Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2209
Cut Nur Cinthia Alamanda, Ida Parwati, Gusti Ayu Prani Pradani, A. Fibriani
Coronavirus Disease 19 (COVID-19), the disease caused by SARS-CoV-2, was declared a pandemic in early 2020. With the emergence of different strains of SARS-CoV-2 mutations, efforts to reduce infection rates and help vulnerable populations remain in question. Genomic surveillance has been carried out on COVID-19 cases to detect new variants and monitor trends in circulating variants. Genomic surveillance is important because it can detect virus characteristics, estimate the prevalence of specific variants in the community, assess the extent to which medication can combat the variants, and analyze virus transmission in outbreaks. The purpose of this study was to investigate the prevalence of SARS-CoV-2 genomic variants in West Java and to inform policymakers in developing strategies to reduce the transmission rate of the SARS-CoV-2 virus. According to the inclusion criteria, variant sequence data were acquired from Global Initiative on Sharing All Influenza Data (GISAID) for the period January 1st, 2021-December 31st, 2022 and evaluated cross-sectional descriptively. This data were obtained from West Java. The majority of the samples came from Bandung Regency, where the Delta (AY), BA1 and BA5 variations predominated. The dynamic of the SARS-CoV-2 cases was influenced by government policies such as imposition of the restriction on community activities and public holiday. Because SARS-CoV-2 is subject to mutations, the various varieties must still be monitored to determine the influence on society. In the future, surveillance for any microorganisms with the potential to cause epidemics is urgently needed in order to mitigate the spread of the disease.
{"title":"Distribution of SARS-CoV-2 Variants in West Java Based on Genomic Surveillance Data, 2021-2022","authors":"Cut Nur Cinthia Alamanda, Ida Parwati, Gusti Ayu Prani Pradani, A. Fibriani","doi":"10.24293/ijcpml.v30i3.2209","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2209","url":null,"abstract":"Coronavirus Disease 19 (COVID-19), the disease caused by SARS-CoV-2, was declared a pandemic in early 2020. With the emergence of different strains of SARS-CoV-2 mutations, efforts to reduce infection rates and help vulnerable populations remain in question. Genomic surveillance has been carried out on COVID-19 cases to detect new variants and monitor trends in circulating variants. Genomic surveillance is important because it can detect virus characteristics, estimate the prevalence of specific variants in the community, assess the extent to which medication can combat the variants, and analyze virus transmission in outbreaks. The purpose of this study was to investigate the prevalence of SARS-CoV-2 genomic variants in West Java and to inform policymakers in developing strategies to reduce the transmission rate of the SARS-CoV-2 virus. According to the inclusion criteria, variant sequence data were acquired from Global Initiative on Sharing All Influenza Data (GISAID) for the period January 1st, 2021-December 31st, 2022 and evaluated cross-sectional descriptively. This data were obtained from West Java. The majority of the samples came from Bandung Regency, where the Delta (AY), BA1 and BA5 variations predominated. The dynamic of the SARS-CoV-2 cases was influenced by government policies such as imposition of the restriction on community activities and public holiday. Because SARS-CoV-2 is subject to mutations, the various varieties must still be monitored to determine the influence on society. In the future, surveillance for any microorganisms with the potential to cause epidemics is urgently needed in order to mitigate the spread of the disease.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"45 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141378255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2125
St. Sandra Karyati Serel, Yuyun Widaningsih, Fitriani Mangarengi
Lupus Nephritis (LN) is a manifestation of Systemic Lupus Erythematosus (SLE), which targets the kidney. Based on histopathology, the World Health Organization divides the disease into five classes: normal pattern, mesangial, focal, diffuse proliferative, and membranous. Albumin to Globulin Ratio (AGR) compares serum albumin with serum globulin levels. Low AGR value is associated with poor prognosis of diseases such as cancer, liver cirrhosis, and other chronic inflammatory diseases such as LN. This study aimed to analyze the AGR value as a prognostic predictor in LN patients based on disease classes with a retrospective descriptive cross-sectional approach. Total subjects were 109, which consisted of class 1 (n=15), class 2 (n=37), class 3 (n=9), class 4 (n=21), and class 5 LN (n=27). Data of disease classes, serum albumin, and serum globulin/total protein levels were collected. SPSS version 25, Mann-Whitney, Kruskal-Wallis, Chi-Square, and Spearman's correlation test were used for statistical analysis. The ROC curve determined the cut-off. Test results were significant if p <0.05. The lowest mean AGR value (0.79) was found in class 4 LN (p<0.05). The optimal cut-off AGR was 1.10 to categorize mild-moderate and severe degrees. AGR prognostic value: sensitivity=95.8%; specificity=78.8%; Positive Prediction Value (PPV)=78.0%; Negative Prediction Value (NPV)=96.0%, accuracy = 86.2%. There was a negative strong correlation between the AGR value and LN class with a correlation coefficient R of -0.777 (p<0.001). AGR marker has a good sensitivity and specificity as a predictor of LN progression.
{"title":"Analysis of Albumin to Globulin Ratio as A Prognostic Predictor in Lupus Nephritis Patients","authors":"St. Sandra Karyati Serel, Yuyun Widaningsih, Fitriani Mangarengi","doi":"10.24293/ijcpml.v30i3.2125","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2125","url":null,"abstract":"Lupus Nephritis (LN) is a manifestation of Systemic Lupus Erythematosus (SLE), which targets the kidney. Based on histopathology, the World Health Organization divides the disease into five classes: normal pattern, mesangial, focal, diffuse proliferative, and membranous. Albumin to Globulin Ratio (AGR) compares serum albumin with serum globulin levels. Low AGR value is associated with poor prognosis of diseases such as cancer, liver cirrhosis, and other chronic inflammatory diseases such as LN. This study aimed to analyze the AGR value as a prognostic predictor in LN patients based on disease classes with a retrospective descriptive cross-sectional approach. Total subjects were 109, which consisted of class 1 (n=15), class 2 (n=37), class 3 (n=9), class 4 (n=21), and class 5 LN (n=27). Data of disease classes, serum albumin, and serum globulin/total protein levels were collected. SPSS version 25, Mann-Whitney, Kruskal-Wallis, Chi-Square, and Spearman's correlation test were used for statistical analysis. The ROC curve determined the cut-off. Test results were significant if p <0.05. The lowest mean AGR value (0.79) was found in class 4 LN (p<0.05). The optimal cut-off AGR was 1.10 to categorize mild-moderate and severe degrees. AGR prognostic value: sensitivity=95.8%; specificity=78.8%; Positive Prediction Value (PPV)=78.0%; Negative Prediction Value (NPV)=96.0%, accuracy = 86.2%. There was a negative strong correlation between the AGR value and LN class with a correlation coefficient R of -0.777 (p<0.001). AGR marker has a good sensitivity and specificity as a predictor of LN progression.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"129 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141377020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2202
Akeyla Tabina Tawangalun, A. Maskoen, Emma Rachmawati, Candra Arumimaniyah, Shinta Asarina, Ratu Safitri, Tri Yuliana
Geobacillus sp. is recognized for its potential to produce bacteriocins, antibacterial substances that hold promise in addressing gastrointestinal illnesses. This study aimed to optimize the medium and pH conditions for producing antibacterial substances by Geobacillus kaustophilus Tm6T2 (a). The research employed a descriptive and experimental methodology. Growth studies were conducted in Mueller Hinton Broth with CaCl2 and MgSO4 and Nutrient Broth with KCl and MgCl2 across 6, 7, and 8 pH values. Subsequently, antibacterial substance production was achieved at the late logarithmic phase and was assessed against the gastrointestinal pathogen Salmonella typhimurium. Interestingly, findings indicated that antibacterial substance production might not solely correlate with bacterial cell count. Despite a lower bacterial cell count, the highest inhibition zone against S.typhimurium was observed at 13.11 mm in NB salt at pH 8. Analytical results show that the variation of pH and both mediums significantly affects the presence of the inhibition zone (p < 0.10). This finding suggests the complexity of factors influencing antibacterial activity. Overall, the optimum condition for antibacterial production in G.kaustophilus Tm6T2(a) was identified at pH 8 using NB salt. These findings have potential implications for developing antibacterial solutions targeting gastrointestinal pathogens.
{"title":"Optimized Novel Antibacterial Production from Geobacillus kaustophilus Tm6T2 (a) as Treatment for Salmonella typhimurium","authors":"Akeyla Tabina Tawangalun, A. Maskoen, Emma Rachmawati, Candra Arumimaniyah, Shinta Asarina, Ratu Safitri, Tri Yuliana","doi":"10.24293/ijcpml.v30i3.2202","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2202","url":null,"abstract":"Geobacillus sp. is recognized for its potential to produce bacteriocins, antibacterial substances that hold promise in addressing gastrointestinal illnesses. This study aimed to optimize the medium and pH conditions for producing antibacterial substances by Geobacillus kaustophilus Tm6T2 (a). The research employed a descriptive and experimental methodology. Growth studies were conducted in Mueller Hinton Broth with CaCl2 and MgSO4 and Nutrient Broth with KCl and MgCl2 across 6, 7, and 8 pH values. Subsequently, antibacterial substance production was achieved at the late logarithmic phase and was assessed against the gastrointestinal pathogen Salmonella typhimurium. Interestingly, findings indicated that antibacterial substance production might not solely correlate with bacterial cell count. Despite a lower bacterial cell count, the highest inhibition zone against S.typhimurium was observed at 13.11 mm in NB salt at pH 8. Analytical results show that the variation of pH and both mediums significantly affects the presence of the inhibition zone (p < 0.10). This finding suggests the complexity of factors influencing antibacterial activity. Overall, the optimum condition for antibacterial production in G.kaustophilus Tm6T2(a) was identified at pH 8 using NB salt. These findings have potential implications for developing antibacterial solutions targeting gastrointestinal pathogens.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"20 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141379195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
COVID-19 antigen is an alternative test for detecting SARS-CoV-2 infection. Viral load represented by the Cycle Threshold (CT) in the Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) affects the diagnostic performance of the test. Higher CT values result in reduced sensitivity of the SARS-CoV-2 antigen. The main objective of this study was to determine the highest CT value in rRT-PCR that still yielded reactive results in the COVID-19 antigen test. This cross-sectional study was conducted at the Fever Outpatient Clinic in Dr. Cipto Mangunkusumo Hospital from July 2020 to June 2021. Two hundred and thirty-five naso-oropharyngeal swabs were taken from patients with confirmed and suspected COVID-19 diagnoses. About 24.7% of subjects were tested positive. The median highest CT value giving reactive COVID-19 antigen results was 28.22 (13.33-39.16), while the median CT value for non-reactive antigen results was 34.45 (26.08-39.65). At a CT value < 40, the COVID-19 antigen test demonstrated 63.8% sensitivity, 99.4% specificity, 89.3% Negative Predictive Value (NPV), and 97.4% Positive Predictive Value (PPV). At the CT value < 25, the test showed 92.3% sensitivity, 99.4% specificity, 99.4% NPV, 92.3% PPV, 163.4 LR+, and 0.1 LR-. The identified cut-off point for the CT value was 29.82, with a sensitivity of 64.9% and specificity of 81%. In conclusion, COVID-19 antigen is a valuable test for screening patients with symptoms of SARS-CoV-2 infection. Understanding the influence of cycle threshold can enhance the interpretation and reliability of the antigen test.
{"title":"The Impact of Cycle Threshold Value in Influencing the Performance of COVID-19 Antigen","authors":"Rivaldi Febrian, July Kumalawati, Nina Dwi Putri, Linny Luciana, Aria Kekalih","doi":"10.24293/ijcpml.v30i3.2217","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2217","url":null,"abstract":"COVID-19 antigen is an alternative test for detecting SARS-CoV-2 infection. Viral load represented by the Cycle Threshold (CT) in the Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) affects the diagnostic performance of the test. Higher CT values result in reduced sensitivity of the SARS-CoV-2 antigen. The main objective of this study was to determine the highest CT value in rRT-PCR that still yielded reactive results in the COVID-19 antigen test. This cross-sectional study was conducted at the Fever Outpatient Clinic in Dr. Cipto Mangunkusumo Hospital from July 2020 to June 2021. Two hundred and thirty-five naso-oropharyngeal swabs were taken from patients with confirmed and suspected COVID-19 diagnoses. About 24.7% of subjects were tested positive. The median highest CT value giving reactive COVID-19 antigen results was 28.22 (13.33-39.16), while the median CT value for non-reactive antigen results was 34.45 (26.08-39.65). At a CT value < 40, the COVID-19 antigen test demonstrated 63.8% sensitivity, 99.4% specificity, 89.3% Negative Predictive Value (NPV), and 97.4% Positive Predictive Value (PPV). At the CT value < 25, the test showed 92.3% sensitivity, 99.4% specificity, 99.4% NPV, 92.3% PPV, 163.4 LR+, and 0.1 LR-. The identified cut-off point for the CT value was 29.82, with a sensitivity of 64.9% and specificity of 81%. In conclusion, COVID-19 antigen is a valuable test for screening patients with symptoms of SARS-CoV-2 infection. Understanding the influence of cycle threshold can enhance the interpretation and reliability of the antigen test.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2199
Sri Widyaningsih, Z. Rofinda
Breast cancer is the most common malignancy in females globally and one of the main causes of cancer death. There are several markers of cancer-related inflammation to help predict the relationship between pathologic characteristics of breast cancer. The research objective was to analyze the correlation between PLR and NLR with associated tumor size in breast cancer. This was a retrospective study with a cross-sectional design. This study used secondary data from the medical records of breast cancer patients who met the inclusion criteria at Siti Khodijah Hospital, Sidoarjo from January 2021 to March 2023. The sample size was 54 subjects, patients with breast cancer confirmed by pathology anatomy. The exclusion criteria were patients with infection, autoimmune disease, and hematology disorder. All the subjects were female. The mean age at the time of breast cancer diagnosis was 50.18±10.23 years, range of 27-80 years old. Most of the patients were over 50 years as much as 28 (51.85 %), while there were 26 (48.14%) > 50 years. The PLR range was 15.45-600.0, the NLR range was 0.58-9.98, tumor size range was 0.5-10.0 cm. Correlation between PLR and NLR with tumor size in breast cancer (p=0.351 and p=0.339). Correlation analysis showed that PLR and NLR had no significant correlation with tumor size ( r= -0.129, p=0.351 and r= -0.133, p=0.339). In conclusion, there is no significant correlation between PLR and NLR with histopathology of tumor size in patients with breast cancer.
{"title":"Correlation between PLR and NLR with Tumor Size in Breast Cancer Patients","authors":"Sri Widyaningsih, Z. Rofinda","doi":"10.24293/ijcpml.v30i3.2199","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2199","url":null,"abstract":"Breast cancer is the most common malignancy in females globally and one of the main causes of cancer death. There are several markers of cancer-related inflammation to help predict the relationship between pathologic characteristics of breast cancer. The research objective was to analyze the correlation between PLR and NLR with associated tumor size in breast cancer. This was a retrospective study with a cross-sectional design. This study used secondary data from the medical records of breast cancer patients who met the inclusion criteria at Siti Khodijah Hospital, Sidoarjo from January 2021 to March 2023. The sample size was 54 subjects, patients with breast cancer confirmed by pathology anatomy. The exclusion criteria were patients with infection, autoimmune disease, and hematology disorder. All the subjects were female. The mean age at the time of breast cancer diagnosis was 50.18±10.23 years, range of 27-80 years old. Most of the patients were over 50 years as much as 28 (51.85 %), while there were 26 (48.14%) > 50 years. The PLR range was 15.45-600.0, the NLR range was 0.58-9.98, tumor size range was 0.5-10.0 cm. Correlation between PLR and NLR with tumor size in breast cancer (p=0.351 and p=0.339). Correlation analysis showed that PLR and NLR had no significant correlation with tumor size ( r= -0.129, p=0.351 and r= -0.133, p=0.339). In conclusion, there is no significant correlation between PLR and NLR with histopathology of tumor size in patients with breast cancer.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"16 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2207
George Arthur Mantiri, Rheza Paleva Uyanto, M. Hendrianingtyas
Antibiotic susceptibility is significant in patient management and needs close monitoring. This study aims to evaluate the Carbapenem susceptibility profiles and correlation between Carbapenem consumption and susceptibility of the most frequent isolates from blood, sputum, and urine in 2020–2022 from the non-intensive inpatients. The proportion of males and females was 54% and 46%, with the median age group of males and females both being 65-74 years. Higher Meropenem susceptibility was shown in urine isolates of female patients. Lower susceptibility to Meropenem was shown in 2021 compared to 2020 and 2022. Lower susceptibility was shown in isolates from sputum compared to blood and urine. The three-year susceptibility of Carbapenem was decreased compared to 3 years before. The susceptibility of E.coli and S.aureus to Meropenem showed relatively high proportions 95% and 88%, compared to K.pneumoniae (46%), A.baumanii (30%), P.aeruginosa (29%), and others. The susceptibility of isolates from non-intensive-care inpatients in 2020-2022 showed lower rates compared to the hospital-wide and the previous three years' rates. Meropenem consumption was highest compared to Imipenem with inhibitor and Doripenem. The susceptibility of Gram-negative rods to Meropenem showed higher proportions (58.9%) compared to Gram-positive cocci (26.2%). Carbapenem susceptibility was decreased, along with increased Carbapenem consumption but no significant statistical correlation between the susceptibility rates and the monthly defined daily dose.
{"title":"Carbapenem Susceptibility Rate Against Gram-Positive and Gram-Negative Bacteria and Its Correlation with Consumption","authors":"George Arthur Mantiri, Rheza Paleva Uyanto, M. Hendrianingtyas","doi":"10.24293/ijcpml.v30i3.2207","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2207","url":null,"abstract":"Antibiotic susceptibility is significant in patient management and needs close monitoring. This study aims to evaluate the Carbapenem susceptibility profiles and correlation between Carbapenem consumption and susceptibility of the most frequent isolates from blood, sputum, and urine in 2020–2022 from the non-intensive inpatients. The proportion of males and females was 54% and 46%, with the median age group of males and females both being 65-74 years. Higher Meropenem susceptibility was shown in urine isolates of female patients. Lower susceptibility to Meropenem was shown in 2021 compared to 2020 and 2022. Lower susceptibility was shown in isolates from sputum compared to blood and urine. The three-year susceptibility of Carbapenem was decreased compared to 3 years before. The susceptibility of E.coli and S.aureus to Meropenem showed relatively high proportions 95% and 88%, compared to K.pneumoniae (46%), A.baumanii (30%), P.aeruginosa (29%), and others. The susceptibility of isolates from non-intensive-care inpatients in 2020-2022 showed lower rates compared to the hospital-wide and the previous three years' rates. Meropenem consumption was highest compared to Imipenem with inhibitor and Doripenem. The susceptibility of Gram-negative rods to Meropenem showed higher proportions (58.9%) compared to Gram-positive cocci (26.2%). Carbapenem susceptibility was decreased, along with increased Carbapenem consumption but no significant statistical correlation between the susceptibility rates and the monthly defined daily dose.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"17 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141378983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The detection of latent tuberculosis (TB) infection to prevent progression to active TB disease is an essential part of the WHO's end-TB strategy. Diagnosis of latent TB infection is based on detecting immune responses to Mycobacterium tuberculosis antigens. Interferon Gamma Release Assays (IGRA) are superior to Tuberculin Skin Tests (TST) for detecting latent infection; however, the performance of IGRA is limited in resource-limited settings. This study evaluated the sensitivity, specificity, and agreement of the lateral-flow nanoparticle fluorescence assay (QIAreach QFT) compared with the ELISA method (QFT-Plus) as a reference test. This cross-sectional study was carried out in the laboratory department of Siloam Hospitals in Lippo Village, Banten, Indonesia, between January and June 2023. A total of 60 samples consisting of both males and females of all age groups were tested for QFT-Plus and were involved in the study using consecutive samples. Sensitivity, specificity, Negative Predictive Value (NPV), and Positive Predictive Value (PPV) of QIAreach QFT were 100% (95% CI 86.28-100), 70.96% (95% CI 51.96-85.78), 100%, (95% CI 84.56-100) and 73.53% (95% CI 55.64-87.12), respectively. The agreement calculation using Cohen's kappa coefficient, excluding indeterminate data, showed a kappa value 0.68 (95% CI 0.507-0.864). QIAreach QFT, with its superiority, could support the expansion of IGRA testing, particularly in remote areas, thereby helping the eradication attempt of TB infection.
检测潜伏肺结核（TB）感染以防止发展为活动性肺结核病是世界卫生组织终结结核病战略的重要组成部分。潜伏结核感染的诊断基于对结核分枝杆菌抗原免疫反应的检测。干扰素γ释放测定（IGRA）在检测潜伏感染方面优于结核菌素皮试（TST）；然而，在资源有限的环境中，IGRA的效果有限。本研究评估了横向流纳米颗粒荧光测定法（QIAreach QFT）与作为参考检验的酶联免疫吸附法（QFT-Plus）相比的灵敏度、特异性和一致性。这项横断面研究于2023年1月至6月期间在印度尼西亚万丹省里波村的西乐庵医院实验室进行。共有 60 份不同年龄段的男性和女性样本接受了 QFT-Plus 检测，并使用连续样本参与了研究。QIAreach QFT的灵敏度、特异性、阴性预测值（NPV）和阳性预测值（PPV）分别为100%（95% CI 86.28-100）、70.96%（95% CI 51.96-85.78）、100%（95% CI 84.56-100）和73.53%（95% CI 55.64-87.12）。使用科恩卡帕系数（Cohen's kappa coefficient）计算的一致性（不包括不确定数据）显示，卡帕值为 0.68（95% CI 0.507-0.864）。QIAreach QFT 的优越性有助于扩大 IGRA 检测范围，尤其是在偏远地区，从而有助于根除结核病感染的努力。
{"title":"Comparison of Lateral-flow Nanoparticle Fluorescence Assay and ELISA Method for Interferon-y Release Assay Test","authors":"Tandry Meriyanti, Maroloan Aruan, Diana Intan Lusiana Gabriella, Justina Andrea Renjaan","doi":"10.24293/ijcpml.v30i3.2212","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2212","url":null,"abstract":"The detection of latent tuberculosis (TB) infection to prevent progression to active TB disease is an essential part of the WHO's end-TB strategy. Diagnosis of latent TB infection is based on detecting immune responses to Mycobacterium tuberculosis antigens. Interferon Gamma Release Assays (IGRA) are superior to Tuberculin Skin Tests (TST) for detecting latent infection; however, the performance of IGRA is limited in resource-limited settings. This study evaluated the sensitivity, specificity, and agreement of the lateral-flow nanoparticle fluorescence assay (QIAreach QFT) compared with the ELISA method (QFT-Plus) as a reference test. This cross-sectional study was carried out in the laboratory department of Siloam Hospitals in Lippo Village, Banten, Indonesia, between January and June 2023. A total of 60 samples consisting of both males and females of all age groups were tested for QFT-Plus and were involved in the study using consecutive samples. Sensitivity, specificity, Negative Predictive Value (NPV), and Positive Predictive Value (PPV) of QIAreach QFT were 100% (95% CI 86.28-100), 70.96% (95% CI 51.96-85.78), 100%, (95% CI 84.56-100) and 73.53% (95% CI 55.64-87.12), respectively. The agreement calculation using Cohen's kappa coefficient, excluding indeterminate data, showed a kappa value 0.68 (95% CI 0.507-0.864). QIAreach QFT, with its superiority, could support the expansion of IGRA testing, particularly in remote areas, thereby helping the eradication attempt of TB infection.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2206
Hidayat Hidayat, Ida Parwati, Eko Agus Srianto
Klebsiella pneumoniae is one of the most common causes of severe hospital-acquired infection. ESBL-producing Klebsiella pneumoniae causes a major problem for clinical management and epidemiological study. The other factor identified was OmpK35 which is often poorly or not expressed and it can be altered by factors such as point mutations. This study aimed to determine the susceptibility pattern, and the genotyping and to investigate the mutations in OmpK35 of Klebsiella.pneumoniae. This is a cross-sectional study using susceptibility pattern data from the ninety isolates of Klebsiella pneumoniae from the patients admitted to Dr. H. Abdul Moeloek General Hospital, Lampung. The Genotype of ESBL genes and OmpK35 gene were determined by polymerase chain reaction and sequencing for identification of the mutation. The susceptibility rate of Klebsiella pneumoniae belonged to Ampicillin was 0%. The susceptibility rate belonged to Amikacin (96.6%), Meropenem (94.4%), and Ertapenem (94.4%). From 90 isolates, the genotype blaSHV was found in 86.7%, and most of the isolates had OmpK35 genes (91.2%). Among the thirty isolates, 20% harbored mutations in the OmpK35 protein with substitution mutations. This finding indicated a high prevalence of antibiotic resistance, a high prevalence rate of ESBL gene production, and a high frequency of porin mutations among Klebsiella pneumoniae isolates.
{"title":"Susceptibility Pattern, Genotyping, and Mutations of Klebsiella pneumoniae at Dr. H. Abdul Moeloek General Hospital","authors":"Hidayat Hidayat, Ida Parwati, Eko Agus Srianto","doi":"10.24293/ijcpml.v30i3.2206","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2206","url":null,"abstract":"Klebsiella pneumoniae is one of the most common causes of severe hospital-acquired infection. ESBL-producing Klebsiella pneumoniae causes a major problem for clinical management and epidemiological study. The other factor identified was OmpK35 which is often poorly or not expressed and it can be altered by factors such as point mutations. This study aimed to determine the susceptibility pattern, and the genotyping and to investigate the mutations in OmpK35 of Klebsiella.pneumoniae. This is a cross-sectional study using susceptibility pattern data from the ninety isolates of Klebsiella pneumoniae from the patients admitted to Dr. H. Abdul Moeloek General Hospital, Lampung. The Genotype of ESBL genes and OmpK35 gene were determined by polymerase chain reaction and sequencing for identification of the mutation. The susceptibility rate of Klebsiella pneumoniae belonged to Ampicillin was 0%. The susceptibility rate belonged to Amikacin (96.6%), Meropenem (94.4%), and Ertapenem (94.4%). From 90 isolates, the genotype blaSHV was found in 86.7%, and most of the isolates had OmpK35 genes (91.2%). Among the thirty isolates, 20% harbored mutations in the OmpK35 protein with substitution mutations. This finding indicated a high prevalence of antibiotic resistance, a high prevalence rate of ESBL gene production, and a high frequency of porin mutations among Klebsiella pneumoniae isolates.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"13 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141379276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2210
J. Sembiring, A. Indrati, Widya Amalia
Infection of Human Immunodeficiency Virus (HIV) lowers the body's immune system, especially CD4+ cells, making it more susceptible to opportunistic infections. Approximately 10-40% of People Living with HIV/AIDS (PLHIV) fail to achieve normal levels of CD4+ T cells despite continued virological suppression, a condition called Immunological Non-Responders (INR). Previous studies have shown that INR is considered a predictor of disease progression in people with HIV receiving antiretroviral (ARV)s through various mechanisms of suppression of the immune system that increases morbidity and mortality. Papua is an HIV epidemic area with a prevalence of 2.3%. This research is a cohort study conducted at Abepura Hospital from June 2019 to February 2023, which aims to identify the factors that influence the occurrence of INR in PLHIV receiving ARV therapy. There were 123 research subjects consisting of 55 people (44.7%) in the INR group and 68 people (55.3%) in the non-INR group. The results showed that the incidence of INR was higher in males than females (p=0.019), INR was significantly associated with increasing age (p=0.013), and CD4 count was low at the start of ARVs (p=0.002). There was a significant difference in CD4 counts between INR and non-INR (p<0.001). Oral candidiasis as a common opportunistic infection is more common in people with INR than in non-INR. (p=0.037). This study suggested that it is necessary to carry out a CD4 examination at the start of therapy and monitoring every 6 months to detect possible INR to prevent an increased risk of AIDS and non-AIDS, which increases mortality.
{"title":"Characteristics of Immunological Non-Responders in People Living with HIV at Abepura Hospital Papua","authors":"J. Sembiring, A. Indrati, Widya Amalia","doi":"10.24293/ijcpml.v30i3.2210","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2210","url":null,"abstract":"Infection of Human Immunodeficiency Virus (HIV) lowers the body's immune system, especially CD4+ cells, making it more susceptible to opportunistic infections. Approximately 10-40% of People Living with HIV/AIDS (PLHIV) fail to achieve normal levels of CD4+ T cells despite continued virological suppression, a condition called Immunological Non-Responders (INR). Previous studies have shown that INR is considered a predictor of disease progression in people with HIV receiving antiretroviral (ARV)s through various mechanisms of suppression of the immune system that increases morbidity and mortality. Papua is an HIV epidemic area with a prevalence of 2.3%. This research is a cohort study conducted at Abepura Hospital from June 2019 to February 2023, which aims to identify the factors that influence the occurrence of INR in PLHIV receiving ARV therapy. There were 123 research subjects consisting of 55 people (44.7%) in the INR group and 68 people (55.3%) in the non-INR group. The results showed that the incidence of INR was higher in males than females (p=0.019), INR was significantly associated with increasing age (p=0.013), and CD4 count was low at the start of ARVs (p=0.002). There was a significant difference in CD4 counts between INR and non-INR (p<0.001). Oral candidiasis as a common opportunistic infection is more common in people with INR than in non-INR. (p=0.037). This study suggested that it is necessary to carry out a CD4 examination at the start of therapy and monitoring every 6 months to detect possible INR to prevent an increased risk of AIDS and non-AIDS, which increases mortality.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"5 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141379709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.24293/ijcpml.v30i3.2231
Elizabeth Sidhartha, Thoeng Ronald
The Urine Albumin/Creatinine Ratio (uACR) is one of the earliest markers of glomerular disorders. A comparative study of semi-quantitative urine uACR and quantitative uACR tests was carried out using Meditape UC-11A test strips on the Sysmex UC-3500 (automated urinalysis instrument) and Roche Cobas 501, respectively. A total of 213 retrospective data of urine chemistry tests were collected. Semi-quantitative urine albumin, creatinine, and uACR data were obtained using Meditape UC-11A strips on Sysmex UC-3500, whereas quantitative data were obtained using Roche Cobas c501. A weighted Cohen's Kappa agreement, sensitivity, specificity, PPV, NPV, and accuracy were analyzed using data from both instruments. The Kappa values for urine albumin, creatinine, and uACR between the semi-quantitative and quantitative methods were 0.83 (CI 0.771– 0.880), 0.535 (CI 0.417–0.652), and 0.691 (CI 0.606–0.775), respectively. The sensitivity, specificity, PPV, NPV, and accuracy of semi-quantitative methods were 90%, 73.3%, 75%, 89.2%, and 81.2%, respectively. The semi-quantitative uACR test on the UC-3500 showed excellent performance and could be used as a screening test for early detection of impaired kidney function.
{"title":"Performance Evaluation of Semi-quantitative Urine Albumin Creatinine Ratio Using Meditape UC-11A Strip Test","authors":"Elizabeth Sidhartha, Thoeng Ronald","doi":"10.24293/ijcpml.v30i3.2231","DOIUrl":"https://doi.org/10.24293/ijcpml.v30i3.2231","url":null,"abstract":"The Urine Albumin/Creatinine Ratio (uACR) is one of the earliest markers of glomerular disorders. A comparative study of semi-quantitative urine uACR and quantitative uACR tests was carried out using Meditape UC-11A test strips on the Sysmex UC-3500 (automated urinalysis instrument) and Roche Cobas 501, respectively. A total of 213 retrospective data of urine chemistry tests were collected. Semi-quantitative urine albumin, creatinine, and uACR data were obtained using Meditape UC-11A strips on Sysmex UC-3500, whereas quantitative data were obtained using Roche Cobas c501. A weighted Cohen's Kappa agreement, sensitivity, specificity, PPV, NPV, and accuracy were analyzed using data from both instruments. The Kappa values for urine albumin, creatinine, and uACR between the semi-quantitative and quantitative methods were 0.83 (CI 0.771– 0.880), 0.535 (CI 0.417–0.652), and 0.691 (CI 0.606–0.775), respectively. The sensitivity, specificity, PPV, NPV, and accuracy of semi-quantitative methods were 90%, 73.3%, 75%, 89.2%, and 81.2%, respectively. The semi-quantitative uACR test on the UC-3500 showed excellent performance and could be used as a screening test for early detection of impaired kidney function.","PeriodicalId":354500,"journal":{"name":"Indonesian Journal of Clinical Pathology and Medical Laboratory","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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