Background: Streptococcus pneumoniae Serotype 3 (SPN3) remains a significant cause of morbidity and mortality worldwide despite of pneumococcal conjugate vaccine (PCV) implementation. We explored genomic profile of SPN3 from children and adult groups to understand population structure and evolution dynamics of SPN3 in Indonesia.
Methods: We undertook whole genome sequencing (WGS) from 19 isolates of SPN3 in Indonesia between 2017 and 2021 prior to PCV introduction. This study assessed sequence types (STs), global pneumococcal sequence cluster (GPSC), genome prediction of antimicrobial resistance (AMR) profile, pangenome analysis, phylogenetic tree, and genome comparative of capsular polysaccharide (cps) locus.
Results: We identified ST451-GPSC234 (n = 5) and ST180-GPSC12 (n = 4), ST458-GPSC51 (n = 2), ST3805-GPSC12 (n = 2), ST4909-GPSC363 (n = 2), ST700-GPSC10 (n = 1), ST5292-GPSC309 (n = 1), ST505-GPSC12 (n = 1), and ST4233 (n = 1). Genome prediction of AMR discover isolates were resistant to tetracycline (n = 5); co-resistant of chloramphenicol and tetracycline (n = 2); co-trimoxazole and tetracycline (n = 1). We observed SPN3 possess closed pangenome characteristic, indicates more stable genetic repertoire. We found 5 absent genes in cps locus including cpsABCD and tnp in ST700-GPSC10 lineage.
Conclusions: SPN3 has potential genomic profile to enhance the ability of this strain to endure selective pressure such as PCV introduction.
{"title":"An insight of Streptococcus pneumoniae serotype 3 genomic profile in Indonesia.","authors":"Ratna Fathma Sari, Fadilah Fadilah, Yustinus Maladan, Rosantia Sarassari, Miftahuddin Majid Khoeri, Kuntjoro Harimurti, Lindawati Alimsardjono, Dodi Safari","doi":"10.1016/j.jmii.2025.01.007","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.01.007","url":null,"abstract":"<p><strong>Background: </strong>Streptococcus pneumoniae Serotype 3 (SPN3) remains a significant cause of morbidity and mortality worldwide despite of pneumococcal conjugate vaccine (PCV) implementation. We explored genomic profile of SPN3 from children and adult groups to understand population structure and evolution dynamics of SPN3 in Indonesia.</p><p><strong>Methods: </strong>We undertook whole genome sequencing (WGS) from 19 isolates of SPN3 in Indonesia between 2017 and 2021 prior to PCV introduction. This study assessed sequence types (STs), global pneumococcal sequence cluster (GPSC), genome prediction of antimicrobial resistance (AMR) profile, pangenome analysis, phylogenetic tree, and genome comparative of capsular polysaccharide (cps) locus.</p><p><strong>Results: </strong>We identified ST451-GPSC234 (n = 5) and ST180-GPSC12 (n = 4), ST458-GPSC51 (n = 2), ST3805-GPSC12 (n = 2), ST4909-GPSC363 (n = 2), ST700-GPSC10 (n = 1), ST5292-GPSC309 (n = 1), ST505-GPSC12 (n = 1), and ST4233 (n = 1). Genome prediction of AMR discover isolates were resistant to tetracycline (n = 5); co-resistant of chloramphenicol and tetracycline (n = 2); co-trimoxazole and tetracycline (n = 1). We observed SPN3 possess closed pangenome characteristic, indicates more stable genetic repertoire. We found 5 absent genes in cps locus including cpsABCD and tnp in ST700-GPSC10 lineage.</p><p><strong>Conclusions: </strong>SPN3 has potential genomic profile to enhance the ability of this strain to endure selective pressure such as PCV introduction.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-10DOI: 10.1016/j.jmii.2025.02.003
Shuangyan Li, Mingming Pan, Hui Zhao, Yanming Li
Respiratory virus infection is an important cause of both community acquired pneumonia and hospital-acquired pneumonia. Various respiratory viruses, including influenza virus, avian influenza virus, respiratory syncytial virus (RSV), SARS-CoV, MERS-CoV, and SARS-CoV-2, result in severe fibrosis sequelae after the acute phase. Since the COVID-19 pandemic, respiratory virus infection, as an important cause of pulmonary fibrosis, has attracted increasing attention around the world. Respiratory virus infection usually triggers robust inflammation responses, leading to large amounts of proinflammatory mediator production, such as chemokine (C-C motif) ligand 2 (CCL2), a critical chemokine involved in the recruitment of various inflammatory cells. Moreover, CCL2 plays a pivotal role in the pathogenesis of fibrosis progression, through regulating recruitment of bone marrow-derived monocytes and increasing the expression of extracellular matrix proteins. This review provided a concise overview of the common fibrosis sequelae after virus infection. Then we discussed the elevated levels of CCL2 in various respiratory virus infection, underscoring its potent profibrotic role. Targeting the CCL2/CCR2 axis holds promise for alleviating fibrosis sequelae post-acute virus infection and warrants further investigation.
{"title":"Role of CCL2/CCR2 axis in pulmonary fibrosis induced by respiratory viruses.","authors":"Shuangyan Li, Mingming Pan, Hui Zhao, Yanming Li","doi":"10.1016/j.jmii.2025.02.003","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.02.003","url":null,"abstract":"<p><p>Respiratory virus infection is an important cause of both community acquired pneumonia and hospital-acquired pneumonia. Various respiratory viruses, including influenza virus, avian influenza virus, respiratory syncytial virus (RSV), SARS-CoV, MERS-CoV, and SARS-CoV-2, result in severe fibrosis sequelae after the acute phase. Since the COVID-19 pandemic, respiratory virus infection, as an important cause of pulmonary fibrosis, has attracted increasing attention around the world. Respiratory virus infection usually triggers robust inflammation responses, leading to large amounts of proinflammatory mediator production, such as chemokine (C-C motif) ligand 2 (CCL2), a critical chemokine involved in the recruitment of various inflammatory cells. Moreover, CCL2 plays a pivotal role in the pathogenesis of fibrosis progression, through regulating recruitment of bone marrow-derived monocytes and increasing the expression of extracellular matrix proteins. This review provided a concise overview of the common fibrosis sequelae after virus infection. Then we discussed the elevated levels of CCL2 in various respiratory virus infection, underscoring its potent profibrotic role. Targeting the CCL2/CCR2 axis holds promise for alleviating fibrosis sequelae post-acute virus infection and warrants further investigation.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-08DOI: 10.1016/j.jmii.2025.01.003
Eloïse Bailly, Chloé Baranton, Stéphane Valot, Anne Vincent, Hervé Begue, Corentin Beclere, Alain Bonnin, Damien Costa, Philippe Poirier, Louise Basmaciyan, Frédéric Dalle
Background: Intestinal parasitic diseases affect millions of people worldwide. Numerous commercial molecular methods detecting digestive parasites have been developed recently, including multiplex PCR assays able to identify multiple parasites at once. Several studies have demonstrated that the efficacy of these molecular methods is dependent on the specific protocols employed at each stage of the process including pretreatment, extraction and amplification. However, previous studies have exclusively focused on one of these steps, without considering the others. The objective of the present study was to evaluate the performances of molecular tools for Cryptosporidium parvum detection in stool samples, considering all steps of the process simultaneously.
Methods: 30 distinct combinations of protocols were evaluated corresponding to three pre-treatment methods, four DNA extraction techniques and six DNA amplification assays. The performances of these combinations were evaluated in terms of detection limit.
Results: We showed that different combinations yielded varying results. The FTD® Stool Parasite technique proved to be the most effective, achieving 100 % detection. Manual extraction methods demonstrated excellent outcomes, although they are time-consuming. The optimal approach for detecting C. parvum DNA is a combination of mechanical pretreatment, the Nuclisens® Easymag® extraction method, and the FTD® Stool Parasite DNA amplification method.
Conclusion: This work shows that the molecular diagnosis should consider all stages. A PCR method may not be effective with an unsuitable extraction technique, but can yield optimal results with an appropriate one.
{"title":"Performance of 30 protocol combinations for the detection of Cryptosporidium parvum in stool samples.","authors":"Eloïse Bailly, Chloé Baranton, Stéphane Valot, Anne Vincent, Hervé Begue, Corentin Beclere, Alain Bonnin, Damien Costa, Philippe Poirier, Louise Basmaciyan, Frédéric Dalle","doi":"10.1016/j.jmii.2025.01.003","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.01.003","url":null,"abstract":"<p><strong>Background: </strong>Intestinal parasitic diseases affect millions of people worldwide. Numerous commercial molecular methods detecting digestive parasites have been developed recently, including multiplex PCR assays able to identify multiple parasites at once. Several studies have demonstrated that the efficacy of these molecular methods is dependent on the specific protocols employed at each stage of the process including pretreatment, extraction and amplification. However, previous studies have exclusively focused on one of these steps, without considering the others. The objective of the present study was to evaluate the performances of molecular tools for Cryptosporidium parvum detection in stool samples, considering all steps of the process simultaneously.</p><p><strong>Methods: </strong>30 distinct combinations of protocols were evaluated corresponding to three pre-treatment methods, four DNA extraction techniques and six DNA amplification assays. The performances of these combinations were evaluated in terms of detection limit.</p><p><strong>Results: </strong>We showed that different combinations yielded varying results. The FTD® Stool Parasite technique proved to be the most effective, achieving 100 % detection. Manual extraction methods demonstrated excellent outcomes, although they are time-consuming. The optimal approach for detecting C. parvum DNA is a combination of mechanical pretreatment, the Nuclisens® Easymag® extraction method, and the FTD® Stool Parasite DNA amplification method.</p><p><strong>Conclusion: </strong>This work shows that the molecular diagnosis should consider all stages. A PCR method may not be effective with an unsuitable extraction technique, but can yield optimal results with an appropriate one.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143473317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-07DOI: 10.1016/j.jmii.2025.02.001
Yong Xiang, Ruoyu Zhang, Jinghong Qiu, Hon-Cheong So
Background: COVID-19 is one of the most pressing public health issues worldwide. The sequelae of COVID-19 however remains unclear. We performed a systematic assessment of sequelae across all body systems, focusing on whether COVID-19 is associated with increased risk of hospitalization for various diseases.
Methods: In this cohort study, we examined 135 disorders in UK biobank (UKBB) (N = 412,096; age: 50-87). We also conducted analysis for new-onset and recurrent cases, and employed the prior event rate adjustment (PERR) approach to minimize effects of unmeasured confounders. Time-dependent effects were also tested.
Results: Compared to individuals with no known COVID-19 history, those with severe COVID-19 (hospitalized) exhibited increased hazards of hospitalization due to multiple disorders (median follow-up = 261 days), including disorders of respiratory, cardiovascular, neurological, gastrointestinal, genitourinary, musculoskeletal systems, as well as injuries, infections and non-specific symptoms. Notably, severe COVID-19 was associated with increased hospitalization risks in 77 out of the 107 disease categories with ≥ 5 events in both groups. These results remained largely consistent in sensitivity analyses. Mild (non-hospitalized) COVID-19 was associated with increased risk of hospitalization for several disorders: aspiration pneumonitis, musculoskeletal pain and other general signs/symptoms. The risk of hospitalizations following infection was generally higher during the pre-vaccination era.
Conclusion: This study revealed increased risk of hospitalization from a wide variety of pulmonary and extra-pulmonary diseases after COVID-19, especially for severe infections. The findings may have important clinical implications, such as the need for closer monitoring and risk assessment of relevant sequelae, and allocating more resources toward prevention and treatment of such sequelae.
{"title":"Increased risk of hospitalization for various disorders after COVID-19 infection: A Cohort study of the UK biobank spanning over a hundred disease categories.","authors":"Yong Xiang, Ruoyu Zhang, Jinghong Qiu, Hon-Cheong So","doi":"10.1016/j.jmii.2025.02.001","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.02.001","url":null,"abstract":"<p><strong>Background: </strong>COVID-19 is one of the most pressing public health issues worldwide. The sequelae of COVID-19 however remains unclear. We performed a systematic assessment of sequelae across all body systems, focusing on whether COVID-19 is associated with increased risk of hospitalization for various diseases.</p><p><strong>Methods: </strong>In this cohort study, we examined 135 disorders in UK biobank (UKBB) (N = 412,096; age: 50-87). We also conducted analysis for new-onset and recurrent cases, and employed the prior event rate adjustment (PERR) approach to minimize effects of unmeasured confounders. Time-dependent effects were also tested.</p><p><strong>Results: </strong>Compared to individuals with no known COVID-19 history, those with severe COVID-19 (hospitalized) exhibited increased hazards of hospitalization due to multiple disorders (median follow-up = 261 days), including disorders of respiratory, cardiovascular, neurological, gastrointestinal, genitourinary, musculoskeletal systems, as well as injuries, infections and non-specific symptoms. Notably, severe COVID-19 was associated with increased hospitalization risks in 77 out of the 107 disease categories with ≥ 5 events in both groups. These results remained largely consistent in sensitivity analyses. Mild (non-hospitalized) COVID-19 was associated with increased risk of hospitalization for several disorders: aspiration pneumonitis, musculoskeletal pain and other general signs/symptoms. The risk of hospitalizations following infection was generally higher during the pre-vaccination era.</p><p><strong>Conclusion: </strong>This study revealed increased risk of hospitalization from a wide variety of pulmonary and extra-pulmonary diseases after COVID-19, especially for severe infections. The findings may have important clinical implications, such as the need for closer monitoring and risk assessment of relevant sequelae, and allocating more resources toward prevention and treatment of such sequelae.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: To determine susceptibility of imipenem-non-susceptible Escherichia coli (INS-EC) and Klebsiella pneumoniae (INS-KP) isolates collected during 2020-2022 through a national surveillance program in Taiwan to novel antibiotics, and to compare the results with those obtained during 2012-2018.
Methods: Minimum inhibitory concentrations were determined by broth microdilution methods. Genes encoding carbapenemases including blaKPC, metallo-β-lactamase (MBL) genes, and blaOXA-48 were detected via multiplex PCR. Data retrieved from our 2012-2018 study were used for comparison.
Results: Of 3260 E. coli and 1457 K. pneumoniae isolates collected during 2020-2022, 0.9 % and 9.5 %, were INS-EC and INS-KP, respectively. Cefepime-zidebactam, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam were active against 100 %, 75.9 %, 65.5 %, and 79.3 % of 29 INS-EC isolates respectively; and against 100 %, 90.6 %, 64.5 %, and 67.4 % of 138 INS- KP isolates, respectively. Susceptibility was contingent upon carbapenemase types. Susceptibility rates of cefepime-zidebactam and ceftazidime-avibactam remained constant from 2012 to 2018 through 2020-2022 but those of imipenem-relebactam and meropenem-vaborbactam decreased significantly, which may be partially attributable to the increasing prevalence of blaOXA-48. Eighteen MBL-gene-positive isolates and two blaKPC-positive isolates were resistant to ceftazidime-avibactam, whereas all were susceptible to cefepime-zidebactam. Tigecycline had a higher susceptibility rate than eravacycline and omadacycline for K. pneumoniae isolates. Lascufloxacin and delafloxacin were effective against fewer than 10 % of INS isolates. Susceptibilities to novel tetracyclines and fluoroquinolones remained similar from 2012 to 2018 through 2020-2022.
Conclusions: This study highlights significant resistance patterns of INS-EC and INS-KP isolates in Taiwan. The declining susceptibility rates and the rising prevalence of genetic resistance determinants highlight the importance of ongoing surveillance and antimicrobial stewardship.
{"title":"Antimicrobial resistance among imipenem-non-susceptible Escherichia coli and Klebsiella pneumoniae isolates, with an emphasis on novel β-lactam/β-lactamase inhibitor combinations and tetracycline derivatives: The Taiwan surveillance of antimicrobial resistance program, 2020-2022.","authors":"Yu-Lin Lee, Chun-Eng Liu, Wei-Yao Wang, Mei-Chen Tan, Pei-Jing Chen, Yih-Ru Shiau, Hui-Ying Wang, Jui-Fen Lai, I-Wen Huang, Ya-Sung Yang, Shu-Chen Kuo","doi":"10.1016/j.jmii.2025.01.006","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.01.006","url":null,"abstract":"<p><strong>Background: </strong>To determine susceptibility of imipenem-non-susceptible Escherichia coli (INS-EC) and Klebsiella pneumoniae (INS-KP) isolates collected during 2020-2022 through a national surveillance program in Taiwan to novel antibiotics, and to compare the results with those obtained during 2012-2018.</p><p><strong>Methods: </strong>Minimum inhibitory concentrations were determined by broth microdilution methods. Genes encoding carbapenemases including bla<sub>KPC</sub>, metallo-β-lactamase (MBL) genes, and bla<sub>OXA-48</sub> were detected via multiplex PCR. Data retrieved from our 2012-2018 study were used for comparison.</p><p><strong>Results: </strong>Of 3260 E. coli and 1457 K. pneumoniae isolates collected during 2020-2022, 0.9 % and 9.5 %, were INS-EC and INS-KP, respectively. Cefepime-zidebactam, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam were active against 100 %, 75.9 %, 65.5 %, and 79.3 % of 29 INS-EC isolates respectively; and against 100 %, 90.6 %, 64.5 %, and 67.4 % of 138 INS- KP isolates, respectively. Susceptibility was contingent upon carbapenemase types. Susceptibility rates of cefepime-zidebactam and ceftazidime-avibactam remained constant from 2012 to 2018 through 2020-2022 but those of imipenem-relebactam and meropenem-vaborbactam decreased significantly, which may be partially attributable to the increasing prevalence of bla<sub>OXA-48</sub>. Eighteen MBL-gene-positive isolates and two bla<sub>KPC</sub>-positive isolates were resistant to ceftazidime-avibactam, whereas all were susceptible to cefepime-zidebactam. Tigecycline had a higher susceptibility rate than eravacycline and omadacycline for K. pneumoniae isolates. Lascufloxacin and delafloxacin were effective against fewer than 10 % of INS isolates. Susceptibilities to novel tetracyclines and fluoroquinolones remained similar from 2012 to 2018 through 2020-2022.</p><p><strong>Conclusions: </strong>This study highlights significant resistance patterns of INS-EC and INS-KP isolates in Taiwan. The declining susceptibility rates and the rising prevalence of genetic resistance determinants highlight the importance of ongoing surveillance and antimicrobial stewardship.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Chlamydia trachomatis infection is one of the most common sexually transmitted infections (STIs). This study investigated the prevalence and genotype distribution of C. trachomatis, and treatment response, focusing on the recent emergence of genovariant L2b in Taiwan.
Methods: This prospective study was conducted from August 2021 to September 2023, enrolling 1023 participants, including 492 people who received pre-exposure prophylaxis (PrEP) for HIV and 531 people with HIV (PWH). Multiple-site sampling and genotyping of C. trachomatis identified were performed. Participants testing positive for C. trachomatis received a 7-day course of doxycycline and test-of-cure (TOC) assessments were conducted post-treatment.
Results: Among the participants, mostly MSM (92.7%), 26.4% tested positive for C. trachomatis, with 77.8% identified in the rectum. The prevalent genotypes were J (26.4%), G (24.0%), and B (17.7%). Treatment with a 7-day course of doxycycline resulted in clearance for most cases (91.1%). Genotyping investigations for those repeatedly testing positive (8.9%) showed reinfections with different genotypes. Eighteen cases of asymptomatic rectal carriage of genovariant L2b were detected, predominantly in PWH (88.9%). The L2b genovariant was cleared with 7 days of doxycycline on TOC assessments. The prevalence of L2b increased over time, with multi-locus sequence typing showing ST53 as the predominant strain.
Conclusions: C. trachomatis was prevalent among PWH and PrEP users and the prevalence of L2b genovariant was increasing in Taiwan. A 7-day course of doxycycline was effective in clearing L2b genovariant in asymptomatic participants. Continued surveillance to monitor the evolving epidemiology of chlamydia in Taiwan is warranted.
{"title":"Chlamydia trachomatis infection among at-risk populations in Taiwan: Emergence of genovariant L2b and treatment response to antimicrobials.","authors":"Chi-Ying Lin, Chin-Shiang Tsai, Hsin-Yun Sun, Yu-Shan Huang, Kuan-Yin Lin, Wang-Da Liu, Guan-Jhou Chen, Tzong-Yow Wu, Li-Hsin Su, Hsin-Hui Huang, Sui-Yuan Chang, Wen-Chien Ko, Chien-Ching Hung","doi":"10.1016/j.jmii.2025.01.008","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.01.008","url":null,"abstract":"<p><strong>Background: </strong>Chlamydia trachomatis infection is one of the most common sexually transmitted infections (STIs). This study investigated the prevalence and genotype distribution of C. trachomatis, and treatment response, focusing on the recent emergence of genovariant L2b in Taiwan.</p><p><strong>Methods: </strong>This prospective study was conducted from August 2021 to September 2023, enrolling 1023 participants, including 492 people who received pre-exposure prophylaxis (PrEP) for HIV and 531 people with HIV (PWH). Multiple-site sampling and genotyping of C. trachomatis identified were performed. Participants testing positive for C. trachomatis received a 7-day course of doxycycline and test-of-cure (TOC) assessments were conducted post-treatment.</p><p><strong>Results: </strong>Among the participants, mostly MSM (92.7%), 26.4% tested positive for C. trachomatis, with 77.8% identified in the rectum. The prevalent genotypes were J (26.4%), G (24.0%), and B (17.7%). Treatment with a 7-day course of doxycycline resulted in clearance for most cases (91.1%). Genotyping investigations for those repeatedly testing positive (8.9%) showed reinfections with different genotypes. Eighteen cases of asymptomatic rectal carriage of genovariant L2b were detected, predominantly in PWH (88.9%). The L2b genovariant was cleared with 7 days of doxycycline on TOC assessments. The prevalence of L2b increased over time, with multi-locus sequence typing showing ST53 as the predominant strain.</p><p><strong>Conclusions: </strong>C. trachomatis was prevalent among PWH and PrEP users and the prevalence of L2b genovariant was increasing in Taiwan. A 7-day course of doxycycline was effective in clearing L2b genovariant in asymptomatic participants. Continued surveillance to monitor the evolving epidemiology of chlamydia in Taiwan is warranted.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-05DOI: 10.1016/j.jmii.2025.02.002
Yu-Shan Shih, Wan-Ting Tsai, Bei-Chia Guo, Aristine Cheng, Jann-Tay Wang
Neutralizing anti-interferon (IFN)-α autoantibodies can lead to immune dysregulation, potentially resulting in critical coronavirus disease 2019 (COVID-19). We report a case presenting with severe COVID-19 who was subsequently diagnosed to have thymoma and neutralizing anti-IFN-α autoantibodies.
{"title":"Life-threatening COVID-19 in a thymoma patient with anti-interferon-α autoantibodies.","authors":"Yu-Shan Shih, Wan-Ting Tsai, Bei-Chia Guo, Aristine Cheng, Jann-Tay Wang","doi":"10.1016/j.jmii.2025.02.002","DOIUrl":"https://doi.org/10.1016/j.jmii.2025.02.002","url":null,"abstract":"<p><p>Neutralizing anti-interferon (IFN)-α autoantibodies can lead to immune dysregulation, potentially resulting in critical coronavirus disease 2019 (COVID-19). We report a case presenting with severe COVID-19 who was subsequently diagnosed to have thymoma and neutralizing anti-IFN-α autoantibodies.</p>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.jmii.2024.09.006
Yu-Chieh Tsai , Wei-Chen Tai , Chih-Ming Liang , Cheng-Kun Wu , Ming-Chao Tsai , Wan-Hsiang Hu , Pao-Yuan Huang , Chien-Hung Chen , Yuan-Hung Kuo , Chih-Chien Yao , Seng-Kee Chuah
Background
The inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC) is a complex disease with multifactorial etiology. The intestinal dysbiosis have been investigated to play an important role in IBD pathogenesis and disease activity. The aim of our study was to analyze the intestinal microbiota composition in IBD across different severity levels and the impact of biologic therapy on microbiota modulation.
Methods
In this study, 27 IBD patients were recruited, including 14 patients undergoing biologic therapy for moderate to severe disease activity and 13 controls with inactive disease. The gut microbial composition was determined by 16 S ribosomal RNA gene sequencing of stool samples.
Results
Biologic therapy led to significant clinical improvement in IBD disease activity after 48 weeks. About species richness, community alpha diversity was significant lower in active CD patients and enriched gradually after biologic therapy. The beta-diversity regard to the difference of bacterial community composition showed significant difference between patients in biologic and control group. A decrease in Firmicutes and increase in Bacteroidetes abundance were observed in patients with active disease, both in CD and UC. Biologic treatment induced shifts in gut microbiota, with increased Firmicutes and decreased Bacteroidetes, as well as improved F/B ratio gradually after treatment, correlating with disease activity.
Conclusions
Our study suggested that gut microbiota differences changed after biologic therapies among IBD with different disease activity, and a rising Firmicutes/Bacteroidetes ratio could be a potential predictor for disease activity and treatment response monitoring.
背景:炎症性肠病(IBD),包括克罗恩病(CD)和溃疡性结肠炎(UC),是一种病因复杂的多因素疾病。据研究,肠道菌群失调在 IBD 发病机制和疾病活动中发挥着重要作用。我们的研究旨在分析不同严重程度的IBD患者的肠道微生物群组成,以及生物治疗对微生物群调节的影响:本研究共招募了 27 名 IBD 患者,包括 14 名因中重度疾病活动而接受生物治疗的患者和 13 名疾病不活跃的对照组患者。通过对粪便样本进行16 S核糖体RNA基因测序,确定肠道微生物组成:结果:48周后,生物疗法明显改善了IBD疾病的临床活动。在物种丰富度方面,活动性 CD 患者的群落α多样性明显较低,生物治疗后逐渐丰富。关于细菌群落组成差异的贝塔多样性显示,生物治疗组和对照组患者之间存在显著差异。在活动性疾病患者中,无论是 CD 还是 UC,都观察到了固醇菌的减少和类杆菌的增加。生物制剂治疗诱导肠道微生物群发生变化,固缩菌增加,类杆菌减少,治疗后F/B比值逐渐改善,这与疾病活动相关:我们的研究表明,不同疾病活动性的 IBD 患者在接受生物制剂治疗后肠道微生物群的差异发生了变化,而固缩菌/类杆菌比值的升高可作为疾病活动性和治疗反应监测的潜在预测指标。
{"title":"Alternations of the gut microbiota and the Firmicutes/Bacteroidetes ratio after biologic treatment in inflammatory bowel disease","authors":"Yu-Chieh Tsai , Wei-Chen Tai , Chih-Ming Liang , Cheng-Kun Wu , Ming-Chao Tsai , Wan-Hsiang Hu , Pao-Yuan Huang , Chien-Hung Chen , Yuan-Hung Kuo , Chih-Chien Yao , Seng-Kee Chuah","doi":"10.1016/j.jmii.2024.09.006","DOIUrl":"10.1016/j.jmii.2024.09.006","url":null,"abstract":"<div><h3>Background</h3><div>The inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC) is a complex disease with multifactorial etiology. The intestinal dysbiosis have been investigated to play an important role in IBD pathogenesis and disease activity. The aim of our study was to analyze the intestinal microbiota composition in IBD across different severity levels and the impact of biologic therapy on microbiota modulation.</div></div><div><h3>Methods</h3><div>In this study, 27 IBD patients were recruited, including 14 patients undergoing biologic therapy for moderate to severe disease activity and 13 controls with inactive disease. The gut microbial composition was determined by 16 S ribosomal RNA gene sequencing of stool samples.</div></div><div><h3>Results</h3><div>Biologic therapy led to significant clinical improvement in IBD disease activity after 48 weeks. About species richness, community alpha diversity was significant lower in active CD patients and enriched gradually after biologic therapy. The beta-diversity regard to the difference of bacterial community composition showed significant difference between patients in biologic and control group. A decrease in <em>Firmicutes</em> and increase in <em>Bacteroidetes</em> abundance were observed in patients with active disease, both in CD and UC. Biologic treatment induced shifts in gut microbiota, with increased <em>Firmicutes</em> and decreased <em>Bacteroidetes</em>, as well as improved F/B ratio gradually after treatment, correlating with disease activity.</div></div><div><h3>Conclusions</h3><div>Our study suggested that gut microbiota differences changed after biologic therapies among IBD with different disease activity, and a rising Firmicutes/Bacteroidetes ratio could be a potential predictor for disease activity and treatment response monitoring.</div></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"58 1","pages":"Pages 62-69"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.jmii.2024.12.010
Ping-Ing Lee , Yhu-Chering Huang , Ching-Chuan Liu , Shee-Uan Chen , Po-Ren Hsueh , Shih-Chi Ku , Po-Yen Chen , Chih-Jung Chen , Yi-Tsung Lin , Chun-Yi Lu , Nan-Chang Chiu , Hsin Chi , Yee-Chun Chen , Feng-Yee Chang , Muh-Yong Yen , Chin-Te Lu , Kuang-Yao Yang , Cheng-Hsun Chiu , Kao-Pin Hwang , Wen-Sen Lee , Tzou-Yien Lin
Respiratory syncytial virus (RSV) is the most common pathogen for young children hospitalized with bronchiolitis and pneumonia. Most infections occur below 1 year of age. RSV is also a significant viral pathogen for adults with respiratory tract infection.
Vaccines targeting the pre-fusion protein of RSV, including recombinant and mRNA vaccines, are now available. A committee of experts from related fields was convened by the Taiwan Immunization Vision and Strategy to develop recommendations for RSV vaccination in the elderly and pregnant women.
The recommendation is not intended as a sole source of guidance in the prevention of RSV infection in children. The provisions listed in this recommendation are comprehensive suggestions made by experts in Taiwan based on existing medical evidence. This recommendation should be subject to modification in light of additional medical research findings in the future, and these provisions should not be cited as a basis for dispute resolution.
{"title":"Recommendation for the use of respiratory syncytial virus vaccines","authors":"Ping-Ing Lee , Yhu-Chering Huang , Ching-Chuan Liu , Shee-Uan Chen , Po-Ren Hsueh , Shih-Chi Ku , Po-Yen Chen , Chih-Jung Chen , Yi-Tsung Lin , Chun-Yi Lu , Nan-Chang Chiu , Hsin Chi , Yee-Chun Chen , Feng-Yee Chang , Muh-Yong Yen , Chin-Te Lu , Kuang-Yao Yang , Cheng-Hsun Chiu , Kao-Pin Hwang , Wen-Sen Lee , Tzou-Yien Lin","doi":"10.1016/j.jmii.2024.12.010","DOIUrl":"10.1016/j.jmii.2024.12.010","url":null,"abstract":"<div><div>Respiratory syncytial virus (RSV) is the most common pathogen for young children hospitalized with bronchiolitis and pneumonia. Most infections occur below 1 year of age. RSV is also a significant viral pathogen for adults with respiratory tract infection.</div><div>Vaccines targeting the pre-fusion protein of RSV, including recombinant and mRNA vaccines, are now available. A committee of experts from related fields was convened by the Taiwan Immunization Vision and Strategy to develop recommendations for RSV vaccination in the elderly and pregnant women.</div><div>The recommendation is not intended as a sole source of guidance in the prevention of RSV infection in children. The provisions listed in this recommendation are comprehensive suggestions made by experts in Taiwan based on existing medical evidence. This recommendation should be subject to modification in light of additional medical research findings in the future, and these provisions should not be cited as a basis for dispute resolution.</div></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"58 1","pages":"Pages 1-6"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.jmii.2024.11.011
Ting-Yu Yen , Ching Hsu , Ni-Chung Lee , Chao-Szu Wu , Hsin Wang , Kuan-Yi Lee , Chia-Ray Lin , Chun-Yi Lu , Mo-Li Tsai , Tzu-Yu Liu , Che Lin , Chien-Yu Chen , Luan-Yin Chang , Feipei Lai , Li-Min Huang
Background
Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.
Methods
We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).
Results
Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.
Conclusion
This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.
{"title":"Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing","authors":"Ting-Yu Yen , Ching Hsu , Ni-Chung Lee , Chao-Szu Wu , Hsin Wang , Kuan-Yi Lee , Chia-Ray Lin , Chun-Yi Lu , Mo-Li Tsai , Tzu-Yu Liu , Che Lin , Chien-Yu Chen , Luan-Yin Chang , Feipei Lai , Li-Min Huang","doi":"10.1016/j.jmii.2024.11.011","DOIUrl":"10.1016/j.jmii.2024.11.011","url":null,"abstract":"<div><h3>Background</h3><div>Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.</div></div><div><h3>Methods</h3><div>We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).</div></div><div><h3>Results</h3><div>Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that <em>Haemophilus influenzae</em> was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. <em>Rothia mucilaginosa, Dolosigranulum pigrum,</em> and <em>Prevotella melaninogenica</em> tended to be present in less severe community-acquired pneumonia group.</div></div><div><h3>Conclusion</h3><div>This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.</div></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"58 1","pages":"Pages 86-93"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}