Limited genomic surveillance data is available for SARS-CoV-2 in Thailand during the second and third wave outbreaks, including both patient and environmental samples. This study investigated the presence of SARS-CoV-2 RNA in patient samples, on frequently touched surfaces, and in environmental swab samples (EVSs) collected from urban markets in Bangkok between April 2021 and August 2022. A total of 78,159 nasopharyngeal swab samples from patients and 327 environmental swab samples from hospital and market settings were collected. SARS-CoV-2 RNA was detected in 3,706 of 78,159 patient samples and one of 327 environmental samples using real-time RT-PCR. In total, 54 patient samples and an environmental sample were subjected to whole-genome sequencing and mass array genotyping, respectively. Only 46 samples passed the quality assessment based on the analysis criteria. The lineages detected included B.1.1.529 (2 samples), B.1.1.7 (15 samples), B.1.351 (3 samples), B.1.36.16 (6 samples), B.1.617.2 (1 sample), AY.102 (1 sample), AY.4 (11 samples), AY.25 (1 sample), BA.1 (1 sample), BA.1.1 (3 samples), and BA.2 (2 samples). The phylogenetic analysis of the viral genome sequences revealed similar lineages during this study period.
{"title":"Severe acute respiratory syndrome coronavirus 2 variants in patients with coronavirus disease 2019 and environmental sampling from the hospital and market during the coronavirus disease 2019 pandemic in Thailand","authors":"Uraporn Phumisantiphong , Kitwadee Rupprom , Thanwa Wongsuk , Anan Manomaipiboon , Jakravoot Maneerit , Ampan Vimonvattana , Wasun Chantratita , Insee Sensorn , Tonsan Hansirisathit , Wipawee Thongsopa , Chayanit Phutthanu , Sunisa Dongphooyao , Chuphong Thongnak","doi":"10.1016/j.diagmicrobio.2024.116604","DOIUrl":"10.1016/j.diagmicrobio.2024.116604","url":null,"abstract":"<div><div>Limited genomic surveillance data is available for SARS-CoV-2 in Thailand during the second and third wave outbreaks, including both patient and environmental samples. This study investigated the presence of SARS-CoV-2 RNA in patient samples, on frequently touched surfaces, and in environmental swab samples (EVSs) collected from urban markets in Bangkok between April 2021 and August 2022. A total of 78,159 nasopharyngeal swab samples from patients and 327 environmental swab samples from hospital and market settings were collected. SARS-CoV-2 RNA was detected in 3,706 of 78,159 patient samples and one of 327 environmental samples using real-time RT-PCR. In total, 54 patient samples and an environmental sample were subjected to whole-genome sequencing and mass array genotyping, respectively. Only 46 samples passed the quality assessment based on the analysis criteria. The lineages detected included B.1.1.529 (2 samples), B.1.1.7 (15 samples), B.1.351 (3 samples), B.1.36.16 (6 samples), B.1.617.2 (1 sample), AY.102 (1 sample), AY.4 (11 samples), AY.25 (1 sample), BA.1 (1 sample), BA.1.1 (3 samples), and BA.2 (2 samples). The phylogenetic analysis of the viral genome sequences revealed similar lineages during this study period.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116604"},"PeriodicalIF":2.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-12DOI: 10.1016/j.diagmicrobio.2024.116593
Chunyan Zhao , Chang Song , Shixiong Yang , Aichun Huang , Yanrong Lin , Chaoyan Xu , Xiaoying Wei , Chunmei Zeng , Yiyi Lan , Xiaoyang Luo , Qingdong Zhu
Objective
To investigate the diagnostic efficacy of nanopore sequencing technology in tuberculous meningitis (TBM).
Methods
Cerebrospinal fluid samples were collected from patients for acid-fast staining microscopy, Mycobacterium tuberculosis solid culture, DNA detection, and nanopore sequencing. Lastly, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) were calculated and compared among these detection methods.
Results
In this study, 30 TBM patients and 18 non-TBM patients were included. Nanopore sequencing showed higher sensitivity (43.30 %) and AUC (0.661) compared to the other methods. Combining nanopore sequencing and imaging achieved the highest diagnostic performance with sensitivity (60.00 %), specificity (88.90 %), PPV (90.00 %), NPV (57.10 %), and AUC (0.744).
Conclusion
Nanopore sequencing demonstrated superior diagnostic accuracy for TBM, outperforming acid-fast staining, Mycobacterium tuberculosis culture, and DNA detection. When combined with imaging, nanopore sequencing significantly enhanced diagnostic sensitivity and accuracy for TBM.
{"title":"Diagnostic value of nanopore sequencing of cerebrospinal fluid samples in tuberculous meningitis","authors":"Chunyan Zhao , Chang Song , Shixiong Yang , Aichun Huang , Yanrong Lin , Chaoyan Xu , Xiaoying Wei , Chunmei Zeng , Yiyi Lan , Xiaoyang Luo , Qingdong Zhu","doi":"10.1016/j.diagmicrobio.2024.116593","DOIUrl":"10.1016/j.diagmicrobio.2024.116593","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the diagnostic efficacy of nanopore sequencing technology in tuberculous meningitis (TBM).</div></div><div><h3>Methods</h3><div>Cerebrospinal fluid samples were collected from patients for acid-fast staining microscopy, Mycobacterium tuberculosis solid culture, DNA detection, and nanopore sequencing. Lastly, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) were calculated and compared among these detection methods.</div></div><div><h3>Results</h3><div>In this study, 30 TBM patients and 18 non-TBM patients were included. Nanopore sequencing showed higher sensitivity (43.30 %) and AUC (0.661) compared to the other methods. Combining nanopore sequencing and imaging achieved the highest diagnostic performance with sensitivity (60.00 %), specificity (88.90 %), PPV (90.00 %), NPV (57.10 %), and AUC (0.744).</div></div><div><h3>Conclusion</h3><div>Nanopore sequencing demonstrated superior diagnostic accuracy for TBM, outperforming acid-fast staining, Mycobacterium tuberculosis culture, and DNA detection. When combined with imaging, nanopore sequencing significantly enhanced diagnostic sensitivity and accuracy for TBM.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116593"},"PeriodicalIF":2.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-08DOI: 10.1016/j.diagmicrobio.2024.116588
Philip Raj Abraham , Ezhil Veeraiyan , Akash Dhotre , Ashwani Kumar
Dengue, a vector-borne disease, affects nearly 400 million people annually. Although commercially available dengue NS1 antigen-based ELISA kits are simple and rapid, they are expensive as monoclonal antibodies are used in these tests, and also, they have short expiry dates. As an alternative, the polyclonal antibodies generated against dengue NS1 antigen from the individuals who recovered from the dengue infection (human polyclonal antibodies against dengue; HuPA-D) can be explored for the detection of NS1 antigen in the dengue virus (DENV) infected patients’ sera. In this study, blood samples were collected from the dengue-recovered patients after obtaining the IHEC approval. The anti-NS1 HuPA-D (IgG) was purified using NAb™ Spin Column kit and tested on SDS-PAGE. HuPA-D ELISA was developed to test the sensitivity and specificity of the antibodies using the recombinant NS1 antigens of dengue serotypes and flaviviruses. Further, the HuPA-D were used to detect the sera of the dengue patients. The assay was found to be sensitive to detect all the serotypes of recombinant dengue NS1 antigen and also NS1 antigen from the sera of DENV infected patients.
{"title":"Exploring potential application of anti-dengue NS1 human polyclonal antibodies for detection of dengue virus infection","authors":"Philip Raj Abraham , Ezhil Veeraiyan , Akash Dhotre , Ashwani Kumar","doi":"10.1016/j.diagmicrobio.2024.116588","DOIUrl":"10.1016/j.diagmicrobio.2024.116588","url":null,"abstract":"<div><div>Dengue, a vector-borne disease, affects nearly 400 million people annually. Although commercially available dengue NS1 antigen-based ELISA kits are simple and rapid, they are expensive as monoclonal antibodies are used in these tests, and also, they have short expiry dates. As an alternative, the polyclonal antibodies generated against dengue NS1 antigen from the individuals who recovered from the dengue infection (human polyclonal antibodies against dengue; HuPA-D) can be explored for the detection of NS1 antigen in the dengue virus (DENV) infected patients’ sera. In this study, blood samples were collected from the dengue-recovered patients after obtaining the IHEC approval. The anti-NS1 HuPA-D (IgG) was purified using NAb™ Spin Column kit and tested on SDS-PAGE. HuPA-D ELISA was developed to test the sensitivity and specificity of the antibodies using the recombinant NS1 antigens of dengue serotypes and flaviviruses. Further, the HuPA-D were used to detect the sera of the dengue patients. The assay was found to be sensitive to detect all the serotypes of recombinant dengue NS1 antigen and also NS1 antigen from the sera of DENV infected patients.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116588"},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-08DOI: 10.1016/j.diagmicrobio.2024.116603
Li Yang , Shaoxiang Ou , Dan Wang, Bihua Gao, Guifang Zhu, Jialun Xie, Liling Zhong
Vector-Borne disease represent a significant global public health issue, with tsutsugamushi disease (TD) being a notable zoonotic disease transmitted through the bites of chigger larvae. TD is associated with a broad spectrum of complications and is characterized by high rates of morbidity and mortality. Diagnostic, therapeutic, and care standards for TD differ across regions worldwide, and there is a dearth of documented care cases. This case report details a critical TD presentation involving infectious shock and multiple organ failure. After nine days of intensive treatment and nursing intervention, which included correction of hypoxemia, anti-infection measures, antispasmodic and asthmatic management, and stabilization of the internal environment, the patient's condition was effectively managed.
{"title":"Clinical management of infectious shock induced by tsutsugamushi disease with multi-organ failure: A case report abstract","authors":"Li Yang , Shaoxiang Ou , Dan Wang, Bihua Gao, Guifang Zhu, Jialun Xie, Liling Zhong","doi":"10.1016/j.diagmicrobio.2024.116603","DOIUrl":"10.1016/j.diagmicrobio.2024.116603","url":null,"abstract":"<div><div>Vector-Borne disease represent a significant global public health issue, with tsutsugamushi disease (TD) being a notable zoonotic disease transmitted through the bites of chigger larvae. TD is associated with a broad spectrum of complications and is characterized by high rates of morbidity and mortality. Diagnostic, therapeutic, and care standards for TD differ across regions worldwide, and there is a dearth of documented care cases. This case report details a critical TD presentation involving infectious shock and multiple organ failure. After nine days of intensive treatment and nursing intervention, which included correction of hypoxemia, anti-infection measures, antispasmodic and asthmatic management, and stabilization of the internal environment, the patient's condition was effectively managed.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116603"},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-07DOI: 10.1016/j.diagmicrobio.2024.116601
Frank L. Spangler , Cheau Williams , Michael E. Aberger , Bradley A. Wilson , Khaled Ajib , Shahram S. Gholami , Henry N. Goodwin Jr. , Lauren Y. Park , Moustafa Kardjadj , DeAndre Derrick , Thomas K. Huard
Purpose
Managing complicated urinary tract infections (cUTIs) poses significant challenges, often resulting in the overprescription of empiric antibiotics. This approach exposes patients to multiple antimicrobials and raises the risk of inadequate treatment efficacy. The purpose of this study is to assess and compare the clinical utility of molecular testing (PCR) versus conventional culture and sensitivity (C&S) in managing cUTI, to identify optimal management strategies for cUTI patients.
Materials and methods
773 symptomatic adult patients with suspected cUTI diagnosis were randomized (1:1) into either the PCR-guided treatment group or the control group (C&S-guided) and followed up for 28 days. The primary outcome measure was the number (and percentage) of patients in each study arm with favorable clinical outcomes at the end of the study visit.
Results
Overall, 468 patients completed all study procedures, and of those, data from 362 patients were analyzed (193 PCR arm, 169 C&S arm) for this Part 1 of the primary study analysis. Treatments guided by PCR results provided significantly better clinical outcomes compared to treatments guided by conventional C&S results (88.08 % vs. 78.11, p = 0.011), with a significantly shorter mean turnaround time (49.68 h vs. 104.4 h, p < 0.001), and a significant higher investigator satisfaction total score (23.95 ± 1.96 vs. 20.64 ± 4.12, p < 0.001).
Conclusions
This data demonstrated the clinical utility of PCR in improving therapeutic clinical outcomes and facilitating expedited, patient-specific management of cUTI for optimal patient care. Furthermore, this study showed a clear preference among investigators for PCR over C&S when making clinical decisions and managing patients with cUTI.
{"title":"Clinical utility of PCR compared to conventional culture and sensitivity testing for the management of complicated urinary tract infections in adults: Part I. Assessment of clinical outcomes, investigator satisfaction scores, and turnaround times","authors":"Frank L. Spangler , Cheau Williams , Michael E. Aberger , Bradley A. Wilson , Khaled Ajib , Shahram S. Gholami , Henry N. Goodwin Jr. , Lauren Y. Park , Moustafa Kardjadj , DeAndre Derrick , Thomas K. Huard","doi":"10.1016/j.diagmicrobio.2024.116601","DOIUrl":"10.1016/j.diagmicrobio.2024.116601","url":null,"abstract":"<div><h3>Purpose</h3><div>Managing complicated urinary tract infections (cUTIs) poses significant challenges, often resulting in the overprescription of empiric antibiotics. This approach exposes patients to multiple antimicrobials and raises the risk of inadequate treatment efficacy. The purpose of this study is to assess and compare the clinical utility of molecular testing (PCR) versus conventional culture and sensitivity (C&S) in managing cUTI, to identify optimal management strategies for cUTI patients.</div></div><div><h3>Materials and methods</h3><div>773 symptomatic adult patients with suspected cUTI diagnosis were randomized (1:1) into either the PCR-guided treatment group or the control group (C&S-guided) and followed up for 28 days. The primary outcome measure was the number (and percentage) of patients in each study arm with favorable clinical outcomes at the end of the study visit.</div></div><div><h3>Results</h3><div>Overall, 468 patients completed all study procedures, and of those, data from 362 patients were analyzed (193 PCR arm, 169 C&S arm) for this Part 1 of the primary study analysis. Treatments guided by PCR results provided significantly better clinical outcomes compared to treatments guided by conventional C&S results (88.08 % vs. 78.11, p = 0.011), with a significantly shorter mean turnaround time (49.68 h vs. 104.4 h, p < 0.001), and a significant higher investigator satisfaction total score (23.95 ± 1.96 vs. 20.64 ± 4.12, p < 0.001).</div></div><div><h3>Conclusions</h3><div>This data demonstrated the clinical utility of PCR in improving therapeutic clinical outcomes and facilitating expedited, patient-specific management of cUTI for optimal patient care. Furthermore, this study showed a clear preference among investigators for PCR over C&S when making clinical decisions and managing patients with cUTI.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116601"},"PeriodicalIF":2.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We evaluated the diagnostic performance of Rapiim SARS-CoV-2-H (Rapiim-H)—a point-of-care qualitative antigen test—using nasopharyngeal swabs (NPS) and saliva samples and compared its results with those from antigen quantification and nucleic acid amplification tests. NPS and saliva were collected from patients with confirmed and suspected coronavirus disease (COVID-19). In total, 142 NPS and saliva samples were collected. In symptomatic cases, in which the first NPS sample was collected within 10 days of disease onset, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for COVID-19 diagnosis were 91.7 %, 88.6 %, 93.2 %, and 86.1 %, respectively. A similar analysis was performed on saliva samples, and the sensitivity, specificity, PPV, and NPV were 50.8 %, 91.4 %, 91.2 %, and 51.6 %, respectively. The Rapiim-H test using NPS demonstrated approximately 90 % sensitivity and specificity, particularly within the first 10 days after disease onset.
{"title":"Evaluation of the COVID-19 diagnostic performance of Rapiim SARS-CoV-2-H, the highly sensitive SARS-CoV-2 antigen qualitative test kit","authors":"Nobumasa Okumura , Hideaki Kato , Kei Yamamoto , Eri Hagiwara , Masami Kurokawa , Sayaka Hikida , Taketomo Maruki , Kazuhisa Mezaki , Katsushi Tanaka , Takashi Ogura , Norio Ohmagari","doi":"10.1016/j.diagmicrobio.2024.116598","DOIUrl":"10.1016/j.diagmicrobio.2024.116598","url":null,"abstract":"<div><div>We evaluated the diagnostic performance of Rapiim SARS-CoV-2-H (Rapiim-H)—a point-of-care qualitative antigen test—using nasopharyngeal swabs (NPS) and saliva samples and compared its results with those from antigen quantification and nucleic acid amplification tests. NPS and saliva were collected from patients with confirmed and suspected coronavirus disease (COVID-19). In total, 142 NPS and saliva samples were collected. In symptomatic cases, in which the first NPS sample was collected within 10 days of disease onset, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for COVID-19 diagnosis were 91.7 %, 88.6 %, 93.2 %, and 86.1 %, respectively. A similar analysis was performed on saliva samples, and the sensitivity, specificity, PPV, and NPV were 50.8 %, 91.4 %, 91.2 %, and 51.6 %, respectively. The Rapiim-H test using NPS demonstrated approximately 90 % sensitivity and specificity, particularly within the first 10 days after disease onset.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116598"},"PeriodicalIF":2.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-07DOI: 10.1016/j.diagmicrobio.2024.116587
E. Çağan , M.A. Kızmaz , E.H. Akalın , H.B. Oral , G Tezcan , F. Budak
Brucellosis remains a significant public health issue in some parts of the world. It is clear that new laboratory methods are needed to diagnose brucellosis. Currently, no test method meets the criteria of high specificity, sensitivity, reliability, and low cost for the diagnosis of brucellosis, which could also predict chronicity. This study was conducted based on the data from a study conducted in 2015, which aimed to reveal genes with different transcript levels in chronic and acute patients and to evaluate their effects on the progression to chronicity by studying mRNA microarray and miRNA array in peripheral blood mononuclear cells in acute, chronic brucellosis and healthy control groups. According to the data obtained in this study, a second study was conducted to determine new markers that could aid in diagnosis and/or predict chronicity, with the most prominent gene products being [ABI3 (ABL interactor), PIAS4 (Protein Inhibitor of Activated STAT 4), PPP2R4 (Protein Phosphatase 2 Phosphatase Activator), DDIT4L (DNA Damage Inducible Transcript 4 Like), WDR33 (WD Repeat-Containing Protein 33), and IDO (Indoleamine 2,3-Dioxygenase)]. The study speculates that increased levels of ABI3, CLEC12B, PPP2R4 and decreased levels of DDIT4L, PIAS4, and IDO may be used as markers for the diagnosis of acute brucellosis, decreased levels of ABI3, CLEC12B, PPP2R4 and increased levels of DDIT4L, PIAS4, IDO may be assessed for treatment response. The study also suggested that maintaining consistent levels of ABI3, CLEC12B, PIAS4, PPP2R4, and IDO in subsequent titers may serve as a potential marker to predict chronic progression.
{"title":"New biological markers in diagnosis and follow-up of brucellosis cases","authors":"E. Çağan , M.A. Kızmaz , E.H. Akalın , H.B. Oral , G Tezcan , F. Budak","doi":"10.1016/j.diagmicrobio.2024.116587","DOIUrl":"10.1016/j.diagmicrobio.2024.116587","url":null,"abstract":"<div><div>Brucellosis remains a significant public health issue in some parts of the world. It is clear that new laboratory methods are needed to diagnose brucellosis. Currently, no test method meets the criteria of high specificity, sensitivity, reliability, and low cost for the diagnosis of brucellosis, which could also predict chronicity. This study was conducted based on the data from a study conducted in 2015, which aimed to reveal genes with different transcript levels in chronic and acute patients and to evaluate their effects on the progression to chronicity by studying mRNA microarray and miRNA array in peripheral blood mononuclear cells in acute, chronic brucellosis and healthy control groups. According to the data obtained in this study, a second study was conducted to determine new markers that could aid in diagnosis and/or predict chronicity, with the most prominent gene products being [ABI3 (ABL interactor), PIAS4 (Protein Inhibitor of Activated STAT 4), PPP2R4 (Protein Phosphatase 2 Phosphatase Activator), DDIT4L (DNA Damage Inducible Transcript 4 Like), WDR33 (WD Repeat-Containing Protein 33), and IDO (Indoleamine 2,3-Dioxygenase)]. The study speculates that increased levels of ABI3, CLEC12B, PPP2R4 and decreased levels of DDIT4L, PIAS4, and IDO may be used as markers for the diagnosis of acute brucellosis, decreased levels of ABI3, CLEC12B, PPP2R4 and increased levels of DDIT4L, PIAS4, IDO may be assessed for treatment response. The study also suggested that maintaining consistent levels of ABI3, CLEC12B, PIAS4, PPP2R4, and IDO in subsequent titers may serve as a potential marker to predict chronic progression.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116587"},"PeriodicalIF":2.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-07DOI: 10.1016/j.diagmicrobio.2024.116602
Felicity Edwards , Kristin H. Edwards , Alexis Tabah , Patrick N.A. Harris , Kevin B. Laupland
Background
Although Providencia species are recognised as important causes of bloodstream infections (BSI), their epidemiology is not well defined due to their infrequent occurrence. Our objective was to determine the overall incidence, determinants, and outcomes of Providencia species BSI, and compare the epidemiology of P. stuartii and P. rettgeri in a large population.
Methods
All patients within Queensland, Australia with Providencia species BSI between 2000-2019 were included with clinical and outcome data collected from state-wide datasets.
Results
Among 268 residents, there was 273 incident episodes of Providencia species BSI; with 118 cases (43.2%) due to P. rettgeri, 150 cases (55.0%) due to P. stuartii, for age and sex adjusted incidence rates of 1.5, and 2.1 per million respectively. Five cases (<2.0%) were due to other Providencia species. The median age was 73.9 years, 80% were male, and most episodes were of community onset. As compared to P. rettgeri, patients with P. stuartii BSI were more likely to have dementia, peptic ulcer disease, and hemiplegia but less likely to have comorbid liver disease. The overall distribution of infection foci were different with P. stuartii more commonly associated with lower respiratory tract source and P. rettgeri with urinary source. All cause 30-day case fatality was significantly higher for P. rettgeri versus P. stuartii (35; 29.7% vs. 24; 16%; p=0.007).
Conclusions
Providencia species are important causes of community onset BSI especially in older males. Although they share similar incidence, P. stuartii and P. rettgeri BSI differ on many clinical aspects.
背景：尽管普罗维登菌被认为是血流感染（BSI）的重要病因，但由于其不常出现，其流行病学尚未得到很好的界定。我们的目的是确定普罗维登菌属 BSI 的总体发病率、决定因素和结果，并比较 P. stuartii 和 P. rettgeri 在大量人群中的流行病学：纳入澳大利亚昆士兰州 2000-2019 年间所有普罗维登菌属 BSI 患者，并从全州数据集中收集临床和结果数据：在268名居民中，有273例普罗维登菌属BSI病例；其中118例（43.2%）为P. rettgeri，150例（55.0%）为P. stuartii，年龄和性别调整后发病率分别为1.5%/百万和2.1%/百万。其中有 5 例（结论：普罗维登菌属是一种重要的致病菌：普罗维登菌是社区发病 BSI 的重要病因，尤其是在老年男性中。虽然它们的发病率相似，但 P. stuartii 和 P. rettgeri BSI 在许多临床方面存在差异。
{"title":"Differentiation of Providencia species bloodstream infections: A population-based analysis","authors":"Felicity Edwards , Kristin H. Edwards , Alexis Tabah , Patrick N.A. Harris , Kevin B. Laupland","doi":"10.1016/j.diagmicrobio.2024.116602","DOIUrl":"10.1016/j.diagmicrobio.2024.116602","url":null,"abstract":"<div><h3>Background</h3><div>Although <em>Providencia</em> species are recognised as important causes of bloodstream infections (BSI), their epidemiology is not well defined due to their infrequent occurrence. Our objective was to determine the overall incidence, determinants, and outcomes of <em>Providencia</em> species BSI, and compare the epidemiology of <em>P. stuartii</em> and <em>P. rettgeri</em> in a large population.</div></div><div><h3>Methods</h3><div>All patients within Queensland, Australia with <em>Providencia</em> species BSI between 2000-2019 were included with clinical and outcome data collected from state-wide datasets.</div></div><div><h3>Results</h3><div>Among 268 residents, there was 273 incident episodes of <em>Providencia</em> species BSI; with 118 cases (43.2%) due to <em>P. rettgeri</em>, 150 cases (55.0%) due to <em>P. stuartii</em>, for age and sex adjusted incidence rates of 1.5, and 2.1 per million respectively. Five cases (<2.0%) were due to other <em>Providencia</em> species. The median age was 73.9 years, 80% were male, and most episodes were of community onset. As compared to <em>P. rettgeri</em>, patients with <em>P. stuartii</em> BSI were more likely to have dementia, peptic ulcer disease, and hemiplegia but less likely to have comorbid liver disease. The overall distribution of infection foci were different with <em>P. stuartii</em> more commonly associated with lower respiratory tract source and <em>P. rettgeri</em> with urinary source. All cause 30-day case fatality was significantly higher for <em>P. rettgeri</em> versus <em>P. stuartii</em> (35; 29.7% vs. 24; 16%; <em>p</em>=0.007).</div></div><div><h3>Conclusions</h3><div><em>Providencia</em> species are important causes of community onset BSI especially in older males<strong>.</strong> Although they share similar incidence, <em>P. stuartii</em> and <em>P. rettgeri</em> BSI differ on many clinical aspects.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116602"},"PeriodicalIF":2.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-07DOI: 10.1016/j.diagmicrobio.2024.116585
Yasemin Çakır Kıymaz , Serkan Bolat , Bilge Katırcı , Özlem Aldemir , Işık Altınkaya , Merdan Mustafa Özcan , Serhat Murat Hopoğlu , Murtaza Öz , Ertuğrul Keskin , Caner Öksüz , Mürşit Hasbek , Ahmet Aksoy , Onur Mahmutoğlu , Duygu Çelik Seyitoğlu , Seyit Ali Büyüktuna , Nazif Elaldi
This study aimed to report a tularemia outbreak in Sivas and describe the epidemiological and diagnostic characteristics of the patients. Patients aged 18 and over followed up with a diagnosis of tularemia in Sivas Cumhuriyet University Hospital, Sivas Numune State Hospital, and Sivas State Hospital Infectious Diseases Outpatient Clinics and wards between November 2023 and May 2024 were evaluated. 205 adult patients with tularemia were included. The most common symptoms were sore throat (73.2 %, n=150), swelling in the neck (70.2 %, n = 144), and fatigue (55.1 %, n = 113). The most common form was oropharyngeal (82.4 %, n = 169) and glandular (14.6 %, n = 30). Lymphadenopathy was detected in 182 (88.8 %) patients, the most is cervical lymphadenopathy (60 %, n = 123). Lymph node drainage/excision was performed on 50 patients (24.3 %). There have been no deaths in this outbreak. This study presents patient data from the tularemia outbreak in Sivas.
{"title":"The great tularemia outbreak in Sivas: Evaluation of 205 cases","authors":"Yasemin Çakır Kıymaz , Serkan Bolat , Bilge Katırcı , Özlem Aldemir , Işık Altınkaya , Merdan Mustafa Özcan , Serhat Murat Hopoğlu , Murtaza Öz , Ertuğrul Keskin , Caner Öksüz , Mürşit Hasbek , Ahmet Aksoy , Onur Mahmutoğlu , Duygu Çelik Seyitoğlu , Seyit Ali Büyüktuna , Nazif Elaldi","doi":"10.1016/j.diagmicrobio.2024.116585","DOIUrl":"10.1016/j.diagmicrobio.2024.116585","url":null,"abstract":"<div><div>This study aimed to report a tularemia outbreak in Sivas and describe the epidemiological and diagnostic characteristics of the patients. Patients aged 18 and over followed up with a diagnosis of tularemia in Sivas Cumhuriyet University Hospital, Sivas Numune State Hospital, and Sivas State Hospital Infectious Diseases Outpatient Clinics and wards between November 2023 and May 2024 were evaluated. 205 adult patients with tularemia were included. The most common symptoms were sore throat (73.2 %, n=150), swelling in the neck (70.2 %, n = 144), and fatigue (55.1 %, n = 113). The most common form was oropharyngeal (82.4 %, n = 169) and glandular (14.6 %, n = 30). Lymphadenopathy was detected in 182 (88.8 %) patients, the most is cervical lymphadenopathy (60 %, n = 123). Lymph node drainage/excision was performed on 50 patients (24.3 %). There have been no deaths in this outbreak. This study presents patient data from the tularemia outbreak in Sivas.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116585"},"PeriodicalIF":2.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1016/j.diagmicrobio.2024.116600
Muammer Çelik , Mehmet Reşit Polat , Vildan Avkan-Oğuz
This study investigates the prevalence and clinical characteristics of respiratory viruses among patients with acute respiratory illness (ARI) in a low-resource setting, using a rapid antigen test as a point-of-care test (POCT). We included 343 patients presenting with ARI symptoms at an outpatient pulmonary clinic from December 2023 to April 2024. Nasopharyngeal swabs were tested for SARS-CoV-2, influenza A/B, respiratory syncytial virus, and adenovirus using POCT. The overall prevalence of respiratory viruses was 21.2 %, with influenza A being the most common (11.4 %). Shorter duration of symptoms and lower lymphocyte counts were associated with higher influenza positivity. Patients who tested positive for influenza received significantly more antiviral therapy (98.1 % vs. 39.4 %, p<0.001) and less antibiotic therapy (1.9 % vs. 28.5 %, p<0.001) compared to those who tested negative. The study highlights the utility of rapid antigen testing in enhancing antiviral and antibiotic stewardship, thereby improving clinical decision-making and patient outcomes in resource-limited settings.
{"title":"Diagnostic utility of rapid antigen testing as point-of-care test for influenza and other respiratory viruses in patients with acute respiratory illness","authors":"Muammer Çelik , Mehmet Reşit Polat , Vildan Avkan-Oğuz","doi":"10.1016/j.diagmicrobio.2024.116600","DOIUrl":"10.1016/j.diagmicrobio.2024.116600","url":null,"abstract":"<div><div>This study investigates the prevalence and clinical characteristics of respiratory viruses among patients with acute respiratory illness (ARI) in a low-resource setting, using a rapid antigen test as a point-of-care test (POCT). We included 343 patients presenting with ARI symptoms at an outpatient pulmonary clinic from December 2023 to April 2024. Nasopharyngeal swabs were tested for SARS-CoV-2, influenza A/B, respiratory syncytial virus, and adenovirus using POCT. The overall prevalence of respiratory viruses was 21.2 %, with influenza A being the most common (11.4 %). Shorter duration of symptoms and lower lymphocyte counts were associated with higher influenza positivity. Patients who tested positive for influenza received significantly more antiviral therapy (98.1 % vs. 39.4 %, p<0.001) and less antibiotic therapy (1.9 % vs. 28.5 %, p<0.001) compared to those who tested negative. The study highlights the utility of rapid antigen testing in enhancing antiviral and antibiotic stewardship, thereby improving clinical decision-making and patient outcomes in resource-limited settings.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116600"},"PeriodicalIF":2.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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