This study aims to analyze clinical isolates of E. coli causing septicemia across various phylogroups utilizing the PFGE method.
Materials and methods
A total of 100 clinical isolates were collected. The presence of CTX-M, TEM, SHV, KPC, MBL and OXA-48 genes was detected by PCR. Additionally, phylotyping, serotyping, and virulence-typing assay were done by PCR and PFGE methods to investigate the genetic diversity of the isolates.
Results
The O1 serotype and the HlyA gene were the most prevalent serotype and virulence gene, respectively. Notably, 34% of the isolates harbored SHV, TEM, and CTX-M-1 β-lactamase genes. All isolates showed resistance to amoxicillin and tetracycline, but no resistance to fosfomycin was seen. The most and least common phylotypes, according to PFGE analysis, belonged to phylogroups B2 and B1, respectively.
Conclusion
The data offers valuable insights into the genetic diversity and antibiotic resistance patterns of E. coli isolates responsible for septicemia.
{"title":"Genetic diversity and antibiotic resistance patterns of Escherichia coli isolates causing septicemia: A phylogenetic typing and PFGE analysis","authors":"Mahshid Vakili , Hamidreza Goli , Javad Javidnia , Tahereh Alipour , Majid Eslami","doi":"10.1016/j.diagmicrobio.2024.116586","DOIUrl":"10.1016/j.diagmicrobio.2024.116586","url":null,"abstract":"<div><h3>Introduction</h3><div>This study aims to analyze clinical isolates of <em>E. coli</em> causing septicemia across various phylogroups utilizing the PFGE method.</div></div><div><h3>Materials and methods</h3><div>A total of 100 clinical isolates were collected. The presence of <em>CTX</em>-<em>M, TEM, SHV, KPC, MBL</em> and <em>OXA</em>-<em>48</em> genes was detected by PCR. Additionally, phylotyping, serotyping, and virulence-typing assay were done by PCR and PFGE methods to investigate the genetic diversity of the isolates.</div></div><div><h3>Results</h3><div>The O1 serotype and the <em>HlyA</em> gene were the most prevalent serotype and virulence gene, respectively. Notably, 34% of the isolates harbored <em>SHV, TEM</em>, and <em>CTX-M-1</em> β-lactamase genes. All isolates showed resistance to amoxicillin and tetracycline, but no resistance to fosfomycin was seen. The most and least common phylotypes, according to PFGE analysis, belonged to phylogroups B2 and B1, respectively.</div></div><div><h3>Conclusion</h3><div>The data offers valuable insights into the genetic diversity and antibiotic resistance patterns of <em>E. coli</em> isolates responsible for septicemia.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116586"},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616590","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 : 2024-10-29DOI: 10.1016/j.diagmicrobio.2024.116584
Ayça Aydın Uysal, Alper Tünger
Purpose
This study aimed to assess the prevalence of colistin resistance in the study group and compare alternative methods with the gold standard. It sought to evaluate the prevalence of plasmid-mediated colistin resistance genes.
Material and methods
The colistin susceptibility of 151 K. pneumoniae strains was determined using Sensititre™, CBDE, ETEST®, and VITEK®2. Results were compared with BMD. The presence of the mcr gene was assessed using polymerase chain reaction.
Results
The colistin resistance rate was 16,6 %. The categorical agreement of Sensititre™, CBDE, and ETEST® was 100 %. VITEK®2 had a CA of 98 %, a major error of 0.79 %, and a very major error of 8 %. Essential agreement for Sensititre™, ETEST®, and VITEK®2 was 92.7 %, 52.3 %, and 78.1 %, respectively. There were no mcr genes in any strains.
Conclusions
Due to the difficulty of applying BMD, colistin resistance data are insufficient globally. Continuous epidemiological studies and validation of alternative methods are needed.
{"title":"Investigation of Colistin resistance and method comparison in Klebsiella pneumoniae strains","authors":"Ayça Aydın Uysal, Alper Tünger","doi":"10.1016/j.diagmicrobio.2024.116584","DOIUrl":"10.1016/j.diagmicrobio.2024.116584","url":null,"abstract":"<div><h3>Purpose</h3><div>This study aimed to assess the prevalence of colistin resistance in the study group and compare alternative methods with the gold standard. It sought to evaluate the prevalence of plasmid-mediated colistin resistance genes.</div></div><div><h3>Material and methods</h3><div>The colistin susceptibility of 151 <em>K. pneumoniae</em> strains was determined using Sensititre™, CBDE, ETEST®, and VITEK®2. Results were compared with BMD. The presence of the <em>mcr</em> gene was assessed using polymerase chain reaction.</div></div><div><h3>Results</h3><div>The colistin resistance rate was 16,6 %. The categorical agreement of Sensititre™, CBDE, and ETEST® was 100 %. VITEK®2 had a CA of 98 %, a major error of 0.79 %, and a very major error of 8 %. Essential agreement for Sensititre™, ETEST®, and VITEK®2 was 92.7 %, 52.3 %, and 78.1 %, respectively. There were no <em>mcr</em> genes in any strains.</div></div><div><h3>Conclusions</h3><div>Due to the difficulty of applying BMD, colistin resistance data are insufficient globally. Continuous epidemiological studies and validation of alternative methods are needed.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116584"},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616609","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 : 2024-10-28DOI: 10.1016/j.diagmicrobio.2024.116577
Tom Fowler , Edward Blandford , David Chapman , Matthias E. Futschik , Raghavendran Kulasegaran-Shylini , Sarah Tunkel , Carolyn Lewis , Alasdair Fellows , Ellie Sheppard , Leanne McCabe , Peter Marks , Paul E. Klapper , Andrew Dodgson , Malur Sudhanva , Mike Kidd , Andy Vail , Susan Hopkins , Tim Peto
Purpose
The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.
Methods
Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.
Results
Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.
Conclusions
Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.
{"title":"Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing","authors":"Tom Fowler , Edward Blandford , David Chapman , Matthias E. Futschik , Raghavendran Kulasegaran-Shylini , Sarah Tunkel , Carolyn Lewis , Alasdair Fellows , Ellie Sheppard , Leanne McCabe , Peter Marks , Paul E. Klapper , Andrew Dodgson , Malur Sudhanva , Mike Kidd , Andy Vail , Susan Hopkins , Tim Peto","doi":"10.1016/j.diagmicrobio.2024.116577","DOIUrl":"10.1016/j.diagmicrobio.2024.116577","url":null,"abstract":"<div><h3>Purpose</h3><div>The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.</div></div><div><h3>Methods</h3><div>Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.</div></div><div><h3>Results</h3><div>Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.</div></div><div><h3>Conclusions</h3><div>Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116577"},"PeriodicalIF":2.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554300","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 : 2024-10-26DOI: 10.1016/j.diagmicrobio.2024.116580
Yushan Liu , Tingting Xu , Qiwen Tan , Lijuan Xiong
Background
In the intensive care unit (ICU), patients undergoing mechanical ventilation (MV) often exhibit Candida colonization. This study aims to systematically review and analyze the effects of Candida colonization on the outcomes of mechanically ventilated patients and its relationship with bacterial pathogens associated with ventilator-associated pneumonia (VAP).
Methods
We conducted a comprehensive search across PubMed, Embase, Web of Science (WOS), and the Cochrane Central Register of Controlled Trials (CENTRAL) without language restrictions to identify eligible studies. Inclusion criteria involved patients undergoing MV for >2 days, encompassing those with clinically suspected VAP (csVAP), and confirmed VAP patients. We assessed the impact of Candida colonization on patient prognosis, length of ICU stay, bacterial pathogens responsible for VAP, and inflammatory markers. The study protocol was registered with PROSPER (CRD42024580547).
Results
Thirteen studies involving 3,802 patients were included in our analysis. The prevalence of Candida colonization among MV patients ranged from 10 % to 56 %. Our findings indicated that Candida airway colonization was associated with poorer patient prognosis (95 % CI 1.13-1.52, p < 0.05, I² = 39 %). Among patients who developed VAP, Candida colonization correlated with increased detection rates of Pseudomonas aeruginosa (RR = 1.37, 95 % CI 1.07-1.75, p = 0.01, I² = 3 %) and Acinetobacter baumannii (RR= 1.48, 95 % CI 1.17-1.86, p < 0.01, I² = 27 %). Additionally, an association with antibiotic resistance was observed, although the quality of evidence was low. In studies that recorded patients' inflammatory markers, no significant effect of Candida colonization on inflammatory markers (procalcitonin, interleukin-6) was observed.
Conclusion
Candida airway colonization is highly prevalent among mechanically ventilated patients and should be considered a marker of poor prognosis when it occurs. Antibiotics should be used more carefully when Candida colonization is detected in the respiratory tract of mechanically ventilated patients.
{"title":"Effects of Candida colonization on patients with ventilator-associated pneumonia and pathogenic microorganisms: Systematic review and meta-analysis","authors":"Yushan Liu , Tingting Xu , Qiwen Tan , Lijuan Xiong","doi":"10.1016/j.diagmicrobio.2024.116580","DOIUrl":"10.1016/j.diagmicrobio.2024.116580","url":null,"abstract":"<div><h3>Background</h3><div>In the intensive care unit (ICU), patients undergoing mechanical ventilation (MV) often exhibit <em>Candida</em> colonization. This study aims to systematically review and analyze the effects of Candida colonization on the outcomes of mechanically ventilated patients and its relationship with bacterial pathogens associated with ventilator-associated pneumonia (VAP).</div></div><div><h3>Methods</h3><div>We conducted a comprehensive search across PubMed, Embase, Web of Science (WOS), and the Cochrane Central Register of Controlled Trials (CENTRAL) without language restrictions to identify eligible studies. Inclusion criteria involved patients undergoing MV for >2 days, encompassing those with clinically suspected VAP (csVAP), and confirmed VAP patients. We assessed the impact of <em>Candida</em> colonization on patient prognosis, length of ICU stay, bacterial pathogens responsible for VAP, and inflammatory markers. The study protocol was registered with PROSPER (CRD42024580547).</div></div><div><h3>Results</h3><div>Thirteen studies involving 3,802 patients were included in our analysis. The prevalence of <em>Candida</em> colonization among MV patients ranged from 10 % to 56 %. Our findings indicated that <em>Candida</em> airway colonization was associated with poorer patient prognosis (95 % CI 1.13-1.52, p < 0.05, I² = 39 %). Among patients who developed VAP, <em>Candida</em> colonization correlated with increased detection rates of <em>Pseudomonas aeruginosa</em> (RR = 1.37, 95 % CI 1.07-1.75, p = 0.01, I² = 3 %) and <em>Acinetobacter baumannii</em> (RR= 1.48, 95 % CI 1.17-1.86, p < 0.01, I² = 27 %). Additionally, an association with antibiotic resistance was observed, although the quality of evidence was low. In studies that recorded patients' inflammatory markers, no significant effect of <em>Candida</em> colonization on inflammatory markers (procalcitonin, interleukin-6) was observed.</div></div><div><h3>Conclusion</h3><div><em>Candida</em> airway colonization is highly prevalent among mechanically ventilated patients and should be considered a marker of poor prognosis when it occurs. Antibiotics should be used more carefully when <em>Candida</em> colonization is detected in the respiratory tract of mechanically ventilated patients.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116580"},"PeriodicalIF":2.1,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564227","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 : 2024-10-26DOI: 10.1016/j.diagmicrobio.2024.116578
Iman Haghani , Seyedeh Mahdieh Hashemi , Mahdi Abastabar , Zahra Yahyazadeh , Robab Ebrahimi-Barough , Akbar Hoseinnejad , Ali Teymoori , Hossein Azadeh , Mohsen Rashidi , Seyed Reza Aghili , Mohammad Taghi Hedayati , Tahereh Shokohi , Suzana Otasevic , Mika Sillanpää , Mohsen Nosratabadi , Hamid Badali
In recent years, the widespread emergence of drug resistance in yeasts and filamentous fungi to existing antifungal armamentariums has become a severe threat to global health. There is also concern regarding increased rates of azole resistance in Aspergillus fumigatus and Terbinafine resistance in Trichophyton species. To overcome this concern of resistance to regular therapies, new antifungal drugs with novel and effective mechanisms are crucially needed. Herbal remedies may be promising strategies for the treatment of resistant infections. We aimed to investigate the in vitro and silico activity of piperlongumine against clinical azole susceptible/resistant A. fumigatus and terbinafine-susceptible/resistant Trichophyton species. In the current study, piperlongumine demonstrated potent antifungal activity, with minimum inhibitory concentrations (MICs) ranging from 0.016-4 μg/mL against Trichophyton isolates and 0.25-2 μg/mL for A. fumigatus isolates. Additionally, molecular docking studies indicated that piperlongumine has a strong binding affinity to the active sites of squalene epoxidase and sterol 14-alpha demethylase. However, further studies are warranted to correlate these findings with clinical outcomes and provide the basis for further investigations to pave the way for developing novel antifungal agents.
{"title":"In vitro and silico activity of piperlongumine against azole-susceptible/resistant Aspergillus fumigatus and terbinafine-susceptible/resistant Trichophyton species","authors":"Iman Haghani , Seyedeh Mahdieh Hashemi , Mahdi Abastabar , Zahra Yahyazadeh , Robab Ebrahimi-Barough , Akbar Hoseinnejad , Ali Teymoori , Hossein Azadeh , Mohsen Rashidi , Seyed Reza Aghili , Mohammad Taghi Hedayati , Tahereh Shokohi , Suzana Otasevic , Mika Sillanpää , Mohsen Nosratabadi , Hamid Badali","doi":"10.1016/j.diagmicrobio.2024.116578","DOIUrl":"10.1016/j.diagmicrobio.2024.116578","url":null,"abstract":"<div><div>In recent years, the widespread emergence of drug resistance in yeasts and filamentous fungi to existing antifungal armamentariums has become a severe threat to global health. There is also concern regarding increased rates of azole resistance in <em>Aspergillus fumigatus</em> and Terbinafine resistance in <em>Trichophyton</em> species. To overcome this concern of resistance to regular therapies, new antifungal drugs with novel and effective mechanisms are crucially needed. Herbal remedies may be promising strategies for the treatment of resistant infections. We aimed to investigate the <em>in vitro</em> and <em>silico</em> activity of piperlongumine against clinical azole susceptible/resistant <em>A. fumigatus</em> and terbinafine-susceptible/resistant <em>Trichophyton</em> species. In the current study, piperlongumine demonstrated potent antifungal activity, with minimum inhibitory concentrations (MICs) ranging from 0.016-4 μg/mL against <em>Trichophyton</em> isolates and 0.25-2 μg/mL for <em>A. fumigatus</em> isolates. Additionally, molecular docking studies indicated that piperlongumine has a strong binding affinity to the active sites of squalene epoxidase and sterol 14-alpha demethylase. However, further studies are warranted to correlate these findings with clinical outcomes and provide the basis for further investigations to pave the way for developing novel antifungal agents.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116578"},"PeriodicalIF":2.1,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142578741","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 : 2024-10-20DOI: 10.1016/j.diagmicrobio.2024.116563
ZhiYong Pan , Wei Wang , Chen Zhang , LiangWei Mao , YiRong Li , LinLing Yuan , ZhiQiang Li
Respiratory infections are one of the leading causes of death worldwide. Rapid and accurate detection of pathogens is crucial for timely treatment. This study established a detection method based on multiplex PCR combined with capillary electrophoresis, capable of simultaneously detecting 28 common respiratory pathogens. We used specially designed homo-tag primers, significantly reducing the formation of primer dimers and improving the specificity and sensitivity of amplification. After two rounds of PCR amplification, the products were subjected to fragment analysis using the ABI 3500XL Genetic Analyzer, enabling automated result interpretation. The detection limit of this method reaches 2.77 × 102 copies/ml, with some pathogens reaching as low as 2.77 × 10 copies/ml. The detection of 147 clinical specimens showed that the overall consistency of this method with culture, colloidal gold, fluorescent quantitative PCR, and NGS was 75.5 %. The multiplex PCR detection method established in this study is rapid, sensitive, and high-throughput, can be used for routine screening of common pathogens in respiratory infections, providing an important basis for clinical diagnosis and treatment.
{"title":"A rapid, sensitive, and high-throughput pathogen detection method and application of identifying pathogens based on multiplex PCR technology combined with capillary electrophoresis","authors":"ZhiYong Pan , Wei Wang , Chen Zhang , LiangWei Mao , YiRong Li , LinLing Yuan , ZhiQiang Li","doi":"10.1016/j.diagmicrobio.2024.116563","DOIUrl":"10.1016/j.diagmicrobio.2024.116563","url":null,"abstract":"<div><div>Respiratory infections are one of the leading causes of death worldwide. Rapid and accurate detection of pathogens is crucial for timely treatment. This study established a detection method based on multiplex PCR combined with capillary electrophoresis, capable of simultaneously detecting 28 common respiratory pathogens. We used specially designed homo-tag primers, significantly reducing the formation of primer dimers and improving the specificity and sensitivity of amplification. After two rounds of PCR amplification, the products were subjected to fragment analysis using the ABI 3500XL Genetic Analyzer, enabling automated result interpretation. The detection limit of this method reaches 2.77 × 10<sup>2</sup> copies/ml, with some pathogens reaching as low as 2.77 × 10 copies/ml. The detection of 147 clinical specimens showed that the overall consistency of this method with culture, colloidal gold, fluorescent quantitative PCR, and NGS was 75.5 %. The multiplex PCR detection method established in this study is rapid, sensitive, and high-throughput, can be used for routine screening of common pathogens in respiratory infections, providing an important basis for clinical diagnosis and treatment.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116563"},"PeriodicalIF":2.1,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560808","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 : 2024-10-20DOI: 10.1016/j.diagmicrobio.2024.116568
Devy M. Emperador , Cassandra Kelly-Cirino , Daniel G. Bausch , Isabella Eckerle
We conducted a systematic review and meta-analysis of studies and reports comparing the performance of antigen rapid diagnostic tests (Ag RDT) for diagnosing Ebola disease (EVD). We searched PubMed, EMBASE, and Web of Science for diagnostic studies published between 1976 and 2023, evaluating them with QUADAS-2. Using a bivariate random-effects model, we estimated the pooled sensitivity and specificity of Ag RDTs. Of 64 eligible full studies and reports, 16 met the inclusion criteria. Pooled sensitivity and specificity were 82.1% (95%CI: 75.2 – 88.0) and 97.0% (95%CI: 95.1-98.2), respectively. We conducted subgroup analysis on 4 Ag RDTs, 3 RT-PCR tests, and 4 sample types, showing varied performance. The high specificity and positive predictive value of Ag RDTs support their use to “rule-in” patients with EVD. However, high-sensitivity RDTs suitable for field settings and capable of detecting multiple ebolavirus species are needed.
{"title":"Systematic review and meta-analysis of antigen rapid diagnostic tests to detect Zaire ebolavirus","authors":"Devy M. Emperador , Cassandra Kelly-Cirino , Daniel G. Bausch , Isabella Eckerle","doi":"10.1016/j.diagmicrobio.2024.116568","DOIUrl":"10.1016/j.diagmicrobio.2024.116568","url":null,"abstract":"<div><div>We conducted a systematic review and meta-analysis of studies and reports comparing the performance of antigen rapid diagnostic tests (Ag RDT) for diagnosing Ebola disease (EVD). We searched PubMed, EMBASE, and Web of Science for diagnostic studies published between 1976 and 2023, evaluating them with QUADAS-2. Using a bivariate random-effects model, we estimated the pooled sensitivity and specificity of Ag RDTs. Of 64 eligible full studies and reports, 16 met the inclusion criteria. Pooled sensitivity and specificity were 82.1% (95%CI: 75.2 – 88.0) and 97.0% (95%CI: 95.1-98.2), respectively. We conducted subgroup analysis on 4 Ag RDTs, 3 RT-PCR tests, and 4 sample types, showing varied performance. The high specificity and positive predictive value of Ag RDTs support their use to “rule-in” patients with EVD. However, high-sensitivity RDTs suitable for field settings and capable of detecting multiple ebolavirus species are needed.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116568"},"PeriodicalIF":2.1,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521353","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 : 2024-10-18DOI: 10.1016/j.diagmicrobio.2024.116566
Xinying Li , Wenxuan Zheng , Tongyu Hao , Ting Yang , Xiaojuan Gao , Xiuming Zhang
This study explores a premature infant with respiratory failure and pneumonia, suggestive of neonatal sepsis. Despite initially negative clinical specimens, blood testing revealed a pathogen. MALDI-TOF-MS and physiological tests initially failed to identify it accurately. Subsequent analysis of the 16S rRNA gene, housekeeping genes, and whole genome sequencing placed it in the genus Massilia. Average Nucleotide Identities (ANIs) indicated 88.47 % similarity with the type strain of Massilia norwichensis. Detailed characterization showed it as Gram-negative, aerobic, flagellated, measuring 0.45–0.55 × 1.75–2.40 μm. Major fatty acids included C16:0, C16:1ω7c, C18:1ω7c, and cyclo-C17:0. Minimum inhibitory concentrations to ceftazidime, penicillin, and meropenem were <0.032 μg/mL, ≤0.75 μg/mL, and <0.002 μg/mL respectively. Phylogenetic analysis, fatty acid composition, and physiological parameters confirmed it as Massilia shenzhen sp. nov., with strain GZ0329T. Given limited research on Massilia drug resistance, ceftazidime and imipenem show promise in treating Massilia infections.
{"title":"Massilia shenzhen sp. nov., isolated from blood of one premature infant, causing sepsis","authors":"Xinying Li , Wenxuan Zheng , Tongyu Hao , Ting Yang , Xiaojuan Gao , Xiuming Zhang","doi":"10.1016/j.diagmicrobio.2024.116566","DOIUrl":"10.1016/j.diagmicrobio.2024.116566","url":null,"abstract":"<div><div>This study explores a premature infant with respiratory failure and pneumonia, suggestive of neonatal sepsis. Despite initially negative clinical specimens, blood testing revealed a pathogen. MALDI-TOF-MS and physiological tests initially failed to identify it accurately. Subsequent analysis of the 16S rRNA gene, housekeeping genes, and whole genome sequencing placed it in the genus <em>Massilia</em>. Average Nucleotide Identities (ANIs) indicated 88.47 % similarity with the type strain of <em>Massilia norwichensis</em>. Detailed characterization showed it as Gram-negative, aerobic, flagellated, measuring 0.45–0.55 × 1.75–2.40 μm. Major fatty acids included C16:0, C16:1ω7c, C18:1ω7c, and cyclo-C17:0. Minimum inhibitory concentrations to ceftazidime, penicillin, and meropenem were <0.032 μg/mL, ≤0.75 μg/mL, and <0.002 μg/mL respectively. Phylogenetic analysis, fatty acid composition, and physiological parameters confirmed it as <em>Massilia shenzhen</em> sp. nov., with strain GZ0329<sup>T</sup>. Given limited research on <em>Massilia</em> drug resistance, ceftazidime and imipenem show promise in treating <em>Massilia</em> infections.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116566"},"PeriodicalIF":2.1,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142529189","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}
Concerning the progression of dermatophytosis and its prognosis, quantification studies play a significant role. Present work aims to develop an automated grading system for quantifying fungal loads in KOH microscopic images of skin scrapings collected from dermatophytosis patients. Fungal filaments in the images were segmented using a U-Net model to obtain the pixel counts. In the absence of any threshold value for pixel counts to grade these images as low, moderate, or high, experts were assigned the task of manual grading. Grades and corresponding pixel counts were subjected to statistical procedures involving cumulative receiver operating characteristic curve analysis for developing an automated grading system. The model’s specificity, accuracy, precision, and sensitivity metrics crossed 92%, 86%, 82%, and 76%, respectively. ’Almost perfect agreement’ with Fleiss kappa of 0.847 was obtained between automated and manual gradings. This pixel count-based grading of KOH images offers a novel, cost-effective solution for quantifying fungal load.
{"title":"Automated grading system for quantifying KOH microscopic images in dermatophytosis","authors":"Rajitha KV , Sreejith Govindan , Prakash PY , Asha Kamath , Raghavendra Rao , Keerthana Prasad","doi":"10.1016/j.diagmicrobio.2024.116565","DOIUrl":"10.1016/j.diagmicrobio.2024.116565","url":null,"abstract":"<div><div>Concerning the progression of dermatophytosis and its prognosis, quantification studies play a significant role. Present work aims to develop an automated grading system for quantifying fungal loads in KOH microscopic images of skin scrapings collected from dermatophytosis patients. Fungal filaments in the images were segmented using a U-Net model to obtain the pixel counts. In the absence of any threshold value for pixel counts to grade these images as low, moderate, or high, experts were assigned the task of manual grading. Grades and corresponding pixel counts were subjected to statistical procedures involving cumulative receiver operating characteristic curve analysis for developing an automated grading system. The model’s specificity, accuracy, precision, and sensitivity metrics crossed 92%, 86%, 82%, and 76%, respectively. ’Almost perfect agreement’ with Fleiss kappa of 0.847 was obtained between automated and manual gradings. This pixel count-based grading of KOH images offers a novel, cost-effective solution for quantifying fungal load.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 1","pages":"Article 116565"},"PeriodicalIF":2.1,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142529148","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}
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