown.

We describe rapid spread of multidrug-resistant gram-negative bacteria among patients in dedicated coronavirus disease care units in a hospital in Maryland, USA, during May–June 2020. Critical illness, high antibiotic use, double occupancy of single rooms, and modified infection prevention practices were key contributing factors. Surveillance culturing aided in outbreak recognition and control.

Introduction: In recent years, there has been an increase in the number of systemic fungal infections among HIV-infected individuals. The article aimed to examine the frequency of invasive mycoses among the HIV-infected patients at the time of their urgent and/or planned admission to a specialized hospital. Methods: The diagnostic methods used in this study involved physical examination, laboratory testing, bacteriological examination, immunological examination, molecular genetic testing, and radiological imaging. The study was conducted under the ethical guidelines for retrospective studies and does not disclose data on individual patients. Results: Between 2016 and 2018, 85 HIV patients who died with HIV history underwent a series of clinical and pathomorphological examinations at the Novgorod Regional Infectious Diseases Hospital. Systemic mycoses frequently occur in the respiratory system and less often in the brain. Their incidence is severe and the mortality rates associated with it are high. In this study, PCP was the most common cause of death provoked by mycoses. Discussion/Conclusion: Systemic fungal disease can be diagnosed through a combination of diagnostic methods. A crucial factor in the reduction of mortality rates for systemic mycosis is the early diagnosis and intensive antimicrobial therapy.

BACKGROUND Previous studies concluded predictors of smear non-conversion pulmonary tuberculosis (TB) globally as well as in Indonesia. However, there is a limited data in hospital setting. This study aimed to explore predictors of smear non-conversion pulmonary TB in hospital setting. METHODS A case-control study was conducted to explore predictors of smear nonconversion among new-treatment pulmonary TB in Dr. Kariadi General Hospital from 2017 to 2019. Number of cases and controls have been determined consecutively. Data were collected from secondary data accessed in medical records and directly from subjects. Non-conversion status in the case group was defined as a persistent sputum smear-positive after 2 months of intensive phase of treatment. The subjects’ characteristics i.e., age, sex, BMI, education level, occupational status, and predictors of smear non-conversion, i.e., patient’s compliance, smoking status, alcohol consumption, presence of drugs side effects, health care access, first acid-fast bacilli (AFB) smear grading, diabetes mellitus (DM), housing condition, housing density, and household income were observed. Chi-square test and binary logistic regression were used. RESULTS 35 subjects were determined in the case group while 76 subjects were the control group and involved in the final analysis. Age, sex, first AFB smear grading, smoking status, housing condition, housing density, and DM were involved in the model of logistic regression. DM (OR = 3.4; 95% CI = 1.19–10.00) and first AFB smear grading (OR = 11.2; 95% CI = 3.86–33.00) were concluded as the predictors of smear nonconversion. CONCLUSIONS DM and first AFB smear grading were the predictors of smear nonconversion among new-treatment pulmonary TB subjects.

Infants and young children are uniquely susceptible to primary viral and bacterial infections, predisposing them to responses of greater frequency and severity than in adults. Etiologies and manifestations of infections in pediatric patients are often different than those in adults. It can be challenging for clinical laboratories to implement appropriate microbiologic methods for rapid and accurate diagnoses in this population. Laboratorians should be cognizant of the distinctive features of children to provide comprehensive pediatric clinical microbiology services. This article discusses laboratory aspects of several clinically significant pediatric pathogens that cause severe harm to patients and impact public health responses.

Anatomic pathology is an important resource for detection and exclusion of infectious diseases in tissue specimens. Detection of a microorganism (i.e. bacteria, fungi, parasite) in tissue sections is frequently the beginning of a work-up and occasionally sufficient for definitive microbiologic identification. Close correlation with cultures and ancillary testing in the microbiology laboratory is of paramount importance in arriving at a diagnosis and identify with certitude causative pathogen(s). This review will discuss the adequacy and limitations of histopathology in the diagnosis of infectious diseases, describe potential pitfalls, and discuss the appropriate use of molecular diagnostics in formalin-fixed, paraffin embedded tissues.

Background and purpose — It is well recognized that some knee arthroplasty (KA) patients present with prolonged postoperative inflammation and some develop persistent pain. It can reasonably be speculated that some of these problems develop because of low-grade infections with low virulence bacteria caused by intraoperative contamination. This prospective study was performed to investigate whether intraoperative contamination results in lower patient-reported outcomes (PRO) for patients who were clinically uninfected in the first year after surgery. Patients and methods — We combined data from 2 major prospective studies on patients undergoing primary KA at 2 Danish hospitals between September 2016 and January 2018. Pre- and postoperative (1.5, 3, 6, and 12 months) PROs and intraoperative microbiological cultures were obtained on a total of 714 patients who were included in the study. Based on the microbiological cultures, the patients were divided into 2 groups, contaminated and non-contaminated, and differences in PROs between the 2 groups were analyzed. Results — 84 of 714 (12%) patients were intraoperatively contaminated; none of the 714 patients developed clinical infection. The preoperative Oxford Knee Score was 24 and 23 for contaminated and non-contaminated patients, respectively, improving to 40 and 39 at 1 year (p = 0.8). 1-year AUC for Oxford Knee Score and absolute improvement at each postoperative time point for Forgotten Joint Score and EQ-5D-5L also were similar between contaminated and non-contaminated patients. Interpretation — Patient-reported outcomes from 714 patients do not indicate that intraoperative contamination affects the knee-specific or general health-related quality of life in primary KA patients who are clinically uninfected 1 year after surgery.

Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.

Neutralization of SARS-CoV-2 Variants by Convalescent and Vaccinee Serum Analysis of serum samples from patients convalescing after SARS-CoV-2 infection and after vaccination with BBIBP-CorV or Cor...

Background: Extended spectrum β-lactamases have addressed the serious challenges worldwide as a threat to favorable outcomes of treatment of common infections in community and hospital settings since it is found to be increasing trends of multidrug resistance. The present study was aimed to determine the antibiotic profile of multidrug resistant E.coli and status of ESBLs producing E.coli. Methods: This was a cross-sectional study conducted over a period of 2 years (September 2017 to April 2019) at microbiology laboratory of Nepal Mediciti Hospital. A total of 16542 samples were processed. Various clinical samples were collected from both inpatients and outpatients aseptically and without contaminating skin commensals. Standard microbiological techniques were used for isolation and identification of pathogens. Extended spectrum beta-lactamases were phenotypically confirmed by combined disc method. Results: Out of 1449 E.coli isolates, 323(22.29%) were found to be MDR E.coli. Isolation rate of ESBL producing E.coli (66.56%) were found to be high among MDR E.coli isolates. Conclusion: There is increasing prevalence of ESBL producing E.coli. It is essential to monitor antibiotic susceptibility pattern and formulate antibiotic policy to prevent the spread of MDR and ESBL producers. Keywords: E.coli, Extended spectrum β-lactamase, Multidrug resistant

Purpose of review Recurrent urinary tract infections (rUTIs) represent a large burden on the healthcare system. Recent guidelines from the AUA/CUA/SUFU and advancements in the field reflect a paradigm shift for clinician and patients, steering away from empiric antibiotic therapy towards judicious antibiotic use. Recent findings Antibiotic stewardship, including increasing awareness of the collateral damage of antibiotics and the risks of bacterial resistance are a major focus of the new guidelines. Accurate diagnosis of rUTIs is imperative. Urine cultures are necessary to document rUTI and should be obtained prior to any treatment. First line treatment options (trimethoprim-sulfamethoxazole, nitrofurantoin, and fosfomycin) should be used whenever possible. Asymptomatic bacteriuria should not be treated in these patients with rUTI. Although antibiotic prophylaxis methods are effective, nonantibiotic regimens show promise. Summary The management of rUTIs has evolved significantly with the goal of antibiotic stewardship. It is increasingly important to ensure the accuracy of diagnosis with a positive urine culture in the setting of cystitis symptoms, and standardize treatment with first-line therapies to minimize antibiotic side effects.

BACKGROUND AND AIM Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs). METHODS Patients with mild to moderate UC (n = 24), ASC (n = 19 with 21 episodes) and HCs (n = 50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria. RESULTS The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P

Clinical mass spectrometry applications have traditionally focused on small molecules, particularly in the areas of therapeutic drug monitoring, toxicology, and measurement of endogenous and exogenous steroids. More recently, the use of matrix assisted laser desorption/ionization time of flight mass spectrometry for the identification of microbial pathogens has been widely implemented. Following this evolution, there has been an expanding role for the measurement of peptides and proteins in pathology and laboratory medicine. This review explores the current state of protein measurement by clinical mass spectrometry and the analytical strategies employed, as well as emerging applications in clinical chemistry, clinical microbiology and anatomical pathology.

We observed bacterial or fungal coinfections in COVID-19 patients admitted between March 1 and April 18, 2020 (152 of 4,267, 3.6%). Among these patients, mortality was 57%; 74% were intubated; 51% with bacteremia had central venous catheters. Time to culture positivity was 6–7 days, and 79% had received prior antibiotics. Metallo-β-lactamase–producing E. cloacae coinfections occurred in 5 patients.

Minimum bactericidal concentration (MBC) assay is an accepted parameter for evaluating new antimicrobial agents, and it is frequently used as a research tool to provide a prediction of bacterial eradication. To the best of our knowledge, there is no standardization among researchers regarding the technique used to detect a drug's MBC in Mycobacterium tuberculosis. Thus, the aim of this systematic review is to discuss the available literature in determining a drug's MBC in M. tuberculosis, to find the most commonly used technique and standardize the process. A broad and rigorous literature search of three electronic databases (PubMed, Web of Knowledge, and LILACS) was performed according to the PRISMA statement. We considered studies that were published from January 1, 1990 to February 19, 2019. Google Scholar was also searched to increase the number of publications. We searched for articles using the MeSH terms "microbiological techniques," "Mycobacterium," "antibacterial agents." In addition, free terms were used in the search. The search yielded 6,674 publications. After filter application, 5,348 publications remained. Of these, we evaluated the full text of 187 publications. By applying the inclusion criteria, 69 studies were included in the present systematic review. In the literature analyzed, a great variety in the techniques used to determine a drug's MBC in M. tuberculosis was observed. The most common variability is related to the culture media used, culture incubation time, and the percentage of bacterial death for the drug to be considered as bactericidal. The most commonly used technique for drug's MBC determination was carried out using the drug's minimum inhibitory concentration (MIC) assay. Aliquots from prior MIC values were subcultured in Middlebrook agar and incubated for 4 weeks at 35°C for determining the colony forming unit (CFU) with relevance to detect 99.9% bacilli killed or reduction in 3 log10 viable bacilli.

Rapid identification of pathogen and its resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment are essential for correct patient outcomes. Conventional detection methods of bacterial resistance, such as disc diffusion, broth microdilution and automated instruments, are constantly widely used and primarily standardized. Nevertheless, the results cannot be obtained earlier than 48 h after receiving a sample, which may lead to prolonged use or overuse of broad-spectrum antibiotics. Hence, there is a drive to develop and introduce novel, faster, standardized, sensitive and specific methods with reliable results into routine microbiological laboratory practice. Recently developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced in recent years into laboratory practice, and methods based on microfluidics and microdroplets might be introduced in the near future. This review is focused on the methods and instruments in use both currently and in the foreseeable future, applicable to determine antimicrobial efficacy in clinical microbiology laboratories.

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

16S ribosomal-ribonucleic acid polymerase chain reaction (PCR) and targeted PCR aid microbiological diagnosis in culture-negative clinical samples. Despite routine clinical use, there remains a paucity of data on their effectiveness across a variety of clinical sample types, and cost-effectiveness. In this 4 year multicentre retrospective observational study, all clinical samples referred for 16S PCR and/or targeted PCR from a laboratory network serving seven London hospitals were identified. Laboratory, clinical, prescribing, and economic variables were analysed. 78/607 samples were 16S PCR positive; pus samples were most frequently positive (29/84; p

Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes. Materials/methods: We evaluated the newly developed Biofire(R) Filmarray(R) Pneumonia Panel plus (Biomerieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy. Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care. Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.

Cystic fibrosis (CF) expert groups globally recommend using selective medium for isolation of Burkholderia cepacia complex (BCC) from respiratory specimens of CF patients. However, there is no consensus available for optimal duration of incubation and recommendations are variable. The purpose of our study was to compare the difference in recovery of BCC in CF samples at 48 hours versus 7 days when inoculated on Burkholderia cepacia selective agar. A total of 307 consecutive clinical respiratory specimens from our local CF unit were studied prospectively (August 2017 to December 2017). All specimens were inoculated on Burkholderia cepacia medium, containing polymyxin B, gentamicin and ticarcillin. In our laboratory, these plates are routinely incubated for 48 hours as per the manufacturer's recommendation. However, for this study all plates with no growth at 48 hours were further incubated for total of 7 days at 35°C in O2. Plates were read daily to look for any growth. Microbial identification was performed using MALDI-TOF Vitek MS (database V3.0). Of the 307 CF respiratory specimens cultured, 177 (58%) were from paediatric and 130 (42%) were from adult patients; 155 (50%) specimens were sputum, 148 (48%) were cough swabs and four (1%) were bronchoalveolar lavage (BAL). All specimens from adults were sputum except one BAL. Thirteen (4%) cultures from eight adult and five paediatric specimens grew BCC. The majority (294, 96%) of specimens had no growth when incubated for 7 days. All 13 positive isolates recovered within 48 hours and there were no additional positive isolates found beyond 48 hours of incubation. We conclude from our analysis that prolonged incubation is not warranted for recovery of BCC in CF specimens if selective medium containing gentamicin and polymyxin is used. By adopting this approach of non-extended incubation, the burden of work on laboratory personnel can be significantly reduced and much faster turnaround time for CF cultures achieved. Our study confirms the results of recently published data on this point and challenges the prevailing dogma of utility of extended incubation for BCC isolation. For devising consensus statements for microbiology laboratories on this issue, CF societies and expert groups should consider reviewing data from the recent studies.

Purpose: This study examines the impacts of a skin and soft tissue infection (SSTI) management program involving a rapid diagnostic algorithm (Gram stain plus real-time PCR, GeneXpert® MRSA/SA SSTI) performed directly on clinical samples plus antimicrobial stewardship (AMS) counseling of the responsible physician. Methods: Participants were 155 consecutive adult inpatients with SSTI and good quality clinical samples submitted to the microbiology laboratory from April 2016 to January 2017. Results of the rapid test and AMS recommendations were phoned through to the responsible physician. The comparison group was a historical cohort. Results: Most SSTI were surgical wound infections (41.3% vs 38.1% for the intervention and comparison groups respectively) followed by diabetic foot (14.2% and 18.1%), abscesses (13.5% both) and cellulitis (12.9% both). Isolated microorganisms were mostly Gram-negative bacilli (two-thirds), followed by Staphylococcus aureus (SA). The ratio methicillin-susceptible SA (MSSA) to methicillin-resistant SA (MRSA) was 4:1. Improvements in the intervention cohort were: DOT (22.0 vs. 24.3 days, p = 0.007), treatment duration per SSTI episode (14.1 vs. 15.0 days, p = 0.072), treatment cost (433.1 vs. 533.3 €, p = 0.039), length of stay (18.6 vs 20.7 days, p = 0.031), related mortality (1 vs. 4 patients, p = 0.022) and Clostridium difficile infection (CDI) (4 vs. 8 patients, p = 0.050). In 48 cases (31.4%) in the intervention group, advice was given to improve empiric antibiotic treatment. Conclusion: This type of program could help adjust antibiotic treatment when inappropriate, reducing antibiotic use and costs, length of stay, CDI and related mortality. Keywords: Antimicrobial stewardship, GeneXpert® MRSA/SA SSTI, Microbiological techniques, Rapid diagnosis, Soft tissue infections

Purpose Even with rapid diagnostic technology to swiftly identify infectious organisms, prompt response is needed to translate results into appropriate actions. The purpose of this study was to determine if the introduction of real-time pharmacist response to positive rapid diagnostic test results would decrease time to antimicrobial therapy for gram-positive bacteremia and candidemia in a community hospital setting. Methods A quasi-experimental study was conducted in 2 community hospitals. The study comprised 2 cohorts of adult patients who tested positive for gram-positive bacteremia involving Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, or Candida species. The preintervention cohort consisted of patients admitted from November 2017 through May 2018. The intervention cohort consisted of patients admitted from July 2018 through January 2019, after the intervention went live. The primary outcomes were time to optimal antimicrobial therapy and time to effective antimicrobial therapy. Results A total of 140 patients were included in the preintervention group, with 124 patients included in the intervention group. The mean (SD) time to effective therapy decreased from 13.9 (21.6) hours in the preintervention group to 8.6 (12.5) hours in the intervention group (hazard ratio [HR], 1.15; 95% confidence interval [CI], 0.89-1.48; P = 0.29). The mean (SD) time to optimal therapy significantly decreased from 53.7 (57.7) hours in the preintervention group to 38.4 (31.5) hours in the intervention group (HR, 1.73; 95% CI, 1.33-2.26; P < 0.001). Conclusion The introduction of real-time pharmacist response to positive rapid diagnostic test results led to a significant decrease in time to optimal antimicrobial therapy but did not significantly affect time to effective therapy. The results showed that the allocation of limited resources of a community hospital to such a stewardship program is justifiable.

Periprosthetic shoulder infection (PSI), although less common than prosthetic hip and knee infections, continues to be a devastating complication of shoulder arthroplasty. Unlike its counterparts in the hip and knee, infection with nonsuppurative bacteria is more common than infection with more virulent bacteria in periprosthetic shoulder infection. The diagnosis of PSI can be challenging because the traditional clinical and laboratory findings are not always present. The authors present a narrative review of the current methods used in the diagnosis of PSI, as well as recently developed tests that may hold promise for the diagnosis of PSI. [ Orthopedics . 2020; 43(2):76–82.]

Background: Because of the everincreasing costs and the complexity of institutional medical reimbursement policies, the necessity for extensive laboratory work-up of potentially infected patients h...

Background and objective Recently, there has been evidence for the accumulation of steroid hormones in the water environment with negative consequences on fish and humans. However, there is paucity of information on how the steroid hormones influence the microbial community in environmental waters. The objective of this study was to determine the occurrence of 17β-estradiol (E2) and its potential influence on the diversity of Aeromonas spp. Materials and methods Wastewater samples were obtained from sewage treatment plants in northern South Africa and fish samples were collected from the Nandoni dam. Aeromonas spp. were isolated using microbiological methods and PCR protocols were used for their identification. A commercial Elisa kit was used for measuring the concentration of 17β-estradiol (E2) from the wastewater samples as well as the fish samples. Results 17β-estradiol (E2) was found in high concentration in sewage samples varying from 0.32-348.6 pg mL-1 while in fish samples, it ranged from 1.1-73.6 pg mL-1. There was a tendency of samples with high E2 concentrations to have higher diversity of Aeromonas spp., implying that steroid hormones may serve as nutrient for Aeromonas spp. Aeromonas hydrophila was the most prevalent species (71%), followed by A. sobria with (68%). Conclusion The presence of Aeromonas spp. in environmental waters and fish that is consumed by the local community poses a serious health concern. The high content of E2 in treated wastewater is of serious concern as well. For the first time, the present study showed a positive impact of E2 on Aeromonas growth.

This paper reviews the most important clinical papers in cystic fibrosis published in 2018, having searched all the literature on Pubmed. Focus is on CFTR modulator therapy, randomised controlled trials, and infection/microbiology issues.

Studies of acute gastroenteritis (AGE) are hampered by the lack of routine diagnostic methods with good sensitivity and specificity. Molecular methods are increasingly used for clinical purposes, but the clinical significance of a positive result remains a challenge. In this study we aimed to compare results of routine diagnostic methods and molecular methods in symptomatic children and asymptomatic controls.Patients presenting to the pediatric emergency departments of two university hospitals in Brussels with AGE were recruited prospectively from May 2015 to October 2016; asymptomatic controls were recruited from the same hospitals. Stool analyses were performed for all participants for common pathogenic bacteria (culture), virus (immunochromatography) and parasites (microscopy). Stools were also analysed with the Luminex Gastrointestinal Pathogen Panel, a multiplex-PCR for common enteropathogens.Stools from 178 patients and 165 controls were analysed. An enteropathogen was detected in 62.4% (111/178) of cases when combining the two methods (56.2% (100/178) by Luminex, 42.7% (76/178) with routine methods) and 29.1% (48/165) of controls (24.2% (40/165) by Luminex and 10.3% (17/165) by routine methods). Some pathogens were detected more often with Luminex than with routine methods, such as Salmonella (16.3% (29/178) with Luminex and 3.9% (7/178) with routine method, p 0.05), whereas others identified by culture methods, such as Campylobacter, Shigella, Yersinia, were missed by Luminex.Molecular tools seem attractive methods, providing high positivity and a rapid turn-around time for the diagnosis of AGE. However, high rates of positivity in both cases and controls highlight the difficulty in interpreting results. Pathogens missed by Luminex but detected by culture methods raise more questions about the true clinical interest of the technique for our patients.

Summary Clostridioides difficile, a spore-forming bacillus, is a major cause of healthcare-associated infection, and can survive for prolonged periods in the inanimate environment. Environmental sampling to detect C. difficile is not routine but may be undertaken as part of outbreak management and during research projects. We conducted a literature search covering the period between 1980 and 2018 to review methods for the detection of this pathogen in the environment. There are many acceptable sampling methods used for environmental screening, including contact plates, cotton swabs, flocked swabs and sponges. Most recent studies suggest that sponges are the most effective method of sampling and have the added benefit of being capable of sampling larger and curved areas. Culture methods are the most common laboratory method of detecting C. difficile from environmental samples. However, the results are variable depending on the type of agar used and the turnaround times can be long. Molecular methods such as real-time polymerase chain reaction (RT-PCR), although more commonly used to detect C. difficile from faecal specimens, has been used with varying degrees of success in environmental sampling. Further studies are needed to determine whether molecular techniques could offer a more reliable, faster method of environmental sampling, giving infection prevention and control teams more reassurance that patients are being placed in adequately decontaminated hospital environments.

Background we evaluated the performance of the flow cytometry-based UF-4000 automated urine analyzer associated with the UD-10 image analyzer (Sysmex), in comparison with optical microscopy and culture. Materials and methods 2,695 consecutive urine samples of patients were included. The cell count was performed using the analyzer and the Kova cell for 316 samples, and compared according to a threshold of 10 white blood cells (WBC) and 10 red blood cells (RBC) /μL. In a second stage, the quantitative threshold of bacteria from which a bacterial alert is triggered was chosen by comparison with the culture. Finally, the reliability (versus Gram staining and culture) of the nature of Gram negative (GN?) and Gram positive (GP?) flags has been tested on 362 samples. Results the microscopy/UF4000 discrepancy rate was 8.5% for WBC, and 16% for RBC which dropped to 6.9% after switching to UD-10. The majority of these discrepancies corresponded to quantities close to the clinical threshold, mostly higher by automatic than by microscopic counts. With a chosen warning threshold of 200 germs/μL, the «GN?» and «GP?» flags resulted in 91%/86% and 79%/20% of Gram/significant cultures of GN bacilli and GP cocci, respectively. Conclusion the correlation UF4000/microscopy is satisfactory for cellularities, the UD10 allowing to correct discrepancies. The «GN?» flag is reliable allowing a quick diagnostic orientation for the clinician. Finally, UF4000/UD10 has shown very good performances, notably thanks to the integration of the UD-10 image analyzer, which eliminates time consuming optical microscopy cell count.

There is increasing evidence that the hospital surface environment contributes to the spread of pathogens. However, evidence on how best to sample these surfaces is inconsistent and there is no guidance or legislation in place on how to do this. The aim of this review was to assess current literature on surface sampling methodologies, including the devices used, processing methods, and the environmental and biological factors that might influence results. Studies published prior to March 2019 were selected using relevant keywords from ScienceDirect, Web of Science, and PubMed. Abstracts were reviewed and all data-based studies in peer-reviewed journals in the English language were included. Microbiological air and water sampling in the hospital environment were not included. Although the numbers of cells or virions recovered from hospital surface environments were generally low, the majority of surfaces sampled were microbiologically contaminated. Of the organisms detected, multidrug-resistant organisms and clinically significant pathogens were frequently isolated and could, therefore, present a risk to vulnerable patients. Great variation was found between methods and the available data were incomplete and incomparable. Available literature on sampling methods demonstrated deficits with potential improvements for future research. Many of the studies included in the review were laboratory-based and not undertaken in the real hospital environment where sampling recoveries could be affected by the many variables present in a clinical environment. It was therefore difficult to draw overall conclusions; however, some recommendations for the design of routine protocols for surface sampling of healthcare environments can be made.

This revision describes in detail the different diagnostic techniques of catheter-related infection, both in terms of catheter removal and preservation. Culture techniques based on catheter withdrawal are classified depending on the detection of extraluminal and/or intraluminal colonization, and new methodologies are described. In general, the most important recommendations are: (a) do not send for culture catheter tips without suspicion of infection, (b) Maki's technique is the standard for detecting extraluminal colonization, (c) take 2 pairs of peripheral blood cultures before starting antibiotic treatment, (d) use skin and connections/connectors cultures for the conservative diagnosis due to their high negative predictive value (Gram and culture), and (e) take differential quantitative blood cultures though all catheter lumens and through a peripheral vein.

Background Tissues are valuable specimens in diagnostic microbiology because they are often obtained by invasive methods, and effort should thus be taken to maximize microbiological yield. The objective of this study was to evaluate the added value of using tissue pre-processing (tissue homogenizer instrument gentleMACS Dissociator) in detecting microorganisms responsible for infections. Methods We included 104 randomly collected tissue samples, 41 (39.4 %) bones and 63 (60.6 %) soft tissues, many of those (42/104 (40.4 %)) were of periprosthetic origins. We compared the agreement between pre-processing tissues using tissue homogenizer with routine microbiology diagnostic procedure, and we calculated the performance of these methods when clinical infections were used as reference standard. Results There was no significant difference between the two methods (McNemar test, p = 0.3). Among the positive culture using both methods (n = 62), 61 (98.4 %) showed at least one similar microorganism. Exactly similar microorganisms were found in 42/62 (67.7 %) of the samples. From the included tissues, 55/ 104 (52.9 %) were deemed as infected. We found that the sensitivity of homogenized tissue procedure was lower (83.6 %) than when tissue was processed using tissue homogenizer (89.1 %). Sub-analysis on periprosthetic tissues and soft or bone tissues showed comparable results. Conclusions The added value of GentleMACS Dissociator tissue homogenizer is limited in comparison to routine tissue processing.

Purpose of Review The aim of this article is to review current and emerging microbiological techniques that support the rapid diagnosis of bacterial infections in critically ill patients, including their performance, strengths and pitfalls, as well as available data evaluating their clinical impact. Recent Findings Bacterial infections and sepsis are responsible for significant morbidity and mortality in patients admitted to the intensive care unit and their management is further complicated by the increase in the global burden of antimicrobial resistance. In this setting, new diagnostic methods able to overcome the limits of traditional microbiology in terms of turn-around time and accuracy are highly warranted. We discuss the following broad themes: optimisation of existing culture-based methodologies, rapid antigen detection, nucleic acid detection (including multiplex PCR assays and microarrays), sepsis biomarkers, novel methods of pathogen detection (e.g. T2 magnetic resonance) and susceptibility testing (e.g. morphokinetic cellular analysis) and the application of direct metagenomics on clinical samples. The assessment of the host response through new “omics” technologies might also aid in early diagnosis of infections, as well as define non-infectious inflammatory states. Summary Despite being a promising field, there is still scarce evidence about the real-life impact of these assays on patient management. A common finding of available studies is that the performance of rapid diagnostic strategies highly depends on whether they are integrated within active antimicrobial stewardship programs. Assessing the impact of these emerging diagnostic methods through patient-centred clinical outcomes is a complex challenge for which large and well-designed studies are awaited.

Background Microbiological tests are required for individuals on HIV Pre-Exposure Prophylaxis (PrEP), but their real-life numbers, types and cost are poorly described. Methods Number, type, and results of microbiological tests performed in a Besancon Hospital-associated laboratory, France, from 2016 to 2019, in the setting of PrEP consultations were retrospectively collected. Costs were estimated by the current reimbursement rate set by the French national protection system. Results 756 consultations for PrEP initiation or follow-up of 135 persons were performed over 4 years. Among 3434 tests performed in the institution-associated laboratory, 1083 and 2351 were virological and bacteriological tests, respectively. Serology was predominant in virology (98% of virological tests), with HIV, HCV, and HBV screening as the 3 more frequent assays, whereas molecular biology was predominant in bacteriology (63.1% of bacteriological tests) with N. gonorrhoeae and C. trachomatis screening as leader assays. Agar-based culture accounted for 1% of bacterial tests. The global cost of microbiological tests was 45,983.20 euros, corresponding to a mean cost of 60.80 euros per consultation. Virological and bacteriological tests accounted for 37.7% and 62.3% of this budget, respectively. No seroconversion was observed for HIV or HCV. N. gonorrhoeae and C. trachomatis were detected at least once in 39.3% and 22.4% of individuals, respectively, with 15% of symptomatic episodes in both cases. Active syphilis infection was detected in 15.4% of individuals. Conclusions Since numerous microbiological tests are required during PrEP, the availability of specific technical platforms should not be neglected by centers wishing to set up PrEP consultations.

With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical–medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.

Background Tuberculous pleural effusion (TPE) is often misdiagnosed as severe Mycoplasma pneumoniae pneumonic effusion (SMPPE) in children at early stage. The aim of this study was to develop a predictive model based on clinical and laboratory indices to make accurate differential diagnosis. Methods Patients included in this study were 167 children (83 patients with TPE and 84 with SMPPE), containing 117 patients for predictive model development and 50 patients for external validation. Multivariate logistic regression analysis was conducted to select potentially useful characteristics for discrimination of TPEs. External validation was performed for model evaluation. Results Multivariate analysis revealed that blood neutrophils and serum lactate dehydrogenase were significant independent factors to discriminate between TPEs and SMPPEs. The results indicated that blood neutrophils ≤69.6% and concentration of serum lactate dehydrogenase ≤297 U/L were the extremely important discrimination factors of TPEs. The area under the receiver operating characteristic curve of the model was 0.9839. The accuracy rate, sensitivity and specificity of the model were 94.02%, 98.28% and 89.83%, respectively. Meanwhile, the accuracy rate of the external validation from the 50 patients was 94.0%. Conclusions Applying a predictive model with clinical and laboratory indices can facilitate the differential diagnosis of TPE from SMPPE in children, which seems helpful when a microbiologic or histologic diagnosis of pleural tuberculosis could not be established.