Diagnostic Microbiology Research Articles

Integrated decentralized blood culture incubation: A step towards a 24/7 microbiology service?

To have an impact on the mortality of bloodstream infections, microbiological diagnostics of blood cultures (BC) should provide first results within 12 h. Here, we show how a decentralized BC incubation connected to the central BC incubators via a browser-based application significantly reduces turnaround times.

Validation of a qualitative real-time PCR assay for the detection of Candida auris in hospital inpatient screening.

This study overviews the validation and implementation of a molecular screening tool for the detection of Candida auris in a College of American Pathologist-accredited clinical laboratory. This molecular laboratory-developed test is both highly sensitive and specific and has significant health-system cost-savings associated with significantly reduced turn-around-time compared to traditional standard-of-care culture-based work up. This method and workflow is of interest to support clinical microbiology diagnostics and to help aid in hospital inpatient, and infection prevention control screening.

Sampling for the diagnosis of orthopaedic surgical infections

Orthopaedic surgical infections, in Denmark, are managed heterogeneously, both within the orthopaedic surgical and the clinical microbiological specialty. More uniform guidelines for sampling and clinical microbiological diagnostics for suspected orthopedic surgical infections would be appropriate. The purpose of this review is therefore to initiate a process aiming for consensus on sampling methods of tissue materials and fluids and clinical microbiological sample handling.

An alternative method for SARS-CoV-2 detection with use modified fluorescent in situ hybridization

The real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) tests are the gold standard in detecting SARS-CoV-2 virus infection. However, despite high sensitivity and specificity, they have limitations that in some cases may result in false negative results. Therefore, it is reasonable to search for additional tools that could support microbiological diagnosis of SARS-CoV-2. The aim of the study was to develop a highly specific molecular test capable of detecting and visualizing SARS-CoV-2 infection. A universal probe and a set of 18 specific oligonucleotides with a FLAP sequence attached to them on both sides were designed to visualize SARS-CoV-2 virus infection based on the fluorescence in situ hybridization method (FISH). FISH conditions using the developed kit were standardized on the Vero CCL-81 cell line infected by SARS-CoV-2 virus. The method was tested on 290 nasopharyngeal swabs (collected in a doublet) from patients with clinical symptoms of SARS-CoV-2. Each one swab from the doublet was subjected to RNA isolation and amplification by rRT-PCR. From the second swab, a microscopic preparation was performed for FISH. The use of the rRT-PCR allowed obtaining 200 positive and 90 negative results, while our FISH method allowed for 220 positive results and 70 negative results. The differences obtained using both methods were statistically significant (p = 0.008). The obtained results support the use of FISH as an additional method in microbiological diagnostics of SARS-CoV-2.

Assessment of Adequate Blood Culture Incubation Time to Accentuate Clinically Relevant Results from Blood Culture Instrument and Media System in a Tertiary Care Hospital Lahore

Background: Bloodstream infections necessitate rapid identification and management. Automated blood culture systems have revolutionized diagnostic microbiology by expediting pathogen detection and enabling effective clinical interventions. This study assesses the optimal incubation period for blood cultures in a tertiary healthcare setting, aiming to enhance diagnostic accuracy and support antibiotic stewardship. Objective: To evaluate the adequacy of incubation times in blood cultures for producing clinically significant results using an automated system in a tertiary care setting. Methods: This cross-sectional descriptive study was conducted at the Microbiology Section of Combined Military Hospital, Lahore, from October 2022 to March 2023. All patient blood samples processed through the Bactec/Alert system were studied. Positive samples were cultured on Blood and MacConkey agar and incubated at 35 ± 2°C for 24 hours. Positivity rates, contamination, and patient demographics were analyzed using the Laboratory Information Management System. Results: Of the 8,216 blood culture bottles processed, 490 (5.96%) were flagged as positive. Early detection within the first 24 hours was noted in 41.63% (n=204) of cases, with subsequent detections on the second day at 58.65% (n=258), the third day at 5.30% (n=26), and the fourth day at 0.20% (n=1). The isolated pathogens included gram-positive organisms (16.32%, n=80), gram-negative organisms (80.20%, n=393), and Candida spp. (3.46%, n=17). Conclusion: Timely and effective blood culturing is crucial for the diagnostic confirmation of bacteremia, enabling appropriate pathogen identification and antimicrobial therapy. Shortening detection times can significantly impact clinical outcomes, reduce healthcare costs, and promote antimicrobial stewardship.

The Impact of Artificial Intelligence on Microbial Diagnosis.

Traditional microbial diagnostic methods face many obstacles such as sample handling, culture difficulties, misidentification, and delays in determining susceptibility. The advent of artificial intelligence (AI) has markedly transformed microbial diagnostics with rapid and precise analyses. Nonetheless, ethical considerations accompany AI adoption, necessitating measures to uphold patient privacy, mitigate biases, and ensure data integrity. This review examines conventional diagnostic hurdles, stressing the significance of standardized procedures in sample processing. It underscores AI's significant impact, particularly through machine learning (ML), in microbial diagnostics. Recent progressions in AI, particularly ML methodologies, are explored, showcasing their influence on microbial categorization, comprehension of microorganism interactions, and augmentation of microscopy capabilities. This review furnishes a comprehensive evaluation of AI's utility in microbial diagnostics, addressing both advantages and challenges. A few case studies including SARS-CoV-2, malaria, and mycobacteria serve to illustrate AI's potential for swift and precise diagnosis. Utilization of convolutional neural networks (CNNs) in digital pathology, automated bacterial classification, and colony counting further underscores AI's versatility. Additionally, AI improves antimicrobial susceptibility assessment and contributes to disease surveillance, outbreak forecasting, and real-time monitoring. Despite a few limitations, integration of AI in diagnostic microbiology presents robust solutions, user-friendly algorithms, and comprehensive training, promising paradigm-shifting advancements in healthcare.

External quality assessment schemes in bacteriology support public health in Germany-results from 2006 to 2023.

External Quality Assessment schemes (EQAS) are mandatory to ensure quality standards in diagnostic methods and achieve laboratory accreditation. As host institution for two German culture-based bacteriology EQAS (RV-A and RV-B), we investigated the obtained data of 590 up to 720 surveys per year in RV-A and 2,151 up to 2,929 in RV-B from 2006 to 2023. As educational instruments, they function to review applied methodology and are valuable to check for systemic- or method-dependent failures in microbiology diagnostics or guidelines. Especially, containment of multi-resistant bacteria in times of rising antibiotic resistance is one major point to assure public health. The correct identification and reporting of these strains is therefore of high importance to achieve this goal. Moreover, correct antimicrobial susceptibility testing (AST) per se is important for selecting appropriate therapy, to restrict broad-spectrum antibiotics and minimize resistance development. The reports of participating laboratories displayed a high level of correct identification results in both schemes with mostly consistent failure rates around 2.2% (RV-A) and 3.9% (RV-B) on average. In contrast, results in AST revealed increasing failure rates upon modification of AST requirements concerning adherence to standards and subsequent bacterial species-specific evaluation. Stratification on these periods revealed in RV-A a moderate increase from 1.3% to 4.5%, while in RV-B failure rates reached 14% coming from 4.3% on average. Although not mandatory, subsequent AST evaluation and consistent reporting are areas of improvement to benefit public health.

How Should We Manage Antimicrobial Resistance in Resource-Limited Settings?

Patients living in low- and middle-income countries (LMICs) shoulder the greatest burden of infections caused by antimicrobial-resistant pathogens. Speedy access to appropriate broad-spectrum antimicrobials significantly improves health outcomes and reduces transmission of antimicrobial-resistant pathogens, but persons living in LMICs have compromised access to these antimicrobials. This article considers how inequities in microbiology diagnostics, antimicrobial access, and antimicrobial affordability influence outcomes for patients infected with antimicrobial-resistant pathogens who live in resource-limited settings.

Oxidative stress induced by the human microbiota yeast component as a micromycetes pathogenicity factor

The introduction of MALDI-ToF mass spectrometry into routine microbiological diagnostics has led to a widely extended list of identified microorganisms. This phenomenon also affected mycological studies. Rare basidiomycetes and ascomycetes began to be detected in various types of pathological material. It is often difficult to assess a role of isolated micromycetes in the pathogenesis of a certain disease. In addition to generally admitted pathogenicity factors, such as aggression enzymes, adhesive activity, and toxin formation, induction or inhibition of reactive oxygen species can play a prominent role in pathogenesis of infectious diseases. In our study, we evaluated the total prooxidant and total antioxidant activity of cultivated ascomycete and basidiomycete yeasts from the human intestinal mycobiome. The strains of micromycetes assessed here were obtained from a fecal culture study from patients with gastrointestinal tract pathology and healthy people undergoing a routine medical examination. Identification was carried out analyzing morphological, cultural, biochemical properties and confirmed by mass spectrometry. The total prooxidant and antioxidant activity was assessed by the induced or inhibited malondialdehyde formation during Tween-80 oxidation. It was found that the level of total prooxidant activity in Rhodotorula mucilaginosa, Geotrichum candidum, Candida albicans, Pichia kudriavzevii significantly exceeds the level of total antioxidant activity, and the Pichia kudriavzevii prooxidase activity was more than twice as high as in other studied micromycetes. The revealed ability of some fungi to induce oxidase stress can be considered as one of significant pathogenicity factors of microorganisms that cause pathomorphological changes in human intestinal tissues.

Antibiotic use and resistance patterns at Rumphi District Hospital in Malawi: a cross-sectional study

BackgroundOveruse of antibiotics is a key driver of antimicrobial resistance (AMR) world-wide. Malawi continues to report rising cases of AMR among both in-patients and out-patients. We investigated antibiotic use and resistance patterns among patients with suspected first line antibiotic treatment failure at Rumphi District Hospital, Malawi.MethodsWe used a cross-sectional study design in which records of patients data on culture and antimicrobial sensitivity tests were extracted, alongside treatment history from 2019 to March, 2023, retrospectively. We also included findings for point prevalence survey (PPS) conducted within four hospital wards in June, 2022 by a well-trained multi-disciplinary team from within the hospital. The data was analyzed for antibiotic use, characterization of pathogens and their susceptibility patterns using Microsoft excel and STATA-14 software.ResultsA total of 85 patients’ data records were reviewed on antibiotics resistance pattern in which 54 (63.5%) were females. Patient antibiotic history captured indicated Metronidazole (23%), Gentamycin (20%) and Doxycycline (23%) as the most frequently used antibiotics among clients referred for microbiological investigations. Among locally available antibiotics with over 50% sensitivity were Chloramphenicol (61%), ciprofloxacin (55%), and ceftriaxone (54%). Penicillins were among antibiotics with highest resistance: ampicillin (100%), amoxyclav (90%), Piperacilin-tazobactam (63%). The majority of patients came from STI clinic and presented with genital discharges 44% (n = 39). Over 80% of the isolated N. gonorrhoeae exhibited a reduced susceptibility to gentamycin. Prevalence of Methicillin resistant staphylococcus Aureus (MRSA) was 46% and were mostly isolated from wound pus. Among 80 data records of the patients reviewed during PPS, Ceftriaxone (54.3%) and Metronidazole (23.3%) emerged as the most frequently used antibiotics in the wards which were prescribed empirically without a microbiological indication.ConclusionIn this study setting, we observed high use of watch antibiotics along with problem of multi-drug resistant infections in patients experiencing clinical failure in a variety of clinical syndromes. The findings underline the need to revamp diagnostic microbiology to increase the uptake of antimicrobial susceptibility testing to guide specific prescriptions of broad-spectrum antibiotics in the watch list.

Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel.

Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.

Total Laboratory Automation in Clinical Microbiology: A Note on Needs, Challenges, and Applications in a Pandemic Scenario

Recently, an increasing number of publications on automation in diagnostic laboratories, especially in microbiology, has illustrated its potential impact on modern medicine by enhancing the overall quality of culture-based microbiology testing. In the context of clinical microbiology, total laboratory automation (TLA) is now defined as automating the testing workflow, which comprises all phases from sample inoculation to outcome analysis. Hence, there is a need to design or implement proper laboratory automation management processes to enhance workflow, reduce analysis time, and deliver high-quality results without delay in treatment initiation. This review-cum-perspective article highlights the need and current advancements in diagnostic microbiology automation that could revolutionize laboratory operations in healthcare settings. Automation of the workflow is a crucial advancement in the recent history of laboratory diagnostics that unites many diagnostic specializations into a single track to increase the effectiveness, administration, standardization, reliability, and safety of lab tests. While clinical chemistry laboratories adopted and deployed laboratory automation decades earlier, the process of implementing them into routine clinical microbiological practices has several bottlenecks and is still a lengthy process and fraught with technical and regulatory challenges. Moreover, due to outbreaks including the COVID-19 pandemic of recent times, testing volumes are increasing, and automation could probably be a great solution for small and mid-sized laboratories. This article lists the TLA remedies and the specimen-processing tools that are presently available. The need and challenges to implementing automation in microbiological laboratories are discussed with a note on applications in pandemic scenarios.

The Credibility of Microbiological Diagnostics in MedicalDiagnostic Laboratories Based on the Results of POLMICROExternal Laboratory Quality Control POLMICRO 2023

<br>Introduction: The article describes results of the 30th edition of the Polish National ExternalQuality Assessment Scheme in Microbiology POLMICRO organised by the Centre of QualityControl in Microbiology (CQCM).</br><br>Aim: The evaluation of the reliability of the microbiological diagnostics performed bymedical diagnostic laboratories in Poland.</br><br>Materials and methods: The organiser analysed the results achieved by participants ofprogrammes conducted by CQCM in 2023 concerning important stages of microbiologicaldiagnostics such the as microscopic analysis of Gram-stained slides, identificationof etiological factors of infections, assessment of antimicrobial susceptibility ofmicroorganisms and the detection of antimicrobial resistance mechanisms.</br><br>Results: A positive annual assessment in the POLMICRO 2023 programme was achieved by98.33%, so 413 of 420 participants of the POLMICRO 2023 programme, and all laboratories participatingin the POLMICRO/SSE (n = 132) and POLMICRO/MIKOLOGIA (n = 139) programmes.</br><br>Conclusions: The results of external quality control programmes confirm the reliability oftesting and the high level of microbiological diagnostics performed by medical diagnosticlaboratories in Poland.</br>

State of the microbial spectrum (microbiome) of the ocular surface of patients with cataracts and glaucoma in the early postoperative period

Background. The occurrence of infectious complications in the early postoperative period in patients undergoing ophthalmic surgery remains a persistent challenge in contemporary clinical practice. Typically the treatment regimen involves the administration of a combination of antibiotics and corticosteroids, often utilized in a fixed-dose combination for simplicity. Despite the prevalent use of these regimens, there’s a notable disregard for comprehensive microbiological diagnostics of the conjunctiva in surgical patients, attributed to various socio-economic factors. However, the significance of such diagnostics in forecasting postoperative outcomes is indisputable. Purpose of the study: to determine the medical and economic feasibility of prescribing individual antibacterial and anti-inflammatory medications in fixed combinations (FC) in postoperative treatment regimens for patients scheduled ophthalmic surgeries. Materials and methods. The study included data from 99 patients (65 males and 34 females, mean age 74 (70–77) years) admitted for elective surgery to address cataracts or glaucoma from May to September 2023. Patients were randomly divided to 2 observation groups. The division into groups was carried out according to the drugs (medicines) used in the postoperative treatment regimens, each of which was further divided into 2 subgroups in accordance with ophthalmopathology. The first group of patients received postoperative therapy with the levofloxacin/dexamethasone FC (L-dexopt, RK.O. Rompharm Company S.R.L., RU LP-007490), the second group was treated with a tobramycin/dexamethasone FC (Tobrazon, Kadila Pharmaceuticals, RU P№015176/01). All subjects underwent a comprehensive ophthalmological examination, as well as a microbiological examination of the conjunctival cavity before surgery and 8 days after surgical treatment. Additionally, all patients completed the Ocular Surface Disease Index (OSDI) questionnaire. Results. Analysis of microbial flora changes during therapy revealed an increase in cultures exhibiting a “zero” degree of growth by 29 and 11,1 % in the “cataract” and “glaucoma” subgroups of the fi rst observation group, respectively. The second group showed a similar increase. “zero” degree of growth (11,7 and 28,6 %, respectively). The treatment costs for patients undergoing cataract surgery and receiving the FC levofloxacin/ dexamethasone were 105.9 rubles per treatment course, compared to 40.5 rubles for those undergoing surgery for glaucoma or complicated cataracts. The cost-effectiveness for those treated with the FC tobramycin/dexamethasone in the early postoperative period was 21,6 and 51,9 rubles. respectively. The OSDI scores across in all subgroups ranged from 16,6 to 25,0 points indicating normal values. The administration of FC levofloxacin/dexamethasone and tobramycin/dexamethasone in the early postoperative period for patients with cataracts and glaucoma was clinically effectively in managing the inflammatory process by influencing the microbial spectrum (microbiome) of the ocular surface. No significant differences were observed in the degrees of microflora growth during the preoperative period between the “cataract” and “glaucoma” subgroups, which does not support the hypothesis regarding the antiseptic action of topical antiglaucoma medications in patients with glaucoma at this stage. Conclusions. The conducted medical and economic analysis proved the feasibility of using both drug combination with a slight preference FC levofloxacin/dexamethasone in patients undergoing surgery for glaucoma and FC tobramycin/dexamethasone for those with uncomplicated cataracts in the early postoperative period.

Retrospective Analysis of Antimicrobial Susceptibility Pattern of Pseudomonas aeruginosa from Clinical Samples of Dogs in Grenada, West Indies

Background: Clinical infections caused by multidrug-resistant pathogenic bacteria are associated with increased morbidity and mortality, imposing a severe economic burden. Pseudomonas aeruginosa, a gram-negative bacterium, had demonstrated a prominent level of acquired antimicrobial resistance to its selective antimicrobials. Currently, there is no updated information about the antimicrobial susceptibility pattern of Pseudomonas aeruginosa in Grenada. Hence, the present study aimed to determine the antimicrobial susceptibility pattern of P. aeruginosa from the clinical isolates of dogs in Grenada. Methods: This retrospective study used the diagnostic reports from January 2015 to December 2022. The diagnostic microbiology laboratory reports of canine patients at the Small Animal Clinic of St. George’s University in Grenada were analyzed to study the antimicrobial susceptibility pattern of P. aeruginosa. Result: Among the various bacterial clinical isolates, ninety-one clinical samples were positive for P. aeruginosa. The antimicrobial susceptibility test pattern of these isolates revealed susceptibility to gentamicin (95.6 %), ceftazidime (96.7%), imipenem (97.7%) and ciprofloxacin (97.8%). The result of the present retrospective study illustrates that P. aeruginosa isolates from canine patients in Grenada are susceptible to the recommended antimicrobial drugs. However, this study also revealed the recent development of progressive antimicrobial resistance. This mandates the judicious use of antibacterial drugs against bacterial infections in Grenada.

The EC-COMPASS: Long-term, multi-centre surveillance of Enterobacter cloacae complex – a clinical perspective

Enterobacter cloacae complex (ECCO) comprises closely related Enterobacterales, causing a variety of infections ranging from mild urinary tract infections to severe bloodstream infections. ECCO has emerged as a significant cause of healthcare-associated infections, particularly in neonatal and adult intensive care. The Enterobacter Cloacae COMplex PASsive Surveillance (EC-COMPASS) aims to provide a detailed multi-centre overview of ECCO epidemiology and resistance patterns detected in routine microbiological diagnostics in four German tertiary-care hospitals. In a sentinel cluster of four German tertiary-care hospitals, all culture-positive ECCO results between 1st January 2020 and 31st December 2022, were analysed based on Hybase® laboratory data. Analysis of 31,193 ECCO datasets from 14,311 patients revealed a higher incidence in male patients (P<0.05), although no significant differences were observed in ECCO infection phenotypes. The most common sources of ECCO were swabs (42.7%), urine (17.5%), respiratory secretions (16.1%), blood cultures (8.9%) and tissue samples (5.6%). The annual bacteraemia rate remained steady at approximately 33 cases per hospital. Invasive ECCO infections were predominantly found in oncology and intensive care units. Incidences of nosocomial outbreaks were infrequent and limited in scope. Notably, resistance to carbapenems was consistently low. EC-COMPASS offers a profound clinical perspective on ECCO infections in German tertiary-healthcare settings, highlighting elderly men in oncology and intensive care units as especially vulnerable to ECCO infections. Early detection strategies targeting at-risk patients could improve ECCO infection management.

Longitudinal analysis of 20Years of external quality assurance schemes for PCR/NAAT-based bacterial genome detection in diagnostic testing.

Quality control (QC), quality assurance, and standardization are crucial for modern diagnostic testing in the field of medical microbiology. The need for efficient QC to ensure accurate laboratory results, treatment, and infection prevention has led to significant efforts in standardizing assay reagents and workflows. External quality assessment (EQA) schemes, like those offered by INSTAND, play a vital role in evaluating in-house and commercial routine diagnostic assays, regarded as mandatory by national and global guidelines. The recent impact of polymerase chain reaction/nucleic acid amplification technology (PCR/NAAT) assays in medical microbiology requires that high-performing assays be distinguished from inadequately performing ones, especially those made by inexperienced suppliers. The study assesses the evolving diagnostic performance trends over 2decades for the detection of EHEC/STEC, Borrelia (B.) burgdorferi, and MRSA/cMRSA. It explores the historical context of assay utilization, participant engagement, and rates of correct results in EQA schemes. The research seeks to identify patterns in assay preferences, participant proficiency, and the challenges encountered in detecting emerging variants or clinical strains. The study highlights the decline in in-house PCR assay usage, the emergence of new diagnostic challenges, and educational aspects within EQA schemes. Specific examples, such as the inclusion, in certain EQA surveys, of EHEC strains carrying stx-2f or B. miyamotoi, highlight the role of EQAs in increasing awareness and diagnostic capabilities. Advancements in MRSA detection, especially through the adoption of commercial assays, demonstrate the impact that technology evolution has had on diagnostic performance. Achieving excellence in diagnostic molecular microbiology involves a multifaceted approach, including well-evaluated assays, careful instrumentation selection, and structured training programs. EQA schemes contribute significantly to this pursuit by providing insights into the evolving diagnostic landscape and identifying areas for improvement in the diagnostic workflow as well as in PCR/NAAT assay design.

The Enterics for Global Health (EFGH) Shigella Surveillance Study in Kenya.

Although Shigella is an important cause of diarrhea in Kenyan children, robust research platforms capable of conducting incidence-based Shigella estimates and eventual Shigella-targeted clinical trials are needed to improve Shigella-related outcomes in children. Here, we describe characteristics of a disease surveillance platform whose goal is to support incidence and consequences of Shigella diarrhea as part of multicounty surveillance aimed at preparing sites and assembling expertise for future Shigella vaccine trials. We mobilized our preexisting expertise in shigellosis, vaccinology, and diarrheal disease epidemiology, which we combined with our experience conducting population-based sampling, clinical trials with high (97%-98%) retention rates, and healthcare utilization surveys. We leveraged our established demographic surveillance system (DSS), our network of healthcare centers serving the DSS, and our laboratory facilities with staff experienced in performing microbiologic and molecular diagnostics to identify enteric infections. We joined these resources with an international network of sites with similar capabilities and infrastructure to form a cohesive scientific network, designated Enterics for Global Health (EFGH), with the aim of expanding and updating our knowledge of the epidemiology and adverse consequences of shigellosis and enriching local research and career development priorities. Shigella surveillance data from this platform could help inform Shigella vaccine trials.

INTERDISCIPLINARY INTEGRATION OF MICROBIOLOGY, VIROLOGY, AND IMMUNOLOGY IN THERAPEUTIC STOMATOLOGY

Introduction: This article examines the potential for integrating Therapeutic Stomatology with Microbiology, Virology, and Immunology. It highlights the significance of studying key concepts in these disciplines, which underpin various methods of microbiological diagnostics utilized in dentistry. Practical skills and theoretical knowledge essential for the study of Therapeutic Stomatology are exemplified. The aim of this paper is to underscore the significance of interdisciplinary integration between Microbiology, Virology, and Immunology with Therapeutic Stomatology in the education and training of future dental practitioners.&#x0D; Results and Discussion: A solid grasp of microbiology is crucial for fostering the clinical acumen of future dental professionals. The integration of disciplines should be systematically woven into all phases of the educational curriculum. By merging fundamental and clinical disciplines, a multidimensional approach to problem-solving is facilitated, highlighting the interconnectedness between fields. This integration enhances students' intellectual, cognitive, and communicative abilities, broadening their educational horizons and enabling the application of foundational knowledge in novel contexts. Consequently, this approach nurtures the development of clinical reasoning skills among aspiring dental practitioners.&#x0D; Conclusions: The interdisciplinary integration of Microbiology, Virology, and Immunology with Therapeutic Stomatology in professional training ensures educational coherence, enhances the organization and refinement of knowledge and skills, and lays the groundwork for cultivating professionals characterized by versatile thinking and comprehensive expertise in their field.

Deficits in blood culture collection in the emergency department if sepsis is suspected: results of a retrospective cohort study

PurposeBlood cultures (BCs) are key for pathogen detection in septic patients. We investigated the extent to which sampling was performed and what factors were associated with the absence of general or inadequate BC sampling.MethodsWe conducted a retrospective cohort study of hospitalized patients with sepsis admitted to one of three EDs in 2018. Primary outcome was the extent of general BC collection of at least 1 set. Secondary outcome was the extent of adequate BC sampling, defined as ≥ 2 sets before antibiotic therapy (AT). Multivariable logistic regression analysis was performed to identify factors associated with deficits in both outcomes.Results1143 patients were analyzed. BCs were collected from 946 patients. Single BCs were taken from 520 patients, ≥ 2 sets from 426 patients. Overall, ≥ 2 BCs were taken from 349 patients before AT. BC sampling before AT occurred significantly more frequently when ≥ 2 BC sets were taken rather than a single one (81.9%, versus 68.4%, p < 0.001) and this also led to the highest pathogen detection rate in our cohort (65.6%). A body temperature of ≥ 38 °C was the a supporting factor for general and adequate BC collection in all three EDs. Retrospective analysis of 533 patients showed that the qSOFA score had no influence on general or adequate BC collection.ConclusionData on everyday clinical practice in the pre-analytical phase of microbiological diagnostics shows considerable deficits and indicates the need for more implementation of best practice. The variations identified in BC sampling between EDs should be further investigated.