Diagnostics

Research

26 pages, 8905 KiB

Open AccessArticle

Investigation of Long-Term CD4+ T Cell Receptor Repertoire Changes Following SARS-CoV-2 Infection in Patients with Different Severities of Disease

by Emma L. Callery, Camilo L. M. Morais, Jemma V. Taylor, Kirsty Challen and Anthony W. Rowbottom

Diagnostics 2024, 14(20), 2330; https://doi.org/10.3390/diagnostics14202330 - 19 Oct 2024

Viewed by 723

Abstract

Background: The difference in the immune response to severe acute respiratory syndrome coro-navirus 2 (SARS-CoV-2) in patients with mild versus severe disease remains poorly understood. Recent scientific advances have recognised the vital role of both B cells and T cells; however, many questions [...] Read more.

Background: The difference in the immune response to severe acute respiratory syndrome coro-navirus 2 (SARS-CoV-2) in patients with mild versus severe disease remains poorly understood. Recent scientific advances have recognised the vital role of both B cells and T cells; however, many questions remain unanswered, particularly for T cell responses. T cells are essential for helping the generation of SARS-CoV-2 antibody responses but have also been recognised in their own right as a major factor influencing COVID-19 disease outcomes. The examination of T cell receptor (TCR) family differences over a 12-month period in patients with varying COVID-19 disease severity is crucial for understanding T cell responses to SARS-CoV-2. Methods: We applied a machine learning approach to analyse TCR vb family responses in COVID-19 patients (n = 151) across multiple timepoints and disease severities alongside SARS-CoV-2 infection-naïve (healthy control) individ-uals (n = 62). Results: Blood samples from hospital in-patients with moderate, severe, or critical disease could be classified with an accuracy of 94%. Furthermore, we identified significant variances in TCR vb family specificities between disease and control subgroups. Conclusions: Our findings suggest advantageous and disadvantageous TCR repertoire patterns in relation to disease severity. Following validation in larger cohorts, our methodology may be useful in detecting protective immunity and the assessment of long-term outcomes, particularly as we begin to unravel the immunological mechanisms leading to post-COVID complications. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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11 pages, 416 KiB

Open AccessArticle

Etiology, Clinical Profiles, and Outcomes of Acute Encephalitis Syndrome Cases Admitted to a Tertiary Care Center in Myanmar in 2023

by Aung Kyaw Kyaw, Ohnmar, Zin Nwe Win, Sai Kyaw Win, Zarni Myint Shwe, Kyaw Lwin Show, Nan Aye Thida Oo, Mya Thandar Win, Khin Zarchi Aung, Win Pa Pa Naing, Phyu Phyu Lay, Hlaing Myat Thu and Zaw Than Htun

Diagnostics 2024, 14(19), 2248; https://doi.org/10.3390/diagnostics14192248 - 9 Oct 2024

Viewed by 779

Abstract

Background/Objectives: The diagnosis of encephalitis is a challenging problem due to the heterogeneity of clinical presentations. The objective was to determine the etiology, clinical features, laboratory parameters, radiological findings, and in-hospital outcome of acute encephalitis syndrome (AES) cases in Myanmar. Methods: A prospective [...] Read more.

Background/Objectives: The diagnosis of encephalitis is a challenging problem due to the heterogeneity of clinical presentations. The objective was to determine the etiology, clinical features, laboratory parameters, radiological findings, and in-hospital outcome of acute encephalitis syndrome (AES) cases in Myanmar. Methods: A prospective descriptive study was conducted at the Neuromedical Ward of Yangon General Hospital from March to August 2023. Eighty-one AES cases were enrolled, and cerebrospinal fluid (CSF) samples were collected. A Qiastat ME Panel was used to detect viral, bacterial, and fungal pathogens. Results: Seventeen out of eighty-one (21%) cases were non-encephalitis with alternative definite diagnosis. Among the remaining 64 encephalitis cases, the exact infectious and immune etiologies were identified in 31 of 64 cases (48.4%); 26 of these (83.9%) were due to infectious causes and 5 (16.1%) were immune encephalitis. Among the infectious causes, six Herpes Simplex Virus-1-, one bacteriologically confirmed and seven probable Mycobacterium tuberculosis-, three Haemophilus influenzae-, two Streptococcus pneumoniae-, one Streptococcus pyogenes-, one Varicella-Zoster Virus (Ramsay Hunt Syndrome with meningoencephalitis)-, and two Cryptococcus neoformans-infected patients and rare causes such as Listeria monocytogenes, Burkholdelria cepacia, Sphingomonas paucimobilis, and Aspergillus were identified. One case was a dual infection with Haemophilus influenzae and Cryptococcus neformans. Abnormal protein levels and CSF pleocytosis were significantly higher among bacterial causes (p < 0.05). In total, 6.45% (2/31) of encephalitis patients with identified causes and 12.12% (4/33) of those without an identified organism had poor outcome. Conclusions: Herpes encephalitis and tuberculous meningoencepalitis were the commonest. This study highlighted that molecular testing with a multidisciplinary approach is required to ensure the right treatment on time. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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12 pages, 1663 KiB

Open AccessArticle

Influence of Hematocrit and Storage Temperature on the Stability of Dried Blood Samples in Serological Analyses of Tetanus, Diphtheria, and Pertussis

by Mariano Rodríguez-Mateos, Silvia Carlos, Javier Jaso, África Holguín and Gabriel Reina

Diagnostics 2024, 14(19), 2195; https://doi.org/10.3390/diagnostics14192195 - 1 Oct 2024

Viewed by 682

Abstract

Background: Dried blood spots (DBSs) enable the study of serological markers of various pathogens without the need to obtain serum/plasma through venipuncture. Methods: Sixty-four blood samples were prepared on Whatman™ 903 cards using specimens obtained by venipuncture to study the detection of serological [...] Read more.

Background: Dried blood spots (DBSs) enable the study of serological markers of various pathogens without the need to obtain serum/plasma through venipuncture. Methods: Sixty-four blood samples were prepared on Whatman™ 903 cards using specimens obtained by venipuncture to study the detection of serological markers of diphtheria, tetanus, and pertussis in DBSs, and their stability 4 months post-collection. An automated chemiluminescent immunoassay was used to investigate diphtheria, tetanus, and pertussis IgG levels from both DBSs and plasma samples. Results: An optimal cut-off value for DBSs was calculated to improve the performance of diphtheria and tetanus serological markers in DBSs, achieving high sensitivity (95% and 98%, respectively) and specificity (91.7% and 92.3%, respectively). No protection against pertussis was found in the population studied. The correlation observed between the plasma and the DBSs processed after sample collection was high (0.967–0.970) for all antibodies studied except pertussis (0.753), both considering hematocrit before sample elution or not. The correlation between DBSs and plasma for diphtheria and tetanus remained strong following a 4-month delay in DBS processing at 4 °C (0.925–0.964) and −20 °C (0.924–0.966), with only a minor decrease observed for diphtheria at room temperature (0.889), while maintaining a strong correlation for tetanus (0.960). For pertussis, the correlation between DBSs and plasma was drastically reduced after delaying its processing for 4 months at any temperature. Conclusions: To summarize, hematocrit levels within the normal range do not affect the processing of DBSs in the study of serological markers of diphtheria, tetanus, and pertussis. The DBS stability for serological diagnosis of diphtheria and tetanus is adequate when samples are stored at −20 °C for a period of 4 months. The pertussis serological marker does not appear to remain stable after 4 months, even when the DBS is stored frozen at −20 °C. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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7 pages, 222 KiB

Open AccessCommunication

Evaluation of the Allplex GI Parasite and Helminth PCR Assay in a Belgian Travel Clinic

by Jasmine Coppens, Charlotte Drieghe, Idzi Potters, Jean-Marc Schwob and Marjan Van Esbroeck

Diagnostics 2024, 14(18), 1998; https://doi.org/10.3390/diagnostics14181998 - 10 Sep 2024

Viewed by 602

Abstract

Recently a number of broad-range stool parasite PCR assays have been developed. However, there is ongoing disagreement regarding their diagnostic performance, as various studies have produced contradictory results. In this study, we compared the diagnostic accuracy of the Seegene Allplex GI-Parasite and Allplex [...] Read more.

Recently a number of broad-range stool parasite PCR assays have been developed. However, there is ongoing disagreement regarding their diagnostic performance, as various studies have produced contradictory results. In this study, we compared the diagnostic accuracy of the Seegene Allplex GI-Parasite and Allplex GI-Helminth assays (SA) with the conventional methods used at the travel clinic of the Institute of Tropical Medicine (ITM) including microscopy, antigen testing, and molecular detection in order to provide insights into the strengths and limitations of this diagnostic tool which may be crucial to select the most appropriate diagnostic tools for the suspected pathogen. A total of 97 native stool samples from 95 patients with suspected gastrointestinal illness were analyzed, including 26 from a frozen collection and 71 prospectively collected samples. The diagnostic performance of SA was notably superior to the conventional workflow in detecting Dientamoeba fragilis (sensitivity 100% vs. 47.4%) and Blastocystis hominis (sensitivity 95% vs. 77.5%). SA had a comparable performance with the conventional workflow in detecting pathogenic protozoa (sensitivity 90% vs. 95%). In contrast, SA had a much lower diagnostic performance in detecting helminths (59.1%) compared to the conventional workflow (100%). We conclude that the Seegene Allplex GI-Parasite assay may be useful for protozoa screening in low-endemic industrialized countries. However, the Allplex GI-Helminth assay is not recommended due to its suboptimal performance compared to microscopy. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

12 pages, 559 KiB

Open AccessArticle

Prognostic Utility of dNLR, ALRI, APRI, and SII in COVID-19 Patients with Diabetes: A Cross-Sectional Study

by Alexandra Ioana Danila, Flavius Cioca, Sai Teja Gadde, Sai Praveen Daruvuri, Romulus Timar and Elena Hogea

Diagnostics 2024, 14(15), 1685; https://doi.org/10.3390/diagnostics14151685 - 4 Aug 2024

Viewed by 1117

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has necessitated the identification of biomarkers that can predict disease severity, particularly in vulnerable populations such as individuals with diabetes. This study aims to evaluate the predictive value of inflammatory and liver function markers, specifically derived Neutrophil [...] Read more.

The coronavirus disease 2019 (COVID-19) pandemic has necessitated the identification of biomarkers that can predict disease severity, particularly in vulnerable populations such as individuals with diabetes. This study aims to evaluate the predictive value of inflammatory and liver function markers, specifically derived Neutrophil to Lymphocyte Ratio (dNLR), aspartate aminotransferase (AST)-to-lymphocyte ratio (ALRI), AST to Platelet Ratio Index (APRI), and Systemic Inflammation Index (SII), in COVID-19 patients with and without diabetes. This cross-sectional study included 336 participants, comprising 168 patients with diabetes matched with 168 without, based on gender, body mass index (BMI), and COVID-19 severity at hospitalization. The study was conducted at Victor Babes Hospital for Infectious Diseases and Pulmonology from January 2021 to December 2023. All participants had a confirmed SARS-CoV-2 infection and met the inclusion criteria of being 18 years or older with type 1 or type 2 diabetes as per American Diabetes Association guidelines. At 3 days post symptom onset, significant differences in inflammatory and liver function markers were observed between the two groups. The dNLR, ALRI, APRI, and SII were notably higher in diabetic patients. At a dNLR cutoff of 2.685, the sensitivity and specificity were 70.312% and 65.978%, respectively, with an AUC of 0.624 (p < 0.001). The ALRI showed a cutoff of 0.812, with a sensitivity of 76.429% and specificity of 69.541% (AUC 0.752, p < 0.001). These markers demonstrated statistically significant hazard ratios at both 3 and 7 days, indicating their predictive relevance for severe COVID-19 outcomes. For instance, at 7 days, SII demonstrated a hazard ratio of 2.62 (CI: 1.29–5.04, p < 0.001), highlighting its strong prognostic capability. The study successfully identified significant differences in inflammatory and liver function markers between COVID-19 patients with and without diabetes, with these markers showing good predictive value for disease severity. The results underscore the potential of these biomarkers, particularly ALRI and SII, as valuable tools in managing COVID-19, aiding in the timely identification of patients at increased risk of severe outcomes. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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11 pages, 1783 KiB

Open AccessArticle

Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens

by Alexandru Botan, Giuseppina Campisciano, Verena Zerbato, Stefano Di Bella, Omar Simonetti, Marina Busetti, Dan Alexandru Toc, Roberto Luzzati and Manola Comar

Diagnostics 2024, 14(13), 1318; https://doi.org/10.3390/diagnostics14131318 - 21 Jun 2024

Viewed by 1848

Abstract

Effective treatment of infectious diseases requires prompt and accurate bacterial identification and tailored antimicrobial treatments. Traditional culture methods are considered the gold standard, but their effectiveness diminishes for fastidious and hard-to-grow microorganisms. In recent years, molecular diagnostic tools such as 16S rRNA gene [...] Read more.

Effective treatment of infectious diseases requires prompt and accurate bacterial identification and tailored antimicrobial treatments. Traditional culture methods are considered the gold standard, but their effectiveness diminishes for fastidious and hard-to-grow microorganisms. In recent years, molecular diagnostic tools such as 16S rRNA gene next-generation sequencing (16S NGS) have gained popularity in the field. We analysed data from samples submitted for 16S NGS between July 2022 and July 2023 at the Department of Advanced Translational Microbiology in Trieste, Italy. The study included samples submitted for both culture-based identification and 16S NGS. Conventional media were used for culture, and bacterial identification was performed using MALDI-TOF mass spectrometry. The V3 region of the 16S rRNA gene was sequenced using the Ion PGM platform. Among the 123 samples submitted, drainage fluids (38%) and blood (23%) were the most common, with requests predominantly from the Infectious Diseases (31.7%) and Orthopedic (21.13%) Units. In samples collected from patients with confirmed infections, 16S NGS demonstrated diagnostic utility in over 60% of cases, either by confirming culture results in 21% or providing enhanced detection in 40% of instances. Among the 71 patients who had received antibiotic therapies before sampling (mean 2.3 prior antibiotic days), pre-sampling antibiotic consumption did not significantly affect the sensitivity of 16S NGS. In routine microbiology laboratories, combining 16S NGS with culture method enhances the sensitivity of microbiological diagnostics, even when sampling is conducted during antibiotic therapy. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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14 pages, 779 KiB

Open AccessArticle

Urine Flow Cytometry and Dipstick Analysis in Diagnosing Bacteriuria and Urinary Tract Infections among Adults in the Emergency Department—A Diagnostic Accuracy Trial

by Mathias Amdi Hertz, Isik Somuncu Johansen, Flemming S. Rosenvinge, Claus Lohman Brasen, Eline Sandvig Andersen, Claus Østergaard, Thor Aage Skovsted, Eva Rabing Brix Petersen, Stig Lønberg Nielsen, Christian Backer Mogensen and Helene Skjøt-Arkil

Diagnostics 2024, 14(4), 412; https://doi.org/10.3390/diagnostics14040412 - 13 Feb 2024

Cited by 1 | Viewed by 2797

Abstract

Urinary tract infections (UTIs) are a leading infectious cause of emergency department admission. Early UTI diagnosis is challenging, and a faster, preferably point-of-care urine analysis is necessary. We aimed to evaluate the diagnostic accuracy of urine flow cytometry (UFC) and urine dipstick analysis [...] Read more.

Urinary tract infections (UTIs) are a leading infectious cause of emergency department admission. Early UTI diagnosis is challenging, and a faster, preferably point-of-care urine analysis is necessary. We aimed to evaluate the diagnostic accuracy of urine flow cytometry (UFC) and urine dipstick analysis (UDA) in identifying bacteriuria and UTIs. This study included adults suspected of an infection admitted to three Danish emergency departments. UFC and UDA were the index tests, and urine culture and an expert panel diagnosis were the reference tests. We used logistic regression and receiver operator characteristics curves to find each test’s optimal model and cut-off. We enrolled 966 patients and performed urine cultures on 786. Urine culture was positive in 337, and 200 patients were diagnosed with a UTI. The UFC model ruled out bacteriuria in 10.9% with a negative predictive value (NPV) of 94.6% and ruled out UTI in 38.6% with an NPV of 97.0%. UDA ruled out bacteriuria in 52.1% with an NPV of 79.2% and UTI in 52.8% with an NPV of 93.9%. Neither UFC nor UDA performed well in ruling out bacteriuria in our population. In contrast, both tests ruled out UTI safely and in clinically relevant numbers. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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11 pages, 2554 KiB

Open AccessArticle

Assessment of Cross-Reactivity of Chimeric Trypanosoma cruzi Antigens with Crithidia sp. LVH-60A: Implications for Accurate Diagnostics

by Emily F. Santos, Ramona T. Daltro, Carlos G. Regis-Silva, Tycha B. S. Pavan, Fabrícia A. de Oliveira, Ângela M. da Silva, Roque P. Almeida, Noilson L. S. Gonçalves, Daniel D. Sampaio, Faber N. Santos, Fabricio K. Marchini, Paola A. F. Celedon, Nilson I. T. Zanchin and Fred L. N. Santos

Diagnostics 2023, 13(22), 3470; https://doi.org/10.3390/diagnostics13223470 - 17 Nov 2023

Cited by 3 | Viewed by 1560

Abstract

This study focuses on developing accurate immunoassays for diagnosing Chagas disease (CD), a challenging task due to antigenic similarities between Trypanosoma cruzi and other parasites, leading to cross-reactivity. To address this challenge, chimeric recombinant T. cruzi antigens (IBMP-8.1, IBMP-8.2, IBMP-8.3, and IBMP-8.4) were [...] Read more.

This study focuses on developing accurate immunoassays for diagnosing Chagas disease (CD), a challenging task due to antigenic similarities between Trypanosoma cruzi and other parasites, leading to cross-reactivity. To address this challenge, chimeric recombinant T. cruzi antigens (IBMP-8.1, IBMP-8.2, IBMP-8.3, and IBMP-8.4) were synthesized to enhance specificity and reduce cross-reactivity in tests. While these antigens showed minimal cross-reactivity with leishmaniasis, their performance with other trypanosomatid infections was unclear. This study aimed to assess the diagnostic potential of these IBMP antigens for detecting CD in patients with Crithidia sp. LVH-60A, a parasite linked to visceral leishmaniasis-like symptoms in Brazil. This study involved seven Crithidia sp. LVH-60A patients and three Leishmania infantum patients. The results indicated that these IBMP antigens displayed 100% sensitivity, with specificity ranging from 87.5% to 100%, and accuracy values between 90% and 100%. No cross-reactivity was observed with Crithidia sp. LVH-60A, and only one L. infantum-positive sample showed limited cross-reactivity with IBMP-8.1. This study suggests that IBMP antigens offer promising diagnostic performance, with minimal cross-reactivity in regions where T. cruzi and other trypanosomatids are prevalent. However, further research with a larger number of Crithidia sp. LVH-60A-positive samples is needed to comprehensively evaluate antigen cross-reactivity. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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17 pages, 1160 KiB

Open AccessArticle

A MicroRNA-Based Method for High-Viremia Detection—A New Approach on a Romanian Lot of Chronically Infected Patients with Hepatitis B Virus

by Marina Manea, Dimitri Apostol and Ileana Constantinescu

Diagnostics 2023, 13(22), 3425; https://doi.org/10.3390/diagnostics13223425 - 10 Nov 2023

Viewed by 1302

Abstract

The HBV (hepatitis B virus) infection is intended for elimination, but evaluating patients is both costly and insufficiently applied in several countries. An expensive analysis in Romania is HBV-DNA quantification, with a limited prognostic potential. Our study intended to find new predictors for [...] Read more.

The HBV (hepatitis B virus) infection is intended for elimination, but evaluating patients is both costly and insufficiently applied in several countries. An expensive analysis in Romania is HBV-DNA quantification, with a limited prognostic potential. Our study intended to find new predictors for high viremia in HBV patients, using molecules involved in the multiple assessment of various HBV complications, such as microRNAs. A total of 61 subjects (48 patients with chronic HBV infection and 13 healthy subjects) were generally evaluated. Using a RT-PCR method, with a 2^−ΔΔCT algorithm, we detected the expressions of miR-122 and miR-146a in 33 subjects. MiR-21 was the internal control. The results were analyzed with the R 4.2.2. software. Kruskal–Wallis’s comparisons, Spearman correlations, and several logistic regression methods were applied. The median age of the patients was over 40 years. Without microRNAs, we could not obtain a good prediction formula. The combination of miR-122 and age proved to be the best prediction method for high viremia, with an AUC of 0.827, and a sensitivity of 89.5%. This is the first study which included age and miR-122 as independent predictors for high viremia in Romanian HBV-positive patients. MiR-122 is a new potential biomarker in the evaluation of Romanian patients. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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9 pages, 641 KiB

Open AccessArticle

Detection of Plasmodium falciparum in Saliva and Stool Samples from Children Living in Franceville, a Highly Endemic Region of Gabon

by Roméo Karl Imboumy-Limoukou, Jean-Claude Biteghe-Bi-Essone, Judicael Boris Lendongo Wombo, Sonia Etenna Lekana-Douki, Virginie Rougeron, Steede-Seinnat Ontoua, Lydie Sandrine Oyegue-Liabagui, Cherone Nancy Mbani Mpega Ntigui, Lady Charlène Kouna and Jean-Bernard Lekana-Douki

Diagnostics 2023, 13(20), 3271; https://doi.org/10.3390/diagnostics13203271 - 20 Oct 2023

Cited by 1 | Viewed by 1486

Abstract

Due to the difficulty of obtaining blood samples, which is the invasive method that is currently used for the detection of Plasmodium spp., alternative diagnostic sampling methods that are effective and non-invasive are needed, particularly for long-term studies. Saliva and stool samples from [...] Read more.

Due to the difficulty of obtaining blood samples, which is the invasive method that is currently used for the detection of Plasmodium spp., alternative diagnostic sampling methods that are effective and non-invasive are needed, particularly for long-term studies. Saliva and stool samples from malaria-infected individuals contain trace amounts of Plasmodium DNA and therefore could be used as alternatives. Malaria was screened using rapid diagnosis tests and confirmed via microscopy. Nested PCR tests targeting the Plasmodium falciparum-specific STEVOR gene were performed for blood, saliva and stool samples that were positive for malaria. Three hundred sixty-seven (367) children were enrolled and eighty (22.22%) were confirmed to be positive for malaria. Matched blood, saliva and stool samples were available for 35 children. By using blood smears as the gold standard for the diagnosis of malaria, our study indicates that Plasmodium DNA was more detectable in blood (100%) than in saliva (22.86%) and stools (14.29%). Applying qPCR to the STEVOR gene to detect Plasmodium falciparum DNA in saliva and stool samples cannot be considered as an alternative to the current malaria detection processes using blood specimens. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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10 pages, 431 KiB

Open AccessArticle

Procalcitonin and Risk Prediction for Diagnosing Bacteremia in Hospitalized Patients: A Retrospective, National Observational Study

by Tristan T. Timbrook, Cherilyn D. Garner, Kyle D. Hueth, Gerald A. Capraro, Louise Zimmer and Hari P. Dwivedi

Diagnostics 2023, 13(20), 3174; https://doi.org/10.3390/diagnostics13203174 - 11 Oct 2023

Cited by 2 | Viewed by 1368

Abstract

Bacteremia is associated with significant morbidity and mortality. Timely, appropriate therapy may improve clinical outcomes, and therefore, determining which patients benefit from more comprehensive diagnostic strategies (i.e., direct specimen testing) could be of value. We performed an assessment of procalcitonin (PCT) and clinical [...] Read more.

Bacteremia is associated with significant morbidity and mortality. Timely, appropriate therapy may improve clinical outcomes, and therefore, determining which patients benefit from more comprehensive diagnostic strategies (i.e., direct specimen testing) could be of value. We performed an assessment of procalcitonin (PCT) and clinical characteristics in the discrimination of bacteremic hospitalizations. We analyzed 71,105 encounters and 14,846 visits of patients with bacteremia alongside 56,259 without an admission. The area under the receiver—operating characteristic (AUROC) curve for the prediction of bacteremia via procalcitonin was 0.782 (95% CI 0.779–0.787). The prediction modeling of clinical factors with or without PCT resulted in a similar performance to PCT alone. However, the clinically predicted risk of bacteremia stratified by PCT thresholds allowed the targeting of high-incidence bacteremia groups (e.g., ≥50% positivity). The combined use of PCT and clinical characteristics could be useful in diagnostic stewardship by targeting further advanced diagnostic testing in patients with a high predicted probability of bacteremia. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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14 pages, 2558 KiB

Open AccessArticle

Exploiting the Potential of Magnetic Nanoparticles for Rapid Diagnosis Tests (RDTs): Nanoparticle-Antibody Conjugates and Color Development Strategies

by Yeonjeong Ha

Diagnostics 2023, 13(19), 3033; https://doi.org/10.3390/diagnostics13193033 - 23 Sep 2023

Cited by 1 | Viewed by 1443

Abstract

Magnetic nanoparticles (MNPs) have emerged as a promising material in disease diagnostics due to their potential to enhance detection sensitivity, facilitate concentration and purification of target substances in diverse samples, and enable favorable color-based detection. In this study, antibody-conjugated MNPs were successfully synthesized [...] Read more.

Magnetic nanoparticles (MNPs) have emerged as a promising material in disease diagnostics due to their potential to enhance detection sensitivity, facilitate concentration and purification of target substances in diverse samples, and enable favorable color-based detection. In this study, antibody-conjugated MNPs were successfully synthesized and validated through two appropriate methods: the measurement of MNPs’ size and the use of phosphatase methods. Additionally, three methods were suggested and implemented for developing color in MNPs-based immunoassay, including the formation of MNP aggregations, utilization of MNPs’ peroxidase-like activity, and synthesis of dually-conjugated MNPs with both enzyme and antibody. In particular, color development utilizing nanoparticle aggregations was demonstrated to result in a more yellowish color as virus concentration increased, while the peroxidase activity of MNPs exhibited a proportional increase in color intensity as the MNP concentration increased. This observation suggests the potential applicability of quantitative analysis using these methods. Furthermore, effective concentration and purification of target substances were demonstrated through the collection of MNPs using an external magnetic field, irrespective of factors such as antibody conjugation, dispersion medium, or virus binding. Finally, based on the key findings of this study, a design proposal for MNPs-based immunoassay is presented. Overall, MNPs-based immunoassays hold significant potential for advancing disease diagnostics. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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18 pages, 956 KiB

Open AccessArticle

Particular Aspects Related to CD4+ Level in a Group of HIV-Infected Patients and Associated Acute Coronary Syndrome

by Mircea Bajdechi, Adriana Gurghean, Vlad Bataila, Alexandru Scafa-Udriște, Georgiana-Elena Bajdechi, Roxana Radoi, Anca Cristiana Oprea, Valentin Chioncel, Iuliana Mateescu, Lucia Zekra, Roxana Cernat, Irina Magdalena Dumitru and Sorin Rugina

Diagnostics 2023, 13(16), 2682; https://doi.org/10.3390/diagnostics13162682 - 15 Aug 2023

Cited by 1 | Viewed by 1433

Abstract

People living with HIV infection are at high risk for cardiovascular events due to inflammation and atherosclerosis. Also, some antiretroviral therapies may contribute to the risk of cardiovascular complications. Immune status is highly dependent on the level of lymphocyte T helper CD4+. There [...] Read more.

People living with HIV infection are at high risk for cardiovascular events due to inflammation and atherosclerosis. Also, some antiretroviral therapies may contribute to the risk of cardiovascular complications. Immune status is highly dependent on the level of lymphocyte T helper CD4+. There are data suggesting that immune status and CD4+ cell count may be involved in the development of cardiovascular complications in these patients. Our study is longitudinal and retrospective and included a total number of 50 patients with HIV infection associated with acute coronary syndrome, divided into two subgroups based on the nadir of CD4+ cells. This study analyzes the relationship between the immune status of HIV patients, assessed by the nadir of the CD4+ T-cell count, and the outcome of these patients. Also, secondary endpoints were the assessment of the magnitude of coronary lesions and of thrombotic and bleeding risk assessed by specific scores. Clinical and biological parameters and also the extension and complexity of coronary lesions were assessed. Although patients with poor immune status had more complex coronary lesions and increased operative risk and bleeding risk at one year, this was not associated with significant differences in major adverse cardiac and cerebrovascular events at the 30-day and 1-year outcomes. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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12 pages, 3732 KiB

Open AccessArticle

Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness

by Pallavi Upadhyay, Jairus Reddy, Teddie Proctor, Oceane Sorel, Harita Veereshlingam, Manoj Gandhi, Xuemei Wang and Vijay Singh

Diagnostics 2023, 13(12), 2014; https://doi.org/10.3390/diagnostics13122014 - 9 Jun 2023

Cited by 2 | Viewed by 2462

Abstract

While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the [...] Read more.

While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36–40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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12 pages, 339 KiB

Open AccessArticle

Cardiovascular Risk Factors, Angiographical Features and Short-Term Prognosis of Acute Coronary Syndrome in People Living with Human Immunodeficiency Virus: Results of a Retrospective Observational Multicentric Romanian Study

by Mircea Bajdechi, Adriana Gurghean, Vlad Bataila, Alexandru Scafa-Udriste, Roxana Radoi, Anca Cristiana Oprea, Adrian Marinescu, Stefan Ion, Valentin Chioncel, Alina Nicula, Achilleas Anastasiou, Georgiana-Elena Bajdechi, Ilinca Savulescu-Fiedler, Irina Magdalena Dumitru and Sorin Rugina

Diagnostics 2023, 13(9), 1526; https://doi.org/10.3390/diagnostics13091526 - 24 Apr 2023

Cited by 2 | Viewed by 1498

Abstract

People living with human immunodeficiency virus have increased cardiovascular risk due to a higher prevalence of traditional and particular risk factors such as chronic inflammation, immune dysregulation, endothelial dysfunction, coagulation abnormalities and antiretroviral therapy. In developed countries, coronary artery disease has become the [...] Read more.

People living with human immunodeficiency virus have increased cardiovascular risk due to a higher prevalence of traditional and particular risk factors such as chronic inflammation, immune dysregulation, endothelial dysfunction, coagulation abnormalities and antiretroviral therapy. In developed countries, coronary artery disease has become the most frequent cardiovascular disease and an important cause of mortality in these patients. The symptomatology of an acute coronary syndrome can be atypical, and the prevalence of each type of acute coronary syndrome is reported differently. Regarding coronary artery disease severity in people living with HIV, the literature data indicates that the presence of single-vessel disease is akin to that of HIV-negative patients, and their short-term prognosis is unclear. This study aims to assess the clinical characteristics, biological parameters, angiographical features and short-term prognosis of acute coronary syndrome in a cohort of Romanian people living with human immunodeficiency virus. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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13 pages, 550 KiB

Open AccessArticle

Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital

by Min-Kyung So, Soo-Kyung Kim, Hae-Sun Chung, Ji-Yun Bae and Miae Lee

Diagnostics 2023, 13(6), 1177; https://doi.org/10.3390/diagnostics13061177 - 19 Mar 2023

Cited by 2 | Viewed by 2076

Abstract

The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying [...] Read more.

The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems—VITEK MS MALDI-TOF Mass Spectrometer and Vitek2—and antibiotic susceptibility testing—Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement—both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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20 pages, 1386 KiB

Open AccessArticle

Platelet Abnormalities in Children with Laboratory-Confirmed Influenza

by August Wrotek, Oliwia Wrotek and Teresa Jackowska

Diagnostics 2023, 13(4), 634; https://doi.org/10.3390/diagnostics13040634 - 8 Feb 2023

Cited by 1 | Viewed by 1779

Abstract

Background: The role of platelets in the immune response against influenza has been raised, and a diagnostic or prognostic value of platelet parameter abnormalities, including platelet count (PLT), or mean platelet volume (MPV), has been suggested. The study aimed to analyze the prognostic [...] Read more.

Background: The role of platelets in the immune response against influenza has been raised, and a diagnostic or prognostic value of platelet parameter abnormalities, including platelet count (PLT), or mean platelet volume (MPV), has been suggested. The study aimed to analyze the prognostic value of platelet parameters in children hospitalized due to laboratory-confirmed influenza. Methods: We retrospectively verified the platelet parameters (PLT, MPV, MPV/PLT, and PLT/lymphocyte ratio regarding the influenza complications (acute otitis media, pneumonia, and lower respiratory tract infection—LRTI), and the clinical course (antibiotic treatment, tertiary care transfer, and death). Results: An abnormal PLT was observed in 84 out of 489 laboratory-confirmed cases (17.2%, 44 thrombocytopaenia cases, and 40 thrombocytoses). Patients’ age correlated negatively with PLT (rho = −0.46) and positively with MPV/PLT (rho = 0.44), while MPV was not age-dependent. The abnormal PLT correlated with increased odds of complications (OR = 1.67), including LRTI (OR = 1.89). Thrombocytosis was related to increased odds of LRTI (OR = 3.64), and radiologically/ultrasound-confirmed pneumonia (OR = 2.15), mostly in children aged under 1 year (OR = 4.22 and OR = 3.79, respectively). Thrombocytopaenia was related to antibiotic use (OR = 2.41) and longer hospital stays (OR = 3.03). A lowered MPV predicted a tertiary care transfer (AUC = 0.77), while MPV/PLT was the most versatile parameter in predicting LRTI (AUC = 0.7 in <1 yo), pneumonia (AUC = 0.68 in <1 yo), and antibiotic treatment (AUC = 0.66 in 1–2 yo and AUC = 0.6 in 2–5 yo). Conclusions: Platelet parameters, including PLT count abnormalities and MPV/PLT ratio, are related to the increased odds of complications and a more severe disease course, and may add important data in assessing pediatric influenza patients, but should be interpreted cautiously due to age-related specificities. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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15 pages, 611 KiB

Open AccessArticle

Evaluation of InTray Cassettes Directly from Blood Cultures for the Diagnosis of Sepsis in Clinical Bacteriology Laboratories as an Alternative to Classic Culture Media

by Alessandra Natale, Saoussen Oueslati, Alice Rochard, Sien Ombelet, Daniel Lopez-Baez, Liselotte Hardy, Jane Cunningham, Céline Franquesa, Olivier Vandenberg, Jean-Baptiste Ronat and Thierry Naas

Diagnostics 2023, 13(3), 523; https://doi.org/10.3390/diagnostics13030523 - 31 Jan 2023

Viewed by 2251

Abstract

Culture media is fundamental in clinical bacteriology for the detection and isolation of bacterial pathogens. However, in-house media preparation could be challenging in low-resource settings. InTray^® cassettes (Biomed Diagnostics) could be a valid alternative as they are compact, ready-to-use media preparations. In [...] Read more.

Culture media is fundamental in clinical bacteriology for the detection and isolation of bacterial pathogens. However, in-house media preparation could be challenging in low-resource settings. InTray^® cassettes (Biomed Diagnostics) could be a valid alternative as they are compact, ready-to-use media preparations. In this study, we evaluate the use of two InTray media as a subculture alternative for the diagnosis of bloodstream infections: the InTray^® Müller-Hinton (MH) chocolate and the InTray^® Colorex™ Screen. The InTray MH chocolate was evaluated in 2 steps: firstly, using simulated positive blood cultures (reference evaluation study), and secondly, using positive blood cultures from a routine clinical laboratory (clinical evaluation study). The Colorex Screen was tested using simulated poly-microbial blood cultures. The sensitivity and specificity of the InTray MH chocolate were respectively 99.2% and 90% in the reference evaluation study and 97.1% and 88.2% in the clinical evaluation study. The time to detection (TTD) was ≤20 h in most positive blood cultures (99.8% and 97% in the two studies, respectively). The InTray^® MH Chocolate agar showed good performance when used directly from clinical blood cultures for single bacterial infections. However, mixed flora is more challenging to interpret on this media than on Colorex™ Screen, even for an experienced microbiologist. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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11 pages, 1956 KiB

Open AccessArticle

Formalin Inactivation of Virus for Safe Downstream Processing of Routine Stool Parasite Examination during the COVID-19 Pandemic

by Pisith Chinabut, Nuntiya Sawangkla, Suphaluck Wattano, Techit Thavorasak, Weluga Bootsongkorn, Anchalee Tungtrongchitr and Pichet Ruenchit

Diagnostics 2023, 13(3), 466; https://doi.org/10.3390/diagnostics13030466 - 27 Jan 2023

Viewed by 2181

Abstract

During the COVID-19 pandemic, the parasitology laboratories dealing with fecal samples for the diagnosis of gastrointestinal parasitic infections are confronting the unsaved virus-containing samples. To allow for safe downstream processing of the fecal samples, a protocol for preparing a fecal smear is urgently [...] Read more.

During the COVID-19 pandemic, the parasitology laboratories dealing with fecal samples for the diagnosis of gastrointestinal parasitic infections are confronting the unsaved virus-containing samples. To allow for safe downstream processing of the fecal samples, a protocol for preparing a fecal smear is urgently needed. Formalin was tested with or without isotonic forms for virus inactivation using porcine epidemic diarrhea virus (PEDV) as a representative, as it belongs to the Coronaviridae family. The results revealed complete inactivation activity of 10% formalin and 10% isotonic formalin on coronavirus after 5 min of treatment at room temperature. Both also inhibited Naegleria fowleri growth after 5 min of treatment at 37 °C without disruption of the structure. In addition to these key findings, it was also found that isotonic formalin could stabilize both red and white blood cells when used as a solution to prepare fecal smears comparable to the standard method, highlighting its value for use instead of 0.9% normal saline solution for the quantification of blood cells without active virus. The 10% isotonic formalin is useful to safely prepare a fecal smear for the diagnosis of parasites and other infections of the gastrointestinal tract during the COVID-19 pandemic. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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9 pages, 804 KiB

Open AccessArticle

Efficacy of Lavage by Tube under Local Anesthesia versus Arthroscopic Treatment of Acute Septic Arthritis of Native Knee

by Byung Hak Oh, Youn Moo Heo, In UK Yeo, Woo Jin Shin and Hyun Jin Yoo

Diagnostics 2023, 13(3), 371; https://doi.org/10.3390/diagnostics13030371 - 19 Jan 2023

Cited by 1 | Viewed by 2985

Abstract

Although arthroscopic treatment is a minimally invasive surgery that effectively treats septic arthritis of the knee joint, it requires general or regional anesthesia. This study aimed to compare the clinical results of lavage after tube insertion versus arthroscopic treatment. Patients treated with arthroscopic [...] Read more.

Although arthroscopic treatment is a minimally invasive surgery that effectively treats septic arthritis of the knee joint, it requires general or regional anesthesia. This study aimed to compare the clinical results of lavage after tube insertion versus arthroscopic treatment. Patients treated with arthroscopic treatment were included in group I (n = 76), while those treated with lavage by tube were included in group II (n = 34). We investigated the following in all patients: demographics, underlying disorders, initial serum white blood cell (WBC) count, C-reactive protein (CRP) level, synovial fluid WBC and polymorphonuclear cell counts, causative organism, initial Kellgren–Lawrence grade, lavage number, interventional delay, hospitalization days, CRP normalization time, and Western Ontario McMaster Universities Osteoarthritis index scores for clinical outcomes at 3 months postoperative. The mean interventional delay was significantly greater in group I (23.6 ± 15.6 h vs. 8.7 ± 9.3 h, p < 0.001). The lavage by tube featured a significantly shorter interventional delay time than arthroscopy, while the CRP decrease rate did not differ between groups. Moreover, lavage by tube showed no significant differences in outcomes, including laboratory results and functional outcomes at 3 months postoperative. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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Review

Jump to: Research, Other

19 pages, 3125 KiB

Open AccessReview

Antimicrobial Resistance: What Lies Beneath This Complex Phenomenon?

by Giedrė Valdonė Sakalauskienė and Aurelija Radzevičienė

Diagnostics 2024, 14(20), 2319; https://doi.org/10.3390/diagnostics14202319 - 18 Oct 2024

Viewed by 1588

Abstract

Antimicrobial Resistance (AMR) has evolved from a mere concern into a significant global threat, with profound implications for public health, healthcare systems, and the global economy. Since the introduction of antibiotics between 1945 and 1963, their widespread and often indiscriminate use in human [...] Read more.

Antimicrobial Resistance (AMR) has evolved from a mere concern into a significant global threat, with profound implications for public health, healthcare systems, and the global economy. Since the introduction of antibiotics between 1945 and 1963, their widespread and often indiscriminate use in human medicine, agriculture, and animal husbandry has led to the emergence and rapid spread of antibiotic-resistant genes. Bacteria have developed sophisticated mechanisms to evade the effects of antibiotics, including drug uptake limitation, drug degradation, target modification, efflux pumps, biofilm formation, and outer membrane vesicles production. As a result, AMR now poses a threat comparable to climate change and the COVID-19 pandemic, and projections suggest that death rates will be up to 10 million deaths annually by 2050, along with a staggering economic cost exceeding $100 trillion. Addressing AMR requires a multifaceted approach, including the development of new antibiotics, alternative therapies, and a significant shift in antibiotic usage and regulation. Enhancing global surveillance systems, increasing public awareness, and prioritizing investments in research, diagnostics, and vaccines are critical steps. By recognizing the gravity of the AMR threat and committing to collaborative action, its impact can be mitigated, and global health can be protected for future generations. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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10 pages, 960 KiB

Open AccessReview

Utilizing Next-Generation Sequencing: Advancements in the Diagnosis of Fungal Infections

by Sheetal Naik, Dharambir Kashyap, Jashan Deep, Saif Darwish, Joseph Cross, Edmond Mansoor, Vivek Kumar Garg and Prasanna Honnavar

Diagnostics 2024, 14(15), 1664; https://doi.org/10.3390/diagnostics14151664 - 1 Aug 2024

Viewed by 1664

Abstract

Next-generation sequencing (NGS) has emerged as a promising tool for diagnosing fungal infections. It enables the identification of a wide range of fungal species and provides more accurate and rapid results than traditional diagnostic methods. NGS-based approaches involve the sequencing of DNA or [...] Read more.

Next-generation sequencing (NGS) has emerged as a promising tool for diagnosing fungal infections. It enables the identification of a wide range of fungal species and provides more accurate and rapid results than traditional diagnostic methods. NGS-based approaches involve the sequencing of DNA or RNA from clinical samples, which can be used to detect and identify fungal pathogens in complex clinical samples. The development of targeted gene panels and whole-genome sequencing has allowed for identifying genetic markers associated with antifungal drug resistance, enabling clinicians to tailor patient treatment options. NGS can also provide insights into the pathogenesis of fungal infections and aid in discovering novel drug targets. Although NGS has some limitations, such as cost and data analysis, it can potentially revolutionize the future diagnosis and treatment of fungal infections. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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11 pages, 269 KiB

Open AccessReview

Is It Useful to Repeat Blood Cultures in Endocarditis Patients? A Critical Appraisal

by Wouter Kok

Diagnostics 2024, 14(14), 1578; https://doi.org/10.3390/diagnostics14141578 - 22 Jul 2024

Viewed by 961

Abstract

Background: Previous guidelines for endocarditis have suggested repeating blood cultures until they become negative, with limited evidence. Methods: Literature reviews were conducted (1) on the incidence of persistent bacteremia and association with outcome and (2) on timing of valve culture negativization to examine [...] Read more.

Background: Previous guidelines for endocarditis have suggested repeating blood cultures until they become negative, with limited evidence. Methods: Literature reviews were conducted (1) on the incidence of persistent bacteremia and association with outcome and (2) on timing of valve culture negativization to examine the claim for prolongation of antibiotic therapy starting from negative blood cultures. Results: Persistent bacteremia and fever may be present in the first 3 days of endocarditis, despite treatment, and are more common in Staphylococcus (especially MRSA) and Enterococcus species. Persistent bacteremia (48–72 h), persistent infection (day 7), and new onset septic shock are related and predict in-hospital mortality. It is, however, persistent infection at day 7 and septic shock that primarily determine the infectious course of endocarditis, and not persistent bacteremia. Valve cultures at surgery become negative in most cases (>85–90%) after 14–21 days of antibiotic therapy, with no calculated benefit for prolonging therapy after 21 days. Conclusions: Persistent infection at 7 days after appropriate antibiotic therapy is a better key event for prognosis then positive or negative blood cultures at 48–72 h. Therapy prolongation from the day of negative blood cultures is not reasonable. There is no need to survey blood cultures in endocarditis patients after starting therapy. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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Graphical abstract

16 pages, 1048 KiB

Open AccessReview

Diagnosis of Human Cytomegalovirus Drug Resistance Mutations in Solid Organ Transplant Recipients—A Review

by Madain S. Alsanea, Ahmed A. Al-Qahtani, Reem S. Almaghrabi, Maha A. AlAbdulkareem, Basma M. Alahideb, Dalia Obeid, Feda A. Alsuwairi and Fatimah S. Alhamlan

Diagnostics 2024, 14(2), 203; https://doi.org/10.3390/diagnostics14020203 - 18 Jan 2024

Viewed by 2209

Abstract

Human cytomegalovirus (HCMV) infection may be asymptomatic in healthy individuals but can cause severe complications in immunocompromised patients, including transplant recipients. Breakthrough and drug-resistant HCMV infections in such patients are major concerns. Clinicians are first challenged to accurately diagnose HCMV infection and then [...] Read more.

Human cytomegalovirus (HCMV) infection may be asymptomatic in healthy individuals but can cause severe complications in immunocompromised patients, including transplant recipients. Breakthrough and drug-resistant HCMV infections in such patients are major concerns. Clinicians are first challenged to accurately diagnose HCMV infection and then to identify the most effective antiviral drug and determine when to initiate therapy, alter drug dosage, or switch medication. This review critically examines HCMV diagnostics approaches, particularly for immunocompromised patients, and the development of genotypic techniques to rapidly diagnose drug resistance mutations. The current standard method to identify prevalent and well-known resistance mutations involves polymerase chain reaction amplification of UL97, UL54, and UL56 gene regions, followed by Sanger sequencing. This method can confirm clinical suspicion of drug resistance as well as determine the level of drug resistance and range of cross-resistance with other drugs. Despite the effectiveness of this approach, there remains an urgent need for more rapid and point-of-care HCMV diagnosis, allowing for timely lifesaving intervention. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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25 pages, 992 KiB

Open AccessReview

Alternate Antimicrobial Therapies and Their Companion Tests

by Sriram Kalpana, Wan-Ying Lin, Yu-Chiang Wang, Yiwen Fu and Hsin-Yao Wang

Diagnostics 2023, 13(15), 2490; https://doi.org/10.3390/diagnostics13152490 - 26 Jul 2023

Cited by 1 | Viewed by 2040

Abstract

New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list [...] Read more.

New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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Other

Jump to: Research, Review

13 pages, 2296 KiB

Open AccessSystematic Review

A Systematic Review and Meta-Analysis of Molecular Characteristics on Colistin Resistance of Acinetobacter baumannii

by Ihsan Hakki Ciftci, Elmas Pinar Kahraman Kilbas and Imdat Kilbas

Diagnostics 2024, 14(22), 2599; https://doi.org/10.3390/diagnostics14222599 - 19 Nov 2024

Viewed by 335

Abstract

Background: This study aimed to determine the molecular epidemiology of colistin-resistant A. baumannii in the last ten years and the frequency of gene regions related to pathogenesis, to compare the methods used to detect genes, and to confirm colistin resistance. Methods: This meta-analysis [...] Read more.

Background: This study aimed to determine the molecular epidemiology of colistin-resistant A. baumannii in the last ten years and the frequency of gene regions related to pathogenesis, to compare the methods used to detect genes, and to confirm colistin resistance. Methods: This meta-analysis study was conducted under Preferred Reporting Items for Systematic Reviews and Meta-Analysis Guidelines. In the meta-analysis, research articles published in English and Turkish in electronic databases between January 2012 and November 2023 were examined. International Business Machines (IBM) Statistical Package for the Social Sciences (SPSS) Statistics for Macbook (Version 25.0. Armonk, NY, USA) was used for statistical analysis. The Comprehensive Meta-Analysis (CMA) (Version 3.0. Biostat, NJ, USA) program was used for heterogeneity assessment in the articles included in the meta-analysis. Results: After evaluating the studies according to the elimination criteria, 18 original articles were included. Among colistin-resistant strains, bla_OXA-51 positivity was 243 (19.61%), bla_OXA-23 was 113 (9.12%), bla_OXA-58 was 7 (0.56%), bla_OXA-143 was 15 (1.21%), and bla_OXA-72 was seen in two (0.16%) strains. The positivity rates of pmrA, pmrB, and pmrC were found to be 22 (1.77%), 26 (2.09%), and 6 (0.48%). The mcr-1 rate was found to be 91 (7.34%), the mcr-2 rate was 78 (6.29%), and the mcr-3 rate was 82 (6.61%). Conclusions: The colistin resistance rate in our study was found to be high. However, only some research articles report and/or investigate more than one resistance gene together. Additionally, it may be challenging to explain colistin resistance solely by expressing resistance genes without discussing accompanying components such as efflux pumps, virulence factors, etc. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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13 pages, 2610 KiB

Open AccessSystematic Review

Age-Specific Seroprevalence of Hepatitis A Virus in Turkey Between 2000 and 2023: Systematic Review and Meta-Analysis

by Ihsan Hakki Ciftci, Mehmet Koroglu, Tayfur Demiray, Huseyin Agah Terzi and Elmas Pinar Kahraman Kilbas

Diagnostics 2024, 14(22), 2464; https://doi.org/10.3390/diagnostics14222464 - 5 Nov 2024

Viewed by 475

Abstract

Background: Hepatitis A virus (HAV) is a leading cause of acute viral hepatitis and is primarily transmitted by the fecal–oral route. The clinical presentation and progression of the disease varies according to the age of the patient. Turkey is classified as a [...] Read more.

Background: Hepatitis A virus (HAV) is a leading cause of acute viral hepatitis and is primarily transmitted by the fecal–oral route. The clinical presentation and progression of the disease varies according to the age of the patient. Turkey is classified as a moderately endemic country, and HAV infection continues to be an important public health problem worldwide. Methods: In this study, a systematic meta-analysis was conducted to evaluate age-specific HAV seroprevalence rates in Turkey between 2000 and 2023. A comprehensive literature review identified 57 articles that met the inclusion criteria. The studies were assessed for quality, and seroprevalence rates were evaluated across four different age groups. Statistical analyses were performed using Comprehensive Meta-Analysis (CMA) software (CMAVersion 3.0) and SPSS (SPSS Statistics 25.0). Results: HAV seroprevalence rates were found to be 73.18% in the 0 < 5 age group and 90.90% in the >35 age group. The overall seroprevalence estimated using a random effects model was 64.5% (95% CI: 58.3–70). High heterogeneity was observed among the studies, and the prevalence estimates changed when low-quality studies were excluded. Conclusions: This meta-analysis suggests that the increasing trend in HAV IgG seroprevalence in Turkey, especially among young populations, is likely due to the vaccination program initiated in 2012. Furthermore, the heterogeneity observed among regions highlights the importance of regional public health strategies. Future studies should focus on providing more detailed data to evaluate the long-term effects of vaccination and to explain regional differences in HAV seroprevalence. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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10 pages, 3114 KiB

Open AccessBrief Report

A Multivariant Surrogate Virus Neutralization Test Demonstrates Distinct SARS-CoV-2-Specific Antibody Responses in People Living with HIV after a Fourth Monovalent mRNA Vaccination or an Omicron Breakthrough Infection

by David Niklas Springer, Simon Daller, Michael Knappik, Katja Prüger, Sylvia Hartl, Robab Breyer-Kohansal, Elisabeth Puchhammer-Stöckl, Judith Helene Aberle, Lukas Weseslindtner and Marie Kathrin Breyer

Diagnostics 2024, 14(8), 822; https://doi.org/10.3390/diagnostics14080822 - 16 Apr 2024

Viewed by 1083

Abstract

While neutralizing antibodies (nAbs) induced by monovalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccinations are primarily directed against the wildtype (WT), subsequent exposure to the Omicron variants may increase the breadth of the antibodies’ cross-neutralizing activity. Here, we analyzed the impact of [...] Read more.

While neutralizing antibodies (nAbs) induced by monovalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccinations are primarily directed against the wildtype (WT), subsequent exposure to the Omicron variants may increase the breadth of the antibodies’ cross-neutralizing activity. Here, we analyzed the impact of an Omicron breakthrough infection (BTI) or a fourth monovalent mRNA vaccination on nAb profiles in people living with human immunodeficiency virus (PLWH). Using a multivariant surrogate virus neutralization test (sVNT), we quantified nAbs in 36 three-times vaccinated PLWH, of whom 9 acquired a serologically confirmed Omicron BTI, 8 received a fourth vaccine dose, and 19 were neither infected nor additionally vaccinated. While nAbs against WT and Delta increased after the BTI and a fourth vaccination, a significant increase against BA.1, BA.2, and BA.5 was only observed after the BTI. However, there was no significant difference in nAb concentrations between the samples obtained after the BTI and fourth vaccination. In contrast, nAb levels were significantly lower in PLWH, who were neither infected nor additionally vaccinated after three vaccinations. Thus, our study demonstrates the suitability of a multivariant sVNT to assess hybrid humoral immunity after Omicron BTIs in PLWH vaccinated against SARS-CoV-2. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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12 pages, 4239 KiB

Open AccessCase Report

A Rare Case of Dirofilariasis in the Genian Region

by Andrei Nicolau, Florin Petrică Sava, Florentina Severin, Mihai Liviu Ciofu, Dan Ferariu, Daniela Dodu and Victor Vlad Costan

Diagnostics 2024, 14(6), 628; https://doi.org/10.3390/diagnostics14060628 - 15 Mar 2024

Viewed by 1173

Abstract

Dirofilariasis is an infectious disease caused by species of the Dirofilaria genus. It is manifested by the appearance of a subcutaneous swelling, especially in the eye region. We present the case of a 29-year-old patient who presented with facial asymmetry in the right [...] Read more.

Dirofilariasis is an infectious disease caused by species of the Dirofilaria genus. It is manifested by the appearance of a subcutaneous swelling, especially in the eye region. We present the case of a 29-year-old patient who presented with facial asymmetry in the right genian region. Following clinical and paraclinical evaluations, the diagnosis of a parasitic cyst was established in the context of dirofilariasis with Dirofilaria repens (D. repens). Treatment consisted of surgical excision of the formation associated with prophylactic antibiotic medication. Macroscopic analysis of the excision piece revealed a structure that contained a cystic cavity and a filamentous form with a length of approximately 10 mm and a diameter of 1 mm. This is the first case of dirofilariasis located in the genian region reported in Romania. The overview of this pathology is important to raise awareness among physicians about its presence and clinical variations. Understanding such cases helps healthcare professionals enhance diagnostic skills, refine treatment strategies, and provide valuable insights into the prevalence and clinical presentation, fostering early detection and timely intervention. Detailed case reports contribute to the understanding of the disease’s epidemiology, including risk factors and transmission patterns, which is essential for effective public health strategies. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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9 pages, 1224 KiB

Open AccessBrief Report

Generation of JC Polyoma Pseudovirus for High-Throughput Measurement of Neutralizing Antibodies

by Mami Matsuda, Tian-Cheng Li, Akira Nakanishi, Kazuo Nakamichi, Makoto Saito, Tadaki Suzuki, Tomokazu Matsuura, Masamichi Muramatsu, Tetsuro Suzuki, Yoshiharu Miura and Ryosuke Suzuki

Diagnostics 2024, 14(3), 311; https://doi.org/10.3390/diagnostics14030311 - 31 Jan 2024

Viewed by 1692

Abstract

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system (CNS) caused by reactivation of dormant JC polyomavirus (JCPyV). PML was mainly observed in immunocompromised individuals, such as HIV-positive patients, autoimmune disease patients, and cancer patients. Given that the presence [...] Read more.

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system (CNS) caused by reactivation of dormant JC polyomavirus (JCPyV). PML was mainly observed in immunocompromised individuals, such as HIV-positive patients, autoimmune disease patients, and cancer patients. Given that the presence of anti-JCPyV antibodies in serum is a risk indicator for PML development, it is essential to monitor anti-JCPyV antibody levels. In the present study, we established reporter-based single-infection neutralization assays for JCPyV and the genetically similar BK polyoma virus (BKPyV). We then confirmed the lack of cross-reactivity between the two viruses using test sera obtained from mice immunized with plasmids encoding the JCPyV or BKPyV capsid. Next, we compared neutralization antibody titers in sera from healthy donors, patients with multiple sclerosis (MS), and HIV-positive patients using an in-house enzyme-linked immunosorbent assay (ELISA) with JCPyV-like particles (virus-like particles; VLPs). A positive correlation was demonstrated between the neutralization titer (75% infectious concentration; IC75) against JCPyV and the antibody titer obtained by VLP-based JCPyV ELISA. This assay system may be applied to detect antibodies against other PyVs by generation of pseudoviruses using the respective capsid expression plasmids, and is expected to contribute to the surveillance of PyV as well as basic research on these viruses. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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9 pages, 1674 KiB

Open AccessBrief Report

Comparative Evaluation of a Standard M10 Assay with Xpert Xpress for the Rapid Molecular Diagnosis of SARS-CoV-2, Influenza A/B Virus, and Respiratory Syncytial Virus

by Azwani Abdullah, I-Ching Sam, Yin Jie Ong, Chun Hao Theo, Muhammad Harith Pukhari and Yoke Fun Chan

Diagnostics 2023, 13(23), 3507; https://doi.org/10.3390/diagnostics13233507 - 22 Nov 2023

Cited by 6 | Viewed by 1798

Abstract

SARS-CoV-2, influenza A/B virus (IAV/IBV), and respiratory syncytial virus (RSV) are among the common viruses causing acute respiratory infections. Clinical diagnosis to differentiate these viruses is challenging due to similar clinical presentations; thus, laboratory-based real-time RT PCR is the gold standard for diagnosis. [...] Read more.

SARS-CoV-2, influenza A/B virus (IAV/IBV), and respiratory syncytial virus (RSV) are among the common viruses causing acute respiratory infections. Clinical diagnosis to differentiate these viruses is challenging due to similar clinical presentations; thus, laboratory-based real-time RT PCR is the gold standard for diagnosis. This retrospective study aimed to evaluate the diagnostic performance of STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor Inc., Seoul, Korea) using archived positive and negative respiratory samples for SARS-CoV-2, IAV, IBV, and RSV. A total of 322 respiratory samples were tested, comprising 215 positive samples (49 SARS-CoV-2, 48 IAV, 53 IBV, 65 RSV) and 107 negative samples. All samples were tested with both STANDARD M10 and compared to either Xpert Xpress SARS-CoV-2 or Xpert Xpress Flu/RSV (Cepheid, Sunnyvale, CA, USA). The sensitivity, specificity, positive predictive value, and negative predictive value rates of STANDARD M10 were very similar to Xpert Xpress SARS-CoV-2 or Xpert Xpress Flu/RSV ranges for each virus (98–100%). The duration of testing and workflows were similar. The overall agreement was 99.4%, including 99.1% agreement for positive samples and 100% agreement for negative samples. In conclusion, the STANDARD M10 point-of-care test is suitable for rapid simultaneous detection of SARS-CoV-2, IAV, IBV, and RSV. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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9 pages, 1234 KiB

Open AccessCase Report

Refractory Bilateral Tubo-Ovarian Abscesses in a Patient with Iatrogenic Hypogammaglobulinemia

by Elizabeth J. Klein, Nouf K. Almaghlouth, Gabriela Weigel, Dimitrios Farmakiotis and Erica Hardy

Diagnostics 2023, 13(22), 3478; https://doi.org/10.3390/diagnostics13223478 - 19 Nov 2023

Viewed by 1740

Abstract

Genital mycoplasmas are sexually transmitted Mollicutes with a high prevalence of urogenital tract colonization among females of reproductive age. Current guidelines recommend against routine screening for these organisms, since their role in the pathogenesis of pelvic inflammatory disease and tubo-ovarian abscesses (TOAs) remains [...] Read more.

Genital mycoplasmas are sexually transmitted Mollicutes with a high prevalence of urogenital tract colonization among females of reproductive age. Current guidelines recommend against routine screening for these organisms, since their role in the pathogenesis of pelvic inflammatory disease and tubo-ovarian abscesses (TOAs) remains unclear. However, genital mycoplasmas harbor pathogenic potential in immunocompromised hosts, especially patients with hypogammaglobulinemia. It is important to identify such infections early, given their potential for invasive spread and the availability of easily accessible treatments. We present a young adult female with multiple sclerosis and iatrogenic hypogammaglobulinemia, with refractory, bilateral pelvic inflammatory disease and TOAs due to Ureaplasma urealyticum, identified as a single pathogen via three distinct molecular tests. To our knowledge, this is the second case of TOAs caused by U. urealyticum in the literature, and the first diagnosed by pathogen cell-free DNA metagenomic next-generation sequencing in plasma. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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8 pages, 1660 KiB

Open AccessBrief Report

A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA

by Sayamon Hongjaisee, Nang Kham-Kjing, Piyagorn Musikul, Wannaporn Daengkaokhew, Nuntita Kongson, Ratchadakorn Guntala, Nitipoom Jaiyapan, Enos Kline, Nuttada Panpradist, Nicole Ngo-Giang-Huong and Woottichai Khamduang

Diagnostics 2023, 13(19), 3040; https://doi.org/10.3390/diagnostics13193040 - 25 Sep 2023

Cited by 2 | Viewed by 1870

Abstract

Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed [...] Read more.

Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65 °C for 30 min using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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6 pages, 616 KiB

Open AccessCase Report

Fatal Fulminant Hepatitis E in a Diabetic Patient on Metformin

by Erika Peroni, Pierre Mora, Anne Motte, René Gerolami, Sarah Aherfi and Philippe Colson

Diagnostics 2022, 12(10), 2385; https://doi.org/10.3390/diagnostics12102385 - 30 Sep 2022

Cited by 2 | Viewed by 1577

Abstract

Hepatitis E is mostly autochthonous in Western developed countries, eating pig-derived products being the most frequently documented source. Hepatitis E virus (HEV) infection is usually asymptomatic or self-limiting, but it can cause acute liver failure. HEV serological testing was performed using EUROIMMUN immunoenzymatic [...] Read more.

Hepatitis E is mostly autochthonous in Western developed countries, eating pig-derived products being the most frequently documented source. Hepatitis E virus (HEV) infection is usually asymptomatic or self-limiting, but it can cause acute liver failure. HEV serological testing was performed using EUROIMMUN immunoenzymatic assays. HEV RNA in the serum was determined using an in-house real-time reverse transcriptase PCR procedure. The HEV genotype was determined through phylogenetic analysis after Sanger sequencing was performed using an in-house procedure. The case patient, an immunocompetent patient in his 60s with type 2 diabetes and no documented chronic liver disease, was hospitalized in February 2021 in an intensive care unit due to an initially unexplained coma. He presented metformin overdose and fulminant hepatitis E (HEV RNA in the serum was 4,140,000 copies/mL) that evolved toward death. The HEV genotype was 3f. We identified eight previous hepatitis E in diabetic patients, but with no metformin excessive plasma concentration, in the literature. Three patients were liver transplant recipients and three died. HEV infection can be severe and life-threatening in diabetic patients, which warrants HEV testing in this special population in the case of an altered general condition and/or liver cytolysis. Full article

(This article belongs to the Special Issue Advances in the Diagnosis of Infectious Diseases and Microorganisms)

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