A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology

Swabs versus native specimens in severe head and neck infections: a prospective pilot study and suggestions for clinical management

INTRODUCTION

Head and neck infections, particularly odontogenic infections, can lead to serious complications if not properly managed. While swabs are commonly used for microbial identification, their reliability in polymicrobial infections is debated. This study evaluates the advantages of native tissue samples over swabs in the management of severe head and neck infections.

MATERIAL AND METHODS

This prospective cohort study included patients with severe acute head and neck infections requiring hospitalization, surgical drainage, and microbiologic analysis. Swabs and native tissue/fluid samples were collected for pathogen cultivation, Gram staining, and resistance testing. Clinical data, infection characteristics, and antimicrobial resistance profiles were analyzed using descriptive and inferential statistics.

RESULTS

60 patients, 55% male (45.7 years) and 45% female (48.1 years) were analyzed. After antibiotic treatment, CRP and leukocyte levels decreased significantly, with higher CRP correlating with longer hospital stays. ICU admission correlated with hospital stay > 7 days. More Actinomyces and fungal species were identified in native tissue samples and more Streptococci in swabs. Antibiotic resistance, especially to clindamycin (1/3 of the cases), was associated with longer hospital and ICU stays. Clindamycin resistance correlated with increased ICU admission, while metronidazole resistance (10% of the cases) was associated with longer ICU stays. ICU admission was also associated with higher Cormack-Lehane scores.

CONCLUSION

Severe head and neck infections require a comprehensive multidisciplinary approach. Native tissue should be obtained whenever possible. While microbiological findings varied between sampling methods, native samples may provide a broader spectrum of detected pathogens, which could be relevant for infection management. Given the increasing resistance to clindamycin, its indications should be critically re-evaluated. The implementation of targeted antimicrobial strategies and a risk-based classification system may help optimize patient management and improve outcomes.

The evolving landscape of live biotherapeutics in the treatment of Clostridioides difficile infection

Clostridioides difficile (C. difficile) infection (CDI) is common after antibiotic exposure and presents significant morbidity, mortality and healthcare costs worldwide. The rising incidence of recurrent CDI, driven by hypervirulent strains, widespread antibiotic use and increased community transmission, has led to an urgent need for novel therapeutic strategies. Conventional antibiotic treatments, although effective, face limitations due to rising antibiotic resistance and high recurrence rates, which can reach up to 60% after multiple infections. This has prompted exploration of alternative therapies such as fecal microbiota-based therapies, including fecal microbiota transplantation (FMT) and live biotherapeutics (LBPs), which demonstrate superior efficacy in preventing recurrence. They are aimed at restoring the gut microbiota. Fecal microbiota, live-jslm and fecal microbiota spores, live-brpk have been approved by the U.S. Food and Drug Administration in individuals aged 18 years or older for recurrent CDI after standard antimicrobial treatment. They have demonstrated high efficacy and a favorable safety profile in clinical trials. Another LBP under study includes VE-303, which is not derived from human donor stool. This review provides a comprehensive overview of the current therapeutic landscape for CDI, including its epidemiology, pathophysiology, risk factors, diagnostic modalities and treatment strategies. The review delves into the emerging role of live biotherapeutics, with a particular focus on fecal microbiota-based therapies. We explore their development, mechanisms of action, clinical applications and potential to revolutionize CDI management.

The Utility of Blood Cultures in Non-Febrile Patients and Patients with Antibiotics Therapy in Internal Medicine Departments

Background: The injudicious use of blood cultures is associated with low cost-effectiveness and leads to unnecessary follow-up tests for false-positive results. In addition, false negatives can result in missed diagnoses, leading to delays in initiating appropriate treatment and potentially worsening patient outcomes. The timing of the blood culture tests related to the highest diagnostic yield is not fully elucidated. We hypothesized that a high proportion of the tests are done within non-optimal timing, resulting in a lower clinical yield. We specifically focused on the consequences of BC obtained in afebrile patients. Methods: We assessed 73,787 blood cultures taken between 2014 and 2020 in patients hospitalized with a suspected infection. Blood cultures were considered taken at optimal timing if the per rectum temperature was 38.3 °C or more and no prior antibiotics were given. Only the first culture per patient was assessed. The primary outcome was a true bacteremia defined by the clinically important pathogen. Results: Therefore, 25,616 blood cultures were obtained at optimal timing (34.7%), with true bacteremia found in 6.15% vs. 5.15% in cultures obtained at non-optimal timing. In a multivariable model, optimal timing adjusted for the variety of the clinical, demographic, and laboratory findings' optimal timing was significantly associated with an increase in the odds of detecting true bacteremia (OR:1.23, 95% CI: 1.12-1.35). Conclusions: Nearly two-thirds of patients hospitalized due to a suspected infection did not have their blood cultures taken at the optimal time. Our findings underscore the importance of integrating clinical judgment, patient-specific risk factors, and evidence-based criteria when deciding to perform blood cultures, rather than relying solely on fever as an indicator.

Clinical characteristics, antimicrobial resistance, and mortality of neonatal bloodstream infections in Northern Tanzania, 2022-2023

Neonatal bloodstream infections (BSI) make a substantial contribution to morbidity and mortality in low- and middle-income countries (LMICs), but data on the epidemiology and antimicrobial resistance (AMR) in Tanzania are limited. We describe the prevalence, resistance patterns, and associated factors of neonatal BSI at the Kilimanjaro Christian Medical Centre (KCMC), a large referral hospital in northern Tanzania. We conducted a prospective, observational study involving infants aged 0-60 days with perinatal risk factors or clinical signs of sepsis. Aerobic blood cultures were obtained at enrollment and monitored using a continuously monitored blood culture instrument. Antimicrobial susceptibility testing was performed using standard phenotypic methods. Vital status was obtained on days 2, 7, and 28 post-enrollment. BSI was defined as the isolation of established neonatal pathogens, including yeast and coagulase-negative Staphylococcus spp. (CoNS). Early-onset BSI occurred on day of life (DOL) 0-2, while late-onset BSI occurred on DOL 3 or later. Among 236 enrolled infants, blood culture was obtained in 233. BSI occurred in 106 (45.5%) of 233 infants, 50 (47.2%) were early-onset, and 56 (52.8%) were late-onset BSI. The isolated pathogens included 58 (54.7%) Gram-positive bacteria, 40 (37.7%) Gram-negative bacteria, and 8 (7.5%) yeast. CoNS (n = 55, 51.9%) and Klebsiella pneumoniae (n = 35, 33.0%) were the most common pathogens. Notably, all K. pneumoniae isolates were extended-spectrum beta-lactamase producers, resistant to ampicillin and ceftriaxone. Among the 56 infants who died, 29 (51.8%) had BSI; 11 (19.6%) infants with EO-BSI, and 18 (32.1%) with LO-BSI. Infants requiring respiratory support at admission had a 1.89-fold increased adjusted odds of BSI (95% CI, 1.05-3.44). We found high prevalence of neonatal BSI due to bacteria with a high prevalence of AMR, and BSI was associated with high mortality. There is an urgent need for effective preventive, diagnostic, and therapeutic interventions to address BSI among hospitalized infants in northern Tanzania.

Survival and risk factor analysis in patients with septic arthritis: a retrospective study of 192 cases

BACKGROUND

Septic arthritis (SA) presents a complex clinical challenge, often resulting in significant morbidity and mortality. This study aimed to (1) assess overall mortality rates and (2) identify potential factors contributing to increased mortality risk in patients with SA.

METHODS

This retrospective study on SA patients treated at a German university hospital between January 1, 2011, and December 31, 2021. Patients were identified using International Classification of Diseases (ICD)-10 codes for septic arthritis, specifically "M00.-". The study evaluated mortality rates and analyzed comorbidities, pathogens, and other potential risk factors. Kaplan-Meier survival curves and odds ratios (OR) were calculated to assess mortality risk.

RESULTS

In a cohort of 192 patients diagnosed with SA, 64 patients (33.3%) died during a mean follow-up period of 54.4 ± 42 months. The overall mortality rate was 17.5% at one year, 19.9% at two years, and 28.3% at five years. Patients aged 65 years or older, as well as those with arterial hypertension, congestive heart failure, chronic renal disease, chronic liver disease, malignancy, steroid use and immunosuppression showed significantly higher mortality rates (p < 0.05). Chronic renal disease (OR = 2.80), malignancy (OR = 3.40), and chronic heart failure (OR = 2.62) were identified as significant notably risk factors for mortality.

CONCLUSION

This study highlights a notably high mortality rate among vulnerable patients with SA, particularly those with pre-existing comorbidities. Recognizing and addressing these risk factors early could improve patient outcomes. These results unterscore the need for close monitoring of SA patients, particularly those with chronic organ conditions, and timely intervention for sepsis to reduce mortality risk.

Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples

Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.

Highly Drug-Resistant Escherichia coli from Hospital Wastewater with Several Evolutionary Mutations: An Integrated Insights from Molecular, Computational, and Biophysics

Many people around the world are still unable to get access to clean drinking water. Escherichia coli is a common waterborne pathogen that frequently results from insufficient hygiene measures and needs attention to address health problems. The present study aimed to evaluate antibiotic resistance of Escherichia coli isolated from wastewater and drinking water samples of hospital and non-hospital settings at Peshawar. Out of 462 samples collected, 111 tested positive for E. coli. The majority of isolates were resistant to many antibiotics including Ampicillin, Gentamicin, Tobramycin, Imipenem, Meropenem, Tetracycline, Cefepime, Amikacin, Piperacillin, Levofloxacin, Ciprofloxacin, Ceftriaxone, and Cefazolin. However, they showed susceptibility to Chloramphenicol, Fosfomycin 200 mg, Colistin, and Tigecycline. Genetic analysis revealed various antibiotic resistance genes within the isolates, i.e., marA(20%), marB(40%) marR(30%), rob(30%), and soxS(35%). Following PCR, the resulting products underwent next-generation sequencing. marA exhibited T10P and D101H mutations, while MarR showed substitutions at M1G, V142S, L143P, and P144C positions. In Rob, D2I, A4P, L10F, I12N, and L253P mutations were observed. The SoxS displayed alterations at H105P, R106A, and L107V positions. Asinex antibacterial library was used to study molecular docking based on virtual screening. SWISS ADME was used to in silico evaluate the pharmacokinetics of these substances. 100 ns molecular dynamics simulation was conducted to estimate free binding energies, confirmation, and stability of the binding mode of the identified compounds. Screening results revealed that LAS-52505571, LAS52171241, LAS52202332, and LAS22461675 compounds showed high affinity to MarA, MarR, SoxS, and Rob proteins, respectively, with the lowest binding energies across the library. In brief, the current study aimed at establishing potential chemical entities that could facilitate the evolution of silicon drugs against antibiotic-resistant E. coli strains.

Fluorescent antibody-based detection and ultrastructural analysis of Streptococcus pneumoniae in human sputum

BACKGROUND

Pneumococcal pneumonia continues to be a significant global health burden, affecting both children and adults. Traditional diagnostic methods for sputum analysis remain challenging. The objective of this study was twofold: to develop a rapid and easy-to-perform assay for the identification of Streptococcus pneumoniae (Spn) directly in sputum specimens using fluorescence microscopy, and to characterize with high-resolution confocal microscopy the ultrastructure of pneumococci residing in human sputum.

METHODS

We fluorescently labeled antibodies against the pneumococcal capsule (Spn-FLUO). The specificity and sensitivity of Spn-FLUO for detecting Spn was evaluated in vitro and in vivo using mouse models of carriage and disease, human nasopharyngeal specimens, and sputum from patients with pneumococcal pneumonia. Spn was confirmed in the specimens using culture and a species-specific qPCR assay. Spn strains were serotyped by Quellung. Confocal microscopy and Imaris software analysis were utilized to resolve the ultrastructure of pneumococci in human sputum.

RESULTS

Compared with cultures and qPCR, Spn-FLUO demonstrated high sensitivity (78-96%) in nasopharyngeal samples from mice and humans. The limit of detection (LOD) in nasopharyngeal samples was ≥ 1.6 × 10⁴ GenEq/ml. The specificity in human nasopharyngeal specimens was 100%. In lung specimens from mice infected with pneumococci, Spn-FLUO reached 100% sensitivity with a LOD of ≥ 1.39 × 10⁴ GenEq/ml. In human sputum, the sensitivity for detecting Spn was 92.7% with a LOD of 3.6 × 10³ GenEq/ml. Ultrastructural studies revealed that pneumococci are expectorated as large aggregates with a median size of 1336 μm².

CONCLUSIONS

Spn-FLUO is a rapid and sensitive assay for detecting Spn in human sputum within 30 min, encompassing a range of both vaccine and non-vaccine serotypes associated with pneumococcal pneumonia. The study highlights that most pneumococci form aggregates in human sputum.

Genital Herpes Simplex Virus Infections in Women-A Clinical Update

Genital herpes is a relatively common chronic lower genital tract sexually transmitted infection caused by herpes simplex virus types 1 and 2 (HSV-1 and HSV-2). It is characterized by recurrent, self-limited genital ulcers, and it is the leading cause of genital ulcer disease worldwide (1). The impact of genital herpes on sexual and reproductive health, including the risk of perinatal infection, necessitates a profound understanding of its clinical presentation, diagnosis, treatment, and prevention. This chapter aims to review the critical clinical aspects of HSV in women, emphasizing relevant evidence-based data.

Adherence to Palivizumab for Respiratory Syncytial Virus Prophylaxis in Romanian Infants

BACKGROUND

In 2022, Romania started an RSV immunoprophylaxis program with Palivizumab for infants at high risk: preterm infants born before 35 weeks of pregnancy, infants born with congenital heart defects, and infants with chronic lung disease. We evaluated treatment adherence from August 2022 to March 2024.

METHOD

We monitored the increase in the number of patients enrolled in the program and the number of collaborating neonatologists, family doctors, and pediatricians. Adherence to all doses of Palivizumab in enrolled patients was assessed by telephone interviews. The factors contributing to reduced adherence were identified.

RESULTS

Between August 2022 and March 2024, 1903 patients and 233 specialists were enrolled, a steady increase in both cohorts. The percentage of patients that complete their full sequence of doses decreases along with the number of doses (99% for one dose, 73% for two doses, 47% for three doses, 35% for four doses, and 22% for five doses) due to several factors.

CONCLUSIONS

The program remains highly regarded by both physicians and caregivers, demonstrating its effectiveness as a valuable resource for educating parents and facilitating monoclonal antibody administration as a prevention method for RSV.

Rate of Urine Culture Contamination with Different Methods of Urine Specimen Collection

BACKGROUND

Midstream urine (MSU) samples are commonly collected at the time of patient evaluation despite known high rates of contamination.

OBJECTIVE

The primary objective of this study was to evaluate the rate of mixed flora results in urine specimens obtained by MSU compared to straight catheterization urine (SCU).

STUDY DESIGN

This was a quality improvement project evaluating urine culture results of women who provided either an MSU or SCU sample for analysis. Adult women seen within urogynecology clinics at a tertiary care center between April and August 2023 who had urine cultures performed for any indication were included. Mixed flora was defined as the presence of ≥ 2 non-uropathogens or 1 uropathogen in low quantity (at least 10 times fewer) compared to the concentration of nonsignificant organisms.

RESULTS

Three hundred forty women provided a urine specimen during the study period. SCU collection was performed for 171 (50.3%) women while 169 (49.7%) provided an MSU sample. Overall, 18.8% of urine cultures were reported as mixed flora (33.1% in MSU and 4.7% in SCU, p < 0.001). Mixed flora was more common with MSU specimens (87.5%, p < 0.001) and associated with a higher BMI compared to positive or negative cultures (mixed flora 29.8 kg/m2 ± 16.3, positive or negative cultures 27.8 kg/m2 ± 7.0, p = 0.04). MSU samples had increased odds of urine contamination compared to SCU collection (7.40 aOR, 95% CI 3.01-18.24).

CONCLUSION

The prevalence of mixed flora was reduced significantly when SCU samples were obtained. Clinicians should consider performing SCU collection when a urine specimen is required for patient evaluation.

Diagnostic value of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

BACKGROUND

Current diagnostic methods of lower respiratory tract infections (LRTIs) often lack specificity, underscoring the necessity for advanced technologies such as metagenomic next-generation sequencing (mNGS).

METHODS

This retrospective study compared bronchoalveolar lavage fluid (BALF) analysis using mNGS and conventional microbiological tests (CMT) to evaluate their effectiveness in pathogen identification and alignment with clinical diagnoses.

RESULTS

In this study involving 369 patients suspected of LTRIs, mNGS identified pathogens in 342 cases (92.7%), showing superior diagnostic performance compared to CMT (58.8%). The positive agreement and negative agreement rates of mNGS were 92.7% and 96.3%, respectively, both significantly higher than those of CMT (both p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were significantly higher than those of CMT, with values of 99.7% vs. 57.1%, 68.4% vs. 26.3%, 96.5% vs. 87.1%, and 96.3% vs. 6.3%, respectively (all p<0.001). Pathogen detection rates among the patients showed that 89.7% had evidence of LRTIs, with bacterial infections (20.1%), mycoplasma (13.6%), mycobacterium (4.3%), fungal (4.1%), viral (3.3%), and mixed infections (44.4%) being the most common. Furthermore, the study also differentiated the distribution of pathogens between adults and pediatric patients, and assessed the impact of pathogen types on severe outcomes using multivariate logistic regression, revealing that viral and fungal infections were more likely associated with severe symptoms, whereas mycoplasma infections typically presented with milder symptoms.

CONCLUSIONS

BALF mNGS proves effective for rapid, comprehensive pathogen detection in LRTIs, warranting its early use for enhanced diagnosis and management, especially across different age groups.

The Diagnostic Efficacy of Rapid Urine Sediment Fluorescence Staining in Urinary Tract Infections: An Exploratory Study

OBJECTIVE

To investigate rapid and early diagnostic approaches for urinary tract infections (UTIs).

METHODS

Coincidence rates, sensitivities, and specificities of fungal fluorescence staining for fungal detection were calculated. Additionally, the positive rate of cellular fluorescence staining was compared with bacterial urine culture, with a focus on the increasing correlation between fluorescently stained bacteria proportions and the concordance between methods. Furthermore, diagnostic performance for detecting cocci and bacilli via histocyte fluorescence staining was evaluated. Receiver Operating Characteristic (ROC) curve analyses were conducted to determine the diagnostic accuracy of urine sediment fluorescence staining for fungal and bacterial UTIs.

RESULTS

Fungal fluorescence staining of urine sediment demonstrated a coincidence rate of 95.90%, sensitivity of 94.44%, and specificity of 96.05%. The positivity of cellular fluorescence staining exceeded that of bacterial culture (P=.014), and an enhanced agreement between the 2 methods was observed with a rise in the proportion of stained bacteria. For histocyte fluorescence staining in identifying cocci and bacilli, coincidence rates were 76.92% and 74.36%, sensitivities were 51.85% and 73.85%, and specificities reached 82.43% and 88.18%, respectively. The ROC curve areas for diagnosing fungal and bacterial UTIs using urine sediment fluorescence staining were 0.952 and 0.87, respectively.

CONCLUSION

Urine sediment fluorescence staining offers promise as a rapid diagnostic tool for UTIs, demonstrating high sensitivity and specificity for fungal detection and a competitive performance in bacterial identification when compared to standard culture methods. These findings highlight the potential utility of this technique in clinical settings for prompt and accurate UTI diagnosis.

Assessment of bacterial isolates and antimicrobial susceptibility patterns in external ocular infections among patients attending eye clinic at Kafrelsheikh University Hospitals

BACKGROUND

Ocular infections can harm the eye's anatomic structure on numerous levels. They are a global health issue. Endophthalmitis, a serious complication following cataract surgery, can result in substantial ocular morbidity and vision loss despite the administration of antibiotics. Bacterial ocular flora are the primary causative agents. This study aimed to assess the types of bacterial isolates on the external ocular surface and evaluate their antimicrobial susceptibility patterns in pre-operative cataract patients at Kafrelsheikh University Hospitals.

METHODS

This cross-sectional study enrolled 691 patients scheduled for routine cataract surgery in the Department of Ophthalmology at Kafrelsheikh University Hospitals, Egypt. Each patient underwent a comprehensive assessment of medical history, including the use of traditional medicine, past eye trauma, and any prior eye surgeries, as well as ophthalmic clinical data such as visual acuity and ocular surface disorders. Conjunctival swabs were collected and processed using standard microbiological procedures to identify bacterial isolates and their respective antimicrobial susceptibility patterns.

RESULTS

Among the 691 patients enrolled (median age 60 years, IQR 54-66), 59.8% were female. Conjunctival cultures yielded positive results in 38 cases (5.6%). The most frequently isolated organisms were Staphylococcus aureus, accounting for 52.6% of isolates, followed by Staphylococcus epidermidis at 15.8%. Notably, S. aureus demonstrated the highest resistance to erythromycin and vancomycin, with all 20 isolates showing resistance. In contrast, linezolid exhibited high efficacy, with 19 isolates showing sensitivity and only one displaying resistance.

CONCLUSION

This study indicated that ocular conditions such as dry eye syndrome, Meibomian gland dysfunction, and scaly blepharitis are strongly associated with the prevalence of culture-confirmed ocular infections. Regarding antibiotic susceptibility, most Staphylococcus species demonstrated the greatest sensitivity to linezolid and trimethoprim/sulfamethoxazole.

A program to improve sepsis management in the Emergency Department: a multicenter prospective study in France

Implementation of a regional sepsis program to improve compliance with sepsis care bundles and optimize septic patient management and outcomes in the Emergency Department (ED). The program included a multifaceted intervention in 8 EDs: creation of a regional sepsis team, meetings, education (yearly 6-h course and site visits) and sepsis alert. Clinical practice was evaluated in each ED during 1 month every year over 3 years. The primary outcome was the initiation of all criteria of the Surviving Sepsis Campaign (SSC) bundle within 3 h after triage. Secondary outcomes were the initiation of the 3-h bundle in patients with hypotension (SBP ≤ 100 mmHg), admission related to infection or not, proportion of organ supports, subsequent intensive care unit (ICU) admission, and early mortality (day 7). During the 3-month study period, 739 patients were identified with a sepsis including 8% with septic shock. Compliance with the SSC bundle improved during the three periods (P1: 28/176 (16%), P2: 42/272 (15%), P3:69/291 (24%), p = 0.023). In patients with hypotension (n = 142, 19%), no improvement was observed (P1:12/38 (32%), P2:18/46 (39%), P3: 28/58 (48%), p = 0.255). Mortality on day 7 was also similar (10% vs 11% vs 9%, p = 0.621). In multivariate analysis, age (OR = 1.03; 95% CI 1.01-1.05, p = 0.003) and confusion (OR = 2.37; 95% CI 1.37-4.14, p = 0.002) were independently associated with D7 mortality. Patients referred to ED for infection had a better prognosis compared to those with a non-specific reason (OR = 0.56; 95% CI 0.32-0.97, p = 0.038). A regional sepsis educational program appears to improve compliance with the SSC bundle. Pre-hospital identification of sepsis appears to improve further management.

Distinct relative abundances in pathogens detected in mechanically ventilated patients with suspected pneumonia in the intensive care unit at King Abdulaziz University Hospital

In this study, we present for the first time the landscape of the lung microbiota in patients with ventilator-associated pneumonia in Intensive Care Units in Saudi Arabia. DNA from 83 deep endotracheal aspirate lung samples was subjected to PacBio sequencing to identify pathogens in comparison with conventional diagnostic techniques. Patients on ventilation with pneumonia presented with similar lung flora to those of patients on ventilation without pneumonia. Proteobacteria, Firmicutes, and Bacteroidetes were detected in the majority of the samples. Samples treated with different antibiotics exhibited similar abundances of phyla and families. In order, the ten most common species detected in 16 clusters were Klebsiella pneumoniae, Stenotrophomonas maltophilia, Haemophilus influenzae, Pseudomonas aeruginosa, Metamycoplasma salivarium, Elizabethkingia anophilis, Staphylococcus aureus, Acinetobacter baumannii, Prevotella oris and Klebsiella africana. Of 51 on ventilation with pneumonia, the pathogens identified through sequencing corresponded with the findings from culture-dependent tests in 26 patients (50.98%), whereas the results differed in 30 patients (58.82%). Of 32 patients on ventilation without pneumonia, the pathogens identified through sequencing matched the conventional diagnostics results in only two patients (6.25%) but differed in 25 patients (78.13%). In summary, patients on mechanical ventilation with pneumonia did not display notable phenotypic traits. K. pneumoniae and S. maltophilia were the most common taxa detected in the samples, although some variations in microbial composition were observed. We conclude that Intensive Care Units exhibit distinct patterns of microbial colonization.

Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future

Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.

Interrupted-time-series analysis of the impact of COVID-19 pandemic on blood culture utilization in Shanghai

BACKGROUND

Limited information is available regarding the changes in blood culture utilization following the COVID-19 pandemic. Blood culture utilization rate is a critical indicator of diagnostic efficiency for infectious diseases. This study aims to describe the impact of the COVID-19 pandemic on blood culture utilization rate in Shanghai.

METHODS

We conducted an interrupted time-series analysis based on electronic health records from the Shanghai Changzheng hospital from January 2014 to October 2023. The outcome measure was the rate of blood culture utilization among inpatients with a temperature of ≥ 39.4 °C. The impact of the COVID-19 pandemic on blood culture utilization was quantified by fitting linear segmented regression models and modelling the relative cumulative effect by the end of the study. The pandemic period was defined from February 2020, following the implementation of strict containment measures in Shanghai.

RESULTS

A total of 23,761 inpatients with a temperature of ≥ 39.4 °C were included in the analysis. From 2014 to 2023, the utilization rate of hospital blood cultures increased initially and then declined, with a significant change point following the onset of the COVID-19 pandemic (Cochran-Armitage trend test, P < 0.001). The COVID-19 pandemic was associated with a significant change in the slope of the blood culture utilization rate (pre-COVID-19 vs. during-COVID-19: 0.31% per month vs. -0.30% per month, P < 0.001), resulting in a relative cumulative effect of -12.55% at the end of the study (95% confidence interval, -19.08 to -6.03). This corresponds to 407 inpatients who did not have blood cultures taken during-pandemic, which represents a significant deviation from pre-pandemic trends.

CONCLUSIONS

The upward trend in blood culture utilization rate among inpatients stalled during the COVID-19 pandemic and did not return to pre-pandemic levels following the pandemic. These findings suggest that the pandemic had a lasting impact on diagnostic practices. More targeted intervention measures are needed to promote appropriate utilization of blood cultures.

Performance of deep learning models in predicting the nugent score to diagnose bacterial vaginosis

The Nugent score is a commonly used diagnostic tool for bacterial vaginosis. However, its accuracy depends on the skills of laboratory technicians. This study aimed to evaluate the performance of deep learning models in predicting the Nugent score to improve diagnostic consistency and accuracy. In total, 1,510 vaginal smear images collected from a hospital in Japan between 2021 and 2023 were assessed. Each image was annotated by laboratory technicians into one of four categories based on the Nugent score-normal vaginal flora, no vaginal flora, altered vaginal flora, or bacterial vaginosis. Deep learning models were developed to predict these categories, and their performance was compared to that of technician annotations. The deep learning models demonstrated 84% accuracy at 400× magnification and 89% at 1,000× magnification. The 1,000× model was further optimized and tested on an independent set of 106 images. After optimization, the advanced model achieved 94% accuracy, outperforming the average 92% accuracy of the technicians. The agreement between the advanced model predictions and technicians was 92% for normal vaginal flora, 100% for no vaginal flora, 91% for altered vaginal flora, and 100% for bacterial vaginosis. Overall, our findings suggest that deep learning models have the potential to diagnose bacterial vaginosis with an accuracy comparable to that of laboratory technicians.IMPORTANCEBacterial vaginosis is a global health issue affecting women, causing symptoms such as abnormal vaginal discharge and discomfort. The Nugent score is a standard method for diagnosing bacterial vaginosis and is based on the manual interpretation of Gram-stained vaginal smears. However, this method relies on the skill and experience of trained professionals, leading to variability in results and poses significant challenges for settings with limited access to experienced technicians. The results of this study indicate that deep learning models can predict the Nugent score with high accuracy, offering the potential to standardize the diagnosis of bacterial vaginosis. By reducing observer variability, these models can facilitate reliable diagnoses, even in settings where experienced personnel are scarce. Although validation is needed on a larger scale, our results suggest that deep learning models may represent a new approach for diagnosing bacterial vaginosis.

Outcomes of Postcataract Surgery Endophthalmitis Managed Without Microbial Cultures

PURPOSE

To evaluate outcomes of eyes with postcataract surgery endophthalmitis that were managed without microbial cultures.

DESIGN

This retrospective, single-center comparative cohort study identified all cases of endophthalmitis after cataract surgery presenting between February 1, 2014, and November 1, 2022.

SUBJECTS

All eyes presenting with presumed endophthalmitis requiring in-office treatment with intravitreal antibiotics and either a vitreous or aqueous tap were included.

METHODS

Endophthalmitis cases were divided into the "culture group," if the vitreous or aqueous specimens were sent for microbiologic sampling, or into the "no culture group" if an aqueous or vitreous tap was performed but not sent for microbiologic sampling.

MAIN OUTCOME MEASURES

Best-corrected visual acuity (VA) 12 months after endophthalmitis presentation, incidence of retinal detachment, and need for subsequent procedures.

RESULTS

Of the 232 endophthalmitis cases identified, 196 (85%) were in the "culture group" and 36 (15%) were in the "no culture group." At endophthalmitis presentation, eyes in the "culture group" had a mean (standard deviation [SD]) logarithm of the minimum angle of resolution (logMAR) VA (Snellen equivalent) of 2.14 (0.8) (20/2760) and mean (SD) logMAR VA in the "no culture group" was 1.93 (0.8) (20/1702) (P = 0.185). At 12-month follow-up, mean (SD) logMAR VA for the "culture group" was 0.80 (1.0) (20/126) and 0.41 (0.5) (20/50) in the "no culture group" (adjusted difference = 0.41, 95% confidence interval = -0.043 to 0.857, P = 0.076). Twenty of 196 (10%) eyes in the "culture group" developed secondary retinal detachments within 12 months of presentation compared with 0 in the "no culture group" (P = 0.045).

CONCLUSIONS

Eyes with endophthalmitis after cataract surgery managed without microbiologic cultures have similar visual outcomes to eyes managed with microbiologic cultures and may be less likely to develop secondary retinal detachments. This may be an acceptable strategy to manage endophthalmitis after cataract surgery when prompt access to a microbiologic facility is unavailable.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Time to positivity of Coagulase Negative Staphylococcus In Neonatal Blood Cultures as an adjunct tool to help discriminate between sepsis and contamination

OBJECTIVE

To assess the usefulness of time to positivity (TTP) to distinguish between sepsis and contamination in coagulase-negative staphylococci (CoNS) isolates.

STUDY DESIGN

Unicentric retrospective observational. Medical records of 168 patients with suspected sepsis and positive blood culture for CoNS were reviewed. Patients were subdivided into sepsis (29%) and probable contamination (71%). Logistic regression analyses were performed to evaluate different risk factors and clinical signs and symptoms associated with sepsis.

RESULTS

TTP cut-off value that best discriminated sepsis from contamination was found to be 18 h. Regression analysis revealed that TTP ≤ 18 h, gestational age ≤32 weeks, taquycardia/bradycardia and hypoactivity/lethargy were independent predictors of sepsis.

CONCLUSION

TTP is useful in distinguishing sepsis from contamination, especially in neonates with lower gestational age (<32 weeks). The clinical signs that most increase the discriminatory power of TTP are the presence of tachycardia/bradycardia or hypoactivity.

Aerobic skin microbiota study in patients with paratraumatic eczema developed as a result of combat injuries

OBJECTIVE

Aim: To establish taxonomic composition, population level and microecological indicators of the "macroorganism-microbiota" ecosystem by determining the expression levels of individual pathogenicity factors of microorganisms isolated from the skin areas of patients with paratraumatic eczema developed as a result of combat injuries.

PATIENTS AND METHODS

Materials and Methods: Studied microbiologically eczematous lesions content in 54 military men to determine the qualitative and quantitative composition of microbiocenosis to analyze the taxonomic composition, population-species level, microecological indicators and expression levels of individual pathogenicity factors.

RESULTS

Results: The results indicate that most eczematized areas are contaminated with S.aureus (48.1% ) with the highest level of quantitative dominance. The rate of quantitative dominance of other strains is significantly lower: S.epidermidis - 2.56 times, S.haemolyticus - 4.56 times, S.pyogenes - 5.86 times, E.faecalis and K.pneumoniae - 20.56 times. When determining the sensitivity of S. aureus clinical strains to antibacterial drugs, we established high levels of sensitivity to mupirocin, fusidic acid, and oxazolidinones - 95.1%, 90.2%, and 87.8%, respectively. Moreover, S. aureus dominated among the strains with a high ability to form biofilms - 68.2%, with an average ability - S epidermidis, 28.8%.

CONCLUSION

Conclusions: S.aureus is the leading pathogen in the infectious-allergic process with paratraumatic eczema according to the constancy index of each taxon, frequency of manifestation, Margalef's species richness index, Whittaker's species diversity, the value of Simpson's and Berger-Parter's species dominance indices, as well as the population level of each taxon, the coefficient of quantitative dominance and the coefficient of significance. We should consider this fact when prescribing therapy.

Development and Validation of a Machine Learning Model for the Prediction of Bloodstream Infections in Patients with Hematological Malignancies and Febrile Neutropenia

Background/Objectives: The rise of multidrug-resistant (MDR) infections demands personalized antibiotic strategies for febrile neutropenia (FN) in hematological malignancies. This study investigates machine learning (ML) for identifying patient profiles with increased susceptibility to bloodstream infections (BSI) during FN onset, aiming to tailor treatment approaches. Methods: From January 2020 to June 2022, we used the unsupervised ML algorithm KAMILA to analyze data from hospitalized hematological malignancy patients. Eleven features categorized clinical phenotypes and determined BSI and multidrug-resistant Gram-negative bacilli (MDR-GNB) prevalences at FN onset. Model performance was evaluated with a validation cohort from July 2022 to March 2023. Results: Among 462 FN episodes analyzed in the development cohort, 116 (25.1%) had BSIs. KAMILA's stratification identified three risk clusters: Cluster 1 (low risk), Cluster 2 (intermediate risk), and Cluster 3 (high risk). Cluster 2 (28.4% of episodes) and Cluster 3 (43.7%) exhibited higher BSI rates of 26.7% and 37.6% and GNB BSI rates of 13.4% and 19.3%, respectively. Cluster 3 had a higher incidence of MDR-GNB BSIs, accounting for 75% of all MDR-GNB BSIs. Cluster 1 (27.9% of episodes) showed a lower BSI risk (<1%) with no GNB infections. Validation cohort results were similar: Cluster 3 had a BSI rate of 38.1%, including 78% of all MDR-GNB BSIs, while Cluster 1 had no GNB-related BSIs. Conclusions: Unsupervised ML-based risk stratification enhances evidence-driven decision-making for empiric antibiotic therapies at FN onset, crucial in an era of rising multi-drug resistance.

Recommendations on Rapid Diagnostic Point-of-care Molecular Tests for Respiratory Infections in the United Arab Emirates

Traditional testing methods in the Middle East Region, including the United Arab Emirates (UAE), particularly the testing of Respiratory Syncytial Virus (RSV), influenza, group A streptococcus (GAS), and COVID-19 have the potential to be upgraded to new and advanced diagnostics methods that improve lead time to diagnosis, consumption of healthcare resources and patient experience. In addition, based on the research, it was reported that there is an underreporting of respiratory cases, overuse of antibiotics, and prolonged hospitalizations which is posing pressure on UAE healthcare stakeholders. A literature review was done exploring UAE's current diagnostic practices, recommended guidelines, diagnostic gaps, and challenges in RSV, GAS, Influenza, and COVID-19. This was followed by stakeholder discussions focusing on assessing current diagnostic practices, usage of rapid molecular point-of-care (POC) diagnostic tests, current gaps in diagnosis, targeted profiles for POC testing, and potential impact on patient management for targeted respiratory infections. A round table discussion with healthcare experts, insurance experts, key opinion leaders, and pulmonologists discussed challenges and opportunities in treating respiratory diseases. UAE healthcare stakeholders suggest that introducing alternative and up-to-date diagnostic methods such as POC molecular testing is expected to improve healthcare outcomes, optimize resources, and develop a robust case management of respiratory tract infections. It is essential to emphasize that by introducing POC testing, precision medicine is reinforced, efficiency is achieved, and the overall management of population health is enhanced.

Laboratory detection of carbapenemases among Gram-negative organisms

SUMMARYThe carbapenems remain some of the most effective options available for treating patients with serious infections due to Gram-negative bacteria. Carbapenemases are enzymes that hydrolyze carbapenems and are the primary method driving carbapenem resistance globally. Detection of carbapenemases is required for patient management, the rapid implementation of infection prevention and control (IP&C) protocols, and for epidemiologic purposes. Therefore, clinical and public health microbiology laboratories must be able to detect and report carbapenemases among predominant Gram-negative organisms from both cultured isolates and direct from clinical specimens for treatment and surveillance purposes. There is not a "one size fits all" laboratory approach for the detection of bacteria with carbapenemases, and institutions need to determine what fits best with the goals of their antimicrobial stewardship and IP&C programs. Luckily, there are several options and approaches available for clinical laboratories to choose methods that best suits their individual needs. A laboratory approach to detect carbapenemases among bacterial isolates consists of two steps, namely a screening process (e.g., not susceptible to ertapenem, meropenem, and/or imipenem), followed by a confirmation test (i.e., phenotypic, genotypic or proteomic methods) for the presence of a carbapenemase. Direct from specimen testing for the most common carbapenemases generally involves detection via rapid, molecular approaches. The aim of this article is to provide brief overviews on Gram-negative bacteria carbapenem-resistant definitions, types of carbapenemases, global epidemiology, and then describe in detail the laboratory methods for the detection of carbapenemases among Gram-negative bacteria. We will specifically focus on the Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii complex.

The value of metagenomic next-generation sequencing with blood samples for the diagnosis of disseminated tuberculosis

Objective

The aim of this study was to assess the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for the identification of disseminated tuberculosis (DTB).

Methods

A total of 48 individuals suspected of DTB were enrolled. All patients underwent mNGS of peripheral blood and conventional microbiological tests. Patient characteristics were collected from their medical records.

Results

A total of 28 patients were diagnosed with DTB, whereas 20 patients were confirmed as non-DTB cases. In the DTB groups, 19 (67.9%) contained TB sequences, with specific reads of TB ranging from 1 to 219. The TB sequence was more detectable by mNGS in male patients, those with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count. The HIV-positive group shows higher TB mNGS reads (p = 0.012) and TB mNGS sensitivity (p = 0.05). The sensitivity of TB mNGS in blood samples was 80% for HIV-infected patients and 44.4% for non-HIV-infected individuals (p = 0.05). The non-HIV group had a higher prevalence of miliary tuberculosis (p = 0.018), and extrapulmonary tuberculosis was more prevalent in the HIV-positive group.

Conclusion

Our research has shown that the mNGS of blood samples has excellent sensitivity for the diagnosis of DTB. The TB sequence was more detectable by mNGS in patients with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count.

BioFire® Joint Infection Panel for Samples Other than Synovial Fluid

Objectives: The early identification of infection-causing microorganisms through multiplex PCR panels enables prompt and targeted antibiotic therapy. This study aimed to assess the performance of the BioFire® Joint Infection Panel (BF-JIP) in analysing non-synovial fluid samples. Methods: We conducted a retrospective cohort study at Trieste University Hospital, Italy, on hospitalised adults with non-synovial fluid samples tested by both BF-JIP and traditional culture methods (November 2022-April 2024). Results: We evaluated 48 samples from 45 patients, including 24 abscess drainage fluids and 10 tissue samples. The BF-JIP showed high concordance (85.4%) and enhanced detection (4.3%) compared to culture methods. The BF-JIP excelled in cerebrospinal fluid (CSF) (100% accuracy and concordance) and in abscess drainage fluid (accuracy: 95.8%; concordance: 91.7%) identification and maintained high performance rates in patients under antibiotics. Conclusions: These findings suggest that BF-JIP is a valuable tool for accurate pathogen detection in various clinical samples, offering the additional advantage of being a rapid method.

A novel ionic liquid-based approach for DNA and RNA extraction simplifies sample preparation for bacterial diagnostics

DNA- and RNA-based diagnostics play a pivotal role in accurately detecting and characterizing health-relevant bacteria, offering insights into bacterial presence, viability and treatment efficacy. Herein, we present the development of a novel extraction protocol for both DNA and RNA, designed to enable simple and rapid molecular diagnostics. The extraction method is based on the hydrophilic ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and silica-coated magnetic beads. First, we developed an IL-based cell lysis protocol for bacteria that operates at room temperature. Subsequently, we established a magnetic bead purification procedure to efficiently and reproducibly extract DNA and RNA from the IL-lysates. The IL not only lyses the cells, but also facilitates the adsorption of nucleic acids (NAs) onto the surface of the magnetic beads, eliminating the need for a chaotropic binding buffer and allowing for purification of NAs without significant effort and materials required. Lastly, we combined the cell lysis step and the purification step and evaluated the novel IL-based extraction method on periopathogenic bacterial cultures, comparing it to commercial DNA and RNA extraction kits via (RT)-qPCR. In comparison to the reference methods, the IL-based extraction protocol yielded similar or superior results. Furthermore, costs are lower, required materials and equipment are minimal and the process is fast (30 min), simple and automatable. These characteristics favour the developed method for use in routine and high-throughput testing as well as in point-of-care, on-site and low-resource settings, thereby advancing the field of molecular diagnostics.

Blood volume collected for cultures in infants with suspected neonatal sepsis

OBJECTIVES

To evaluate blood culture sample volumes, identify factors linked to insufficient samples, and compare volumes among neonates treated for culture-negative-sepsis, sepsis-rule-outs, and bloodstream infections (BSI).

METHODS

Observational cohort of blood cultures collected during NICU stay. Association of age, weight, gender, source, and collection time with lower-than-recommended volumes was determined by logistic regression. Blood culture inocula of patients with culture-negative-sepsis, sepsis rule-out, and BSI were compared using ANOVA.

RESULTS

742 blood cultures were obtained from 292 neonates. Median inoculum was 1 mL (IQR:0.6-1.4), and 259 bottles (35%) had inocula <0.9 mL. Night shift sample collection was associated with lower-than-recommended volumes (p = 0.006). No difference in sample volumes was observed between culture-negative-sepsis, sepsis-rule-outs, and BSI (p = 0.5).

CONCLUSIONS

Median NICU blood culture volumes align with recommendations. Night shift collections correlate with lower volumes. Sample volumes don't differ in patients with culture-negative-sepsis, BSI, and sepsis-rule-out, and should not be a justification for longer duration of antibiotics.

Non-hepatotropic viral hepatitis: a narrative review

Non-hepatotropic viral hepatitis (NHVH) refers to acute hepatitis or acute liver failure caused by viruses that do not primarily target the liver. These viruses include the Epstein-Barr virus (EBV), cytomegalovirus (CMV), herpes simplex virus (HSV)-1 and -2, varicella zoster, parvovirus, adenovirus, adeno-associated virus type 2, measles, and severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). The epidemiology, pathogenesis, and clinical manifestations of hepatitis due to hepatotropic viruses (hepatitis A-E) have been well studied. However, there is a paucity of data on NHVH due to its rarity, self-limiting clinical course, and vague presentation. NHVH can occur as an isolated illness or as part of a disseminated disease, and its clinical features range from self-limiting transaminitis to acute liver failure. This activity reviews the most common non-hepatotropic viruses (NHV), with a focus on their biology, etiopathogenesis, clinical manifestations, and management.

Transforming respiratory tract infection diagnosis in the kingdom of saudi arabia through point-of-care testing: A white paper for policy makers

With the evident increased prevalence of respiratory tract infections (RTIs) such as Respiratory Syncytial Virus (RSV), influenza, Group A Streptococcus (GAS), and COVID-19, the conventional diagnostic methods are considered sub-optimal in providing timely management to patients in the Kingdom of Saudi Arabia (KSA). Gaps in current diagnostics are magnified by the Kingdom's unique demographic composition, comprising 11.9 million foreign workers, and the annual influx of over 10 million pilgrims. Current gaps in timely diagnosis leads to delays in treatment, misuse of antibiotics, and protracted hospital stays, subsequently compromising patient care, and escalating healthcare costs. KSA healthcare stakeholders suggest that the integration of rapid molecular Point-of-Care Testing (POCT) into the Kingdom's healthcare infrastructure is an absolute necessity. This publication serves as an urgent call for action aimed at healthcare policymakers in Saudi Arabia, to review the existing diagnostic challenges and include rapid POCTs in the Saudi healthcare strategy for respiratory infections.

D-PRISM: a global survey-based study to assess diagnostic and treatment approaches in pneumonia managed in intensive care

BACKGROUND

Pneumonia remains a significant global health concern, particularly among those requiring admission to the intensive care unit (ICU). Despite the availability of international guidelines, there remains heterogeneity in clinical management. The D-PRISM study aimed to develop a global overview of how pneumonias (i.e., community-acquired (CAP), hospital-acquired (HAP), and Ventilator-associated pneumonia (VAP)) are diagnosed and treated in the ICU and compare differences in clinical practice worldwide.

METHODS

The D-PRISM study was a multinational, survey-based investigation to assess the diagnosis and treatment of pneumonia in the ICU. A self-administered online questionnaire was distributed to intensive care clinicians from 72 countries between September to November 2022. The questionnaire included sections on professional profiles, current clinical practice in diagnosing and managing CAP, HAP, and VAP, and the availability of microbiology diagnostic tests. Multivariable analysis using multiple regression analysis was used to assess the relationship between reported antibiotic duration and organisational variables collected in the study.

RESULTS

A total of 1296 valid responses were collected from ICU clinicians, spread between low-and-middle income (LMIC) and high-income countries (HIC), with LMIC respondents comprising 51% of respondents. There is heterogeneity across the diagnostic processes, including clinical assessment, where 30% (389) did not consider radiological evidence essential to diagnose pneumonia, variable collection of microbiological samples, and use and practice in bronchoscopy. Microbiological diagnostics were least frequently available in low and lower-middle-income nation settings. Modal intended antibiotic treatment duration was 5-7 days for all types of pneumonia. Shorter durations of antibiotic treatment were associated with antimicrobial stewardship (AMS) programs, high national income status, and formal intensive care training.

CONCLUSIONS

This study highlighted variations in clinical practice and diagnostic capabilities for pneumonia, particularly issues with access to diagnostic tools in LMICs were identified. There is a clear need for improved adherence to existing guidelines and standardized approaches to diagnosing and treating pneumonia in the ICU. Trial registration As a survey of current practice, this study was not registered. It was reviewed and endorsed by the European Society of Intensive Care Medicine.

Noninferiority of Multiplex Polymerase Chain Reaction Compared to Standard Urine Culture for Urinary Tract Infection Diagnosis in Pediatric Patients at Hackensack Meridian Health Children's Hospital Emergency Department

Objective

To establish the noninferiority of the rapid and sensitive multiplex polymerase chain reaction (M-PCR) method versus standard urine culture (SUC) in pediatric urinary tract infection (UTI) diagnostic testing.

Methods

A United States of America (USA)-based single-center prospective observational study of 44 female and four male patients aged 3-21 years old presenting to a Pediatric Emergency Department in New Jersey with clinically suspected UTI. Urine specimens were primarily collected via midstream voiding. Patients with antibiotic exposure within the week prior to presentation were excluded. Patient demographic data, clinical manifestations, and urinalysis results were recorded. Noninferiority testing comparing M-PCR and SUC was conducted using a method for paired binary data, with a noninferiority margin set at 5%. Noninferiority was concluded if the lower bound of the 95% confidence interval of the difference in detection rates between M-PCR and SUC lies entirely to the right of the value minus the noninferiority margin. All statistical calculations were performed using Python 3.10.12.

Results

The two methods were concordant in two-thirds of cases. Of the 14 M-PCR-positive/SUC-negative discordant specimens, 13 (93%) contained a fastidious and/or emerging uropathogen (A. urinae, A. schaalii, G. vaginalis, C. riegelii, U. urealyticum, Viridans group Streptococci (VGS), and/or Coagulase-negative Staphylococci (CoNS)). Neither symptom presentation nor urinalysis results differed significantly between participants with concordant positive results for UTI diagnosis and those with concordant negative results (non-UTI group).

Conclusion

In this pediatric population, similar to previous findings in an older adult population, M-PCR established not only noninferiority but also superiority over SUC in detecting microorganisms in the urine.

Utilization of Syndromic Vaginitis Diagnostic Testing Reduces 6-Month Follow-Up Outpatient Service Healthcare Costs-A Real-World Data Analysis

BACKGROUND/OBJECTIVES

Vaginitis is a common infection among women of reproductive age. Although various diagnostic methodologies exist, diagnosis without the utilization of available diagnostic tests remains prevalent. This study aimed to assess downstream healthcare utilization and the cost of patients with and without diagnostic testing.

METHODS

This retrospective, observational study utilized the IQVIA PharMetrics® Plus database from July 2020 to October 2023. Patients with an index claim (ICD-10 code indicating vaginitis) were categorized into two cohorts: those who received a syndromic polymerase chain reaction (PCR) test and those who had no documented test on the index date or within two days. Total and service-specific healthcare resource utilization and costs were assessed for 6 months following the index event. This study was designed to inform how Syndromic Vaginitis PCR testing is used to make treatment decisions and to track outpatient and inpatient healthcare utilization for 6 months post index date represented by cost.

RESULTS

Patients who received a Syndromic Vaginitis PCR test had significantly fewer outpatient medical services in the 6 months following initial diagnosis compared to those who received no diagnostic test. This was largely attributed to a substantial decrease in other medical service visits, resulting in mean cost savings of USD 2067 (Syndromic PCR = USD 6675, SD = USD 17,187; No Test = USD 8742, SD = USD 29,894) (p-value 0.0009).

CONCLUSIONS

Many vaginitis patients do not receive testing, but Syndromic Vaginitis PCR testing may be an effective diagnostic tool for reducing costs associated with vaginitis infections.

Clinical Microbiome Testing for Urology

The urine culture is imperfect, and a series of alternative approaches are in development to assist in diagnosis, treatment, and prevention of urinary tract infection (UTI). Culture-independent approaches typically do not distinguish between viable and nonviable bacteria, and are generally not included in current clinical guidance. Next-generation sequencing may play an important future role in precise targeting of antibiotic treatment of asymptomatic bacteriuria prior to endourologic surgery or in pregnancy. Future studies are needed to determine whether microbiota modulation could prevent UTI. Possible modulation mechanisms may include fecal microbiota transplant, application of topical vaginal estrogen or probiotics, and bacteriophage therapy.

Defining the value of medical microbiology consultation

Medical microbiologists, defined as doctoral-level laboratory directors with subspecialty training in medical microbiology, lead the clinical laboratory operations through activities such as clinical consultations, oversight of diagnostic testing menu, institutional leadership, education, and scholastic activities. However, unlike their clinical colleagues, medical microbiologists are largely unable to bill for clinical consultations performed within the hospital and, therefore, unable to generate relative value units or a similar quantifiable metric. As hospital budgets tighten and justification of staffing becomes a necessity, this may present a challenge to the medical microbiologist attempting to prove their value to the organization. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. Consults were generated equally from internal (laboratory-based) and external (hospital-based) parties, with the majority directly impacting patient management. Near universal acceptance of the medical microbiologist's recommendation highlights the worth derived from their expertise. External consults required more time commitment from the medical microbiologist than internal consults, although both presented ample opportunity for secondary value, including impact through stewardship, education, clinical guidance, and cost reduction. This study is a description of the content and impact of consultations that underscore the importance of the medical microbiologist as a key member of the healthcare team.

IMPORTANCE

Medical microbiologists are invaluable to the clinical microbiology laboratory and the healthcare system as a whole. However, as medical microbiologists do not regularly generate relative value units, capturing and quantifying the value provided is challenging. As hospital budgets tighten, justification of staffing becomes a necessity. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. To our knowledge, this is the first study to provide detailed evaluation of the consultative value provided by medical microbiologists.

2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Utility of Intra-abdominal Fluid Cultures in Adults, Children, and Pregnant People

This paper is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America. In this paper, the panel provides recommendations for obtaining cultures of intra-abdominal fluid in patients with known or suspected intra-abdominal infection. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach.

2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Utility of Blood Cultures in Adults, Children, and Pregnant People

This article is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America. In this guideline, the panel provides recommendations for obtaining blood cultures in patients with known or suspected intra-abdominal infection. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

Measuring the Direct Medical Costs of Hospital-Onset Infections Using an Analogy Costing Framework

BACKGROUND

The majority of recent estimates on the direct medical cost attributable to hospital-onset infections (HOIs) has focused on device- or procedure-associated HOIs. The attributable costs of HOIs that are not associated with device use or procedures have not been extensively studied.

OBJECTIVE

We developed simulation models of attributable cost for 16 HOIs and estimated the total direct medical cost, including nondevice-related HOIs in the USA for 2011 and 2015.

DATA AND METHODS

We used total discharge costs associated with HOI-related hospitalization from the National Inpatient Sample and applied an analogy costing methodology to develop simulation models of the costs attributable to HOIs. The mean attributable cost estimate from the simulation analysis was then multiplied by previously published estimates of the number of HOIs for 2011 and 2015 to generate national estimates of direct medical costs.

RESULTS

After adjusting all estimates to 2017 US dollars, attributable cost estimates for select nondevice-related infections attributable cost estimates ranged from $7661 for ear, eye, nose, throat, and mouth (EENTM) infections to $27,709 for cardiovascular system infections in 2011; and from $8394 for EENTM to $26,445 for central nervous system infections in 2016 (based on 2015 incidence data). The national direct medical costs for all HOIs were $14.6 billion in 2011 and $12.1 billion in 2016. Nondevice- and nonprocedure-associated HOIs comprise approximately 26-28% of total HOI costs.

CONCLUSION

Results suggest that nondevice- and nonprocedure-related HOIs result in considerable costs to the healthcare system.

Bacterial identification in herniated intervertebral discs: a prospective cohort study

BACKGROUND CONTEXT

Reports of Cutibacterium acnes isolated in cultures of intervertebral disc samples suggest it as possibly responsible for inflammatory conditions causing Modic changes on spinal magnetic resonance imaging (MRI).

PURPOSE

Our objective was to investigate the prevalence of C. acnes in samples of intervertebral disc of patients with lumbar disc herniation; to investigate prognostic factors and the relationship of Modic changes with infection 1 year after microdiscectomy.

STUDY DESIGN

Prospective cohort study.

PATIENT SAMPLE

In this single-center study, patients consecutively operated on for disc herniation had samples of the disc, multifidus muscle and ligamentum flavum (as an indication of contamination) extracted for culture.

OUTCOME MEASURES

Age, sex, alcohol and tobacco consumption, body mass index; function, pain, and Modic chances in MRI before surgery and MRI 1 year later; rate of disc, muscle and ligament infection (primary outcome); diabetes and corticoid use (confoundings).

METHODS

The protruded disc, muscle and ligament samples were sent for culture analysis in up to 30 minutes. A subsample of 17 patients underwent next-generation sequencing (NGS) molecular analysis too. We performed descriptive analysis and comparison of groups of patients with and without infection or contamination using Student's t, Mann-Whitney, chi-square, or Fisher's exact tests as appropriate, and pre- and postsurgical comparisons with the Wilcoxon test.

RESULTS

From January 2018 to September 2019, 112 patients underwent open lumbar microdiscectomy, 67 (59.8%) men. Cultures showed 7 (6.3%) positive cases in the disc (2 with C. acnes), 3 (2.7%) in the ligament, and 12 (10, 7%) in muscle. No evidence of a difference in Modic alterations pre- or postoperatively was found between patients with and without positive culture 1 year after surgery. No association was found between culture positivity and functional or pain differences either. NGS results were all negative for C. acnes.

CONCLUSIONS

We identified infective bacterial presence in the herniated disc in less than 2% of patients with disc herniation. C. acnes was not identified in any disc microbiome analysis. No significant association was observed between positivity for tissue infection and any clinical prognostic factor.

The Adequacy of Current Legionnaires' Disease Diagnostic Practices in Capturing the Epidemiology of Clinically Relevant Legionella: A Scoping Review

Legionella is an underdiagnosed and underreported etiology of pneumonia. Legionella pneumophila serogroup 1 (LpSG1) is thought to be the most common pathogenic subgroup. This assumption is based on the frequent use of a urinary antigen test (UAT), only capable of diagnosing LpSG1. We aimed to explore the frequency of Legionella infections in individuals diagnosed with pneumonia and the performance of diagnostic methods for detecting Legionella infections. We conducted a scoping review to answer the following questions: (1) "Does nucleic acid testing (NAT) increase the detection of non-pneumophila serogroup 1 Legionella compared to non-NAT?"; and (2) "Does being immunocompromised increase the frequency of pneumonia caused by non-pneumophila serogroup 1 Legionella compared to non-immunocompromised individuals with Legionnaires' disease (LD)?". Articles reporting various diagnostic methods (both NAT and non-NAT) for pneumonia were extracted from several databases. Of the 3449 articles obtained, 31 were included in our review. The most common species were found to be L. pneumophila, L. longbeachae, and unidentified Legionella species appearing in 1.4%, 0.9%, and 0.6% of pneumonia cases. Nearly 50% of cases were caused by unspecified species or serogroups not detected by the standard UAT. NAT-based techniques were more likely to detect Legionella than non-NAT-based techniques. The identification and detection of Legionella and serogroups other than serogroup 1 is hampered by a lack of application of broader pan-Legionella or pan-serogroup diagnostics.

Recent Challenges in Diagnosis and Treatment of Invasive Candidiasis in Neonates

Invasive Candida infections represent a significant cause of morbidity and mortality in the neonatal intensive care unit (NICU), particularly among preterm and low birth weight neonates. The nonspecific clinical presentation of invasive candidiasis, resembling that of bacterial sepsis with multiorgan involvement, makes the diagnosis challenging. Given the atypical clinical presentation and the potential detrimental effects of delayed treatment, empirical treatment is often initiated in cases with high clinical suspicion. This underscores the need to develop alternative laboratory methods other than cultures, which are known to have low sensitivity and a prolonged detection time, to optimize therapeutic strategies. Serum biomarkers, including mannan antigen/anti-mannan antibody and 1,3-β-D-glucan (BDG), both components of the yeast cell wall, a nano-diagnostic method utilizing T2 magnetic resonance, and Candida DNA detection by PCR-based techniques have been investigated as adjuncts to body fluid cultures and have shown promising results in improving diagnostic efficacy and shortening detection time in neonatal populations. This review aims to provide an overview of the diagnostic tools and the current management strategies for invasive candidiasis in neonates. Timely and accurate diagnosis followed by targeted antifungal treatment can significantly improve the survival and outcome of neonates affected by Candida species.

From Awareness to Action: Pioneering Solutions for Women's UTI Challenges in the Era of Precision Medicine

This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.

Barriers to implementation of rapid identification and antimicrobial susceptibility testing technologies in the clinical microbiology laboratory: an American perspective

Clinical microbiology laboratories are responsible for confirming the aetiology of infectious diseases and providing antimicrobial susceptibility testing results. Traditional culture-based testing can be augmented by more rapid testing modalities to provide clinically actionable information as quickly as possible. Despite improvements in patient outcomes, many clinical microbiology laboratories are facing challenges to in-sourcing these technologies. Depending on a multitude of factors, including size, location and patient population served, these barriers may affect some laboratories and hospital systems to greater or lesser extents than others. It will be up to each individual facility to ascertain its ability to overcome barriers. To aid in this self-assessment, we present for thoughtful consideration a discussion of the barriers to implementation of rapid identification and antimicrobial susceptibility testing technologies, with specific attention to matters of financial cost, staff expertise, operational issues and stakeholder buy-in.

Five-year analysis of isolated pathogens and antibiotic resistance of ocular infections from two large tertiary comprehensive hospitals in east China

AIM

To analyze the spectrum of isolated pathogens and antibiotic resistance for ocular infections within 5y at two tertiary hospitals in east China.

METHODS

Ocular specimen data were collected from January 2019 to October 2023. The pathogen spectrum and positive culture rate for different infection location, such as keratitis, endophthalmitis, and periocular infections, along with antibiotic resistance were analyzed.

RESULTS

We included 2727 specimens, including 827 (30.33%) positive cultures. A total of 871 strains were isolated, 530 (60.85%) bacterial and 341 (39.15%) fungal strains were isolated. Gram-positive cocci (GPC) were the most common ocular pathogens. The most common bacterial isolates were Staphylococcus epidermidis (25.03%), Staphylococcus aureus (7.46%), Streptococcus pneumoniae (4.59%), Corynebacterium macginleyi (3.44%), and Pseudomonas aeruginosa (3.33%). The most common fungal genera were Fusarium spp. (12.74%), Aspergillus spp. (6.54%), and Scedosporium spp. (5.74%). Staphylococcus epidermidis strains showed more than 50% resistance to fluoroquinolones. Streptococcus pneumoniae and Corynebacterium macginleyi showed more than 90% resistance to erythromycin. The percentage of bacteria showing multidrug resistance (MDR) significantly decreased (χ 2=17.44, P=0.002).

CONCLUSION

GPC are the most common ocular pathogens. Corynebacterium macginleyi, as the fourth common bacterium, may currently be the local microbiological feature of east China. Fusarium spp. is the most common fungus. More than 50% of the GPC are resistant to fluoroquinolones, penicillins, and macrolides. However, the proportion of MDR strains has been reduced over time.

Diagnostic performance of metagenomic sequencing in patients with suspected infection: a large-scale retrospective study

Background

Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method.

Methods

A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated.

Results

Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay (n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched.

Conclusion

Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection.

Clinical evaluation of the T2Candida assay for the rapid diagnosis of candidemia

We evaluated the clinical performance of the T2Candida assay. The overall agreement of the T2Candida assay results with the blood culture results was 95.3 % (121/127). The T2Candida assay detected three Candida albicans/tropicalis-positive specimens and one Candida krusei/glabrata-positive specimen; however, it did not detect two Candida glabrata specimens.