Pub Date : 2025-12-01DOI: 10.1016/j.ijmm.2025.151691
Nicolas Heyer , Tobias Grebe , Andreas Schlattmann , Ahmed Mostafa Abdrabou , Jonel Trebicka , Frieder Schaumburg
Clostridioides difficile infection (CDI) is mediated by the cytotoxins TcdA and/or TcdB. The reliable detection of these toxins using enzyme immunoassays (EIA) could be affected by toxin stability. We assessed the toxin stability in stool samples spiked with TcdA or TcdB and in stool samples from CDI patients under transport conditions. In the spiked samples, the concentration of TcdB decreased faster than TcdA within 72 h. In contrast, toxin levels in stool samples from CDI patients remained stable within 24 h, while viable C. difficile slightly increased. In conclusion, toxin instability did not affect C. difficile toxin detection in our study.
{"title":"Stability of Clostridioides difficile toxins in stool samples","authors":"Nicolas Heyer , Tobias Grebe , Andreas Schlattmann , Ahmed Mostafa Abdrabou , Jonel Trebicka , Frieder Schaumburg","doi":"10.1016/j.ijmm.2025.151691","DOIUrl":"10.1016/j.ijmm.2025.151691","url":null,"abstract":"<div><div><em>Clostridioides difficile</em> infection (CDI) is mediated by the cytotoxins TcdA and/or TcdB. The reliable detection of these toxins using enzyme immunoassays (EIA) could be affected by toxin stability. We assessed the toxin stability in stool samples spiked with TcdA or TcdB and in stool samples from CDI patients under transport conditions. In the spiked samples, the concentration of TcdB decreased faster than TcdA within 72 h. In contrast, toxin levels in stool samples from CDI patients remained stable within 24 h, while viable <em>C. difficile</em> slightly increased. In conclusion, toxin instability did not affect <em>C. difficile</em> toxin detection in our study.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151691"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.ijmm.2025.151687
Yutong Liu , Lin Wan , Xiong Li , Yingshun Zhou , Renjing Hu
<div><h3>Objective</h3><div>KL57 <em>Klebsiella pneumoniae</em> (<em>K. pneumoniae</em>) is an emerging serotype with epidemiological characteristics and pathogenic mechanisms that remain incompletely understood. This study comprehensively analyzed the genomic features of KL57 <em>K. pneumoniae</em> strains isolated in Wuxi from 2016 to 2023, and investigated the global molecular epidemiology and population dynamics of KL57 <em>K. pneumoniae</em>.</div></div><div><h3>Methods</h3><div>From January 2016 to December 2023, 17 KL57 <em>K. pneumoniae</em> isolates were collected from various clinical specimens at the Wuxi No.2 People's Hospital, Jiangsu Province, China. Antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and bioinformatics analysis including evaluation of virulence genes, resistance genes, and plasmid replicon types were performed on these strains. To elucidate the genetic relationships and global distribution of the KL57 <em>K. pneumoniae</em>, phylogenetic trees were constructed through comparative analyses of our KL57 strains alongside those obtained from public databases. Additionally, the distribution patterns of serotypes and carbapenemase genes among these strains were examined.</div></div><div><h3>Results</h3><div>Seventeen KL57 <em>K. pneumoniae</em> strains were categorized into four distinct sequence types (STs), with ST412 being the most prevalent in Wuxi, and ST2846, which was identified for the first time. Analysis of virulence genes indicated KL57 <em>K. pneumoniae</em> isolates often express multiple virulence factors. Antimicrobial resistance profiling revealed that only one ST218 isolate contained the <em>bla</em><sub>KPC-2</sub> gene, which was located on an IncFII<sub>K34</sub> plasmid. Geographically, ST412, ST218, and ST592 were the main predominant epidemic sequence types of the KL57 <em>K. pneumoniae</em>. A global analysis indicated that KL57 carbapenem-resistant <em>K. pneumoniae</em> (CRKp) strains predominantly harbored the <em>bla</em><sub>NDM-1</sub>, <em>bla</em><sub>OXA-48</sub>, <em>bla</em><sub>KPC-2</sub>, and <em>bla</em><sub>OXA-181</sub> genes. Furthermore, phylogenetic analysis demonstrated significant diversity in the sequence types of KL57 <em>K. pneumoniae</em> strains across continents, with notable variations even between countries.</div></div><div><h3>Conclusion</h3><div>Our study corroborates the widespread occurrence of the ST412 KL57 <em>K. pneumoniae</em> in China and identifies a specific strain harboring the IncFII<sub>K34</sub> resistance plasmid. Additionally, the KL57 CRKp strain carries a variety of carbapenemase genes, and some of these strains simultaneously harbor multiple such genes. Our findings suggest that this subtype demonstrates enhanced resistance adaptability and may facilitate the dissemination of drug resistance through horizontal gene transfer. Consequently, it is necessary to develop more targeted surveillance strategies that focus on resistan
{"title":"Emergence of KL57 hypervirulent Klebsiella pneumoniae in Wuxi, China: Genomic insights into virulence plasmid evolution and blaKPC-2-bearing IncFIIK34 plasmid transmission","authors":"Yutong Liu , Lin Wan , Xiong Li , Yingshun Zhou , Renjing Hu","doi":"10.1016/j.ijmm.2025.151687","DOIUrl":"10.1016/j.ijmm.2025.151687","url":null,"abstract":"<div><h3>Objective</h3><div>KL57 <em>Klebsiella pneumoniae</em> (<em>K. pneumoniae</em>) is an emerging serotype with epidemiological characteristics and pathogenic mechanisms that remain incompletely understood. This study comprehensively analyzed the genomic features of KL57 <em>K. pneumoniae</em> strains isolated in Wuxi from 2016 to 2023, and investigated the global molecular epidemiology and population dynamics of KL57 <em>K. pneumoniae</em>.</div></div><div><h3>Methods</h3><div>From January 2016 to December 2023, 17 KL57 <em>K. pneumoniae</em> isolates were collected from various clinical specimens at the Wuxi No.2 People's Hospital, Jiangsu Province, China. Antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and bioinformatics analysis including evaluation of virulence genes, resistance genes, and plasmid replicon types were performed on these strains. To elucidate the genetic relationships and global distribution of the KL57 <em>K. pneumoniae</em>, phylogenetic trees were constructed through comparative analyses of our KL57 strains alongside those obtained from public databases. Additionally, the distribution patterns of serotypes and carbapenemase genes among these strains were examined.</div></div><div><h3>Results</h3><div>Seventeen KL57 <em>K. pneumoniae</em> strains were categorized into four distinct sequence types (STs), with ST412 being the most prevalent in Wuxi, and ST2846, which was identified for the first time. Analysis of virulence genes indicated KL57 <em>K. pneumoniae</em> isolates often express multiple virulence factors. Antimicrobial resistance profiling revealed that only one ST218 isolate contained the <em>bla</em><sub>KPC-2</sub> gene, which was located on an IncFII<sub>K34</sub> plasmid. Geographically, ST412, ST218, and ST592 were the main predominant epidemic sequence types of the KL57 <em>K. pneumoniae</em>. A global analysis indicated that KL57 carbapenem-resistant <em>K. pneumoniae</em> (CRKp) strains predominantly harbored the <em>bla</em><sub>NDM-1</sub>, <em>bla</em><sub>OXA-48</sub>, <em>bla</em><sub>KPC-2</sub>, and <em>bla</em><sub>OXA-181</sub> genes. Furthermore, phylogenetic analysis demonstrated significant diversity in the sequence types of KL57 <em>K. pneumoniae</em> strains across continents, with notable variations even between countries.</div></div><div><h3>Conclusion</h3><div>Our study corroborates the widespread occurrence of the ST412 KL57 <em>K. pneumoniae</em> in China and identifies a specific strain harboring the IncFII<sub>K34</sub> resistance plasmid. Additionally, the KL57 CRKp strain carries a variety of carbapenemase genes, and some of these strains simultaneously harbor multiple such genes. Our findings suggest that this subtype demonstrates enhanced resistance adaptability and may facilitate the dissemination of drug resistance through horizontal gene transfer. Consequently, it is necessary to develop more targeted surveillance strategies that focus on resistan","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151687"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-13DOI: 10.1016/j.ijmm.2025.151684
Muhammad Tahir Khan , Chendi Zhu , Arwa Omar Al Khatib , Dalal Sulaiman Alshaya , Ahmed A. Al-Qahtani , Irfan Ahmad , Taane G. Clark
Introduction
Understanding the distribution and prevalence of different M. tuberculosis lineages can help public health authorities and researchers track the spread of tuberculosis (TB). Some lineages are thought to be more virulent, transmissible, and prone to drug resistance. Here, we sought to find the major lineages and sublineages of M. tuberculosis circulating in Pakistan. Methods: A total of 396 whole-genome sequencing datasets were retrieved from NCBI and TB research centers. Results: In the current study, only four lineages and 21 sublineages have been detected in 396 genomic isolates in which lineages 3 (n = 274/396, 69.19 %) was the predominant, followed by lineage 4 (77/396, 19.4 %), lineage 2 (31/396, 7.8 %), and lineage 1 (14/396, 3.5 %). Lineage 3 was the most common, in which sublineage 3.1.1 (n = 254/274, 93.79 %) was dominant, followed by sublineage 3.1.2.1 (n = 11/274, 4 %) and 3.1.2 (n = 8/274, 2.9 %). 8 sublineages are likely reported for the first time in Pakistan based on current genomic surveillance including sublineage 3.1.2.1 (n = 11/274, 4 %). There were 14 sublineages in lineage 4, of which sublineage L4.5 (23/77, 29.8 %) was the most common, followed by sublineage 4.9 (22/77, 28.5 %). Conclusion: Collectively, these observations highlight Lineage 3’s ability to acquire first-line drug resistance continued transmission. Its predominance in the current study highlights the urgent need for lineage-specific diagnostics, enhanced drug susceptibility testing and tailored therapeutic regimens. The detection of diverse Mtb sublineages, including L3.1.2.1 and various sublineages of L4 (e.g., 4.1.1.1, 4.1.2.1, 4.3.4.2, and 4.6.2.2), signifies advancement in understanding the genetic landscape of TB in the region.
{"title":"Emergence of novel sublineages of Mycobacterium tuberculosis in Pakistan","authors":"Muhammad Tahir Khan , Chendi Zhu , Arwa Omar Al Khatib , Dalal Sulaiman Alshaya , Ahmed A. Al-Qahtani , Irfan Ahmad , Taane G. Clark","doi":"10.1016/j.ijmm.2025.151684","DOIUrl":"10.1016/j.ijmm.2025.151684","url":null,"abstract":"<div><h3>Introduction</h3><div>Understanding the distribution and prevalence of different <em>M. tuberculosis</em> lineages can help public health authorities and researchers track the spread of tuberculosis (TB). Some lineages are thought to be more virulent, transmissible, and prone to drug resistance. Here, we sought to find the major lineages and sublineages of <em>M. tuberculosis</em> circulating in Pakistan. Methods: A total of 396 whole-genome sequencing datasets were retrieved from NCBI and TB research centers. Results: In the current study, only four lineages and 21 sublineages have been detected in 396 genomic isolates in which lineages 3 (n = 274/396, 69.19 %) was the predominant, followed by lineage 4 (77/396, 19.4 %), lineage 2 (31/396, 7.8 %), and lineage 1 (14/396, 3.5 %). Lineage 3 was the most common, in which sublineage 3.1.1 (n = 254/274, 93.79 %) was dominant, followed by sublineage 3.1.2.1 (n = 11/274, 4 %) and 3.1.2 (n = 8/274, 2.9 %). 8 sublineages are likely reported for the first time in Pakistan based on current genomic surveillance including sublineage 3.1.2.1 (n = 11/274, 4 %). There were 14 sublineages in lineage 4, of which sublineage L4.5 (23/77, 29.8 %) was the most common, followed by sublineage 4.9 (22/77, 28.5 %). Conclusion: Collectively, these observations highlight Lineage 3’s ability to acquire first-line drug resistance continued transmission. Its predominance in the current study highlights the urgent need for lineage-specific diagnostics, enhanced drug susceptibility testing and tailored therapeutic regimens. The detection of diverse Mtb sublineages, including L3.1.2.1 and various sublineages of L4 (e.g., 4.1.1.1, 4.1.2.1, 4.3.4.2, and 4.6.2.2), signifies advancement in understanding the genetic landscape of TB in the region.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151684"},"PeriodicalIF":3.6,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145551654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-11DOI: 10.1016/j.ijmm.2025.151683
Christian W. Böing , Julia S. Schneider , Neele J. Froböse , Annette Jurke , Stefanie Kampmeier , Alexander Mellmann
Introduction
Vancomycin-resistant Enterococcus faecium (VREfm) are multidrug-resistant pathogens that cause severe nosocomial infections. The knowledge of virulence profiles of VREfm for the development of invasive infections is still limited. The aim of this study was to analyse gene profiles and genetic variants of VREfm and their association with the development of VREfm bloodstream infections (VRE-BSI).
Methods
One-hundred twenty randomly selected VRE-BSI isolates from a state-wide surveillance study in the German state of North Rhine-Westphalia were included in the analysis and matched with one-hundred twenty VREfm colonization (VRE-COL) isolates from a tertiary hospital in North Rhine-Westphalia. All isolates were subjected to whole genome sequencing (WGS) and analysed for the presence or absence of known or putative virulence genes of E. faecium. A genome-wide association study (GWAS) approach was conducted to identify potential associations of genes and genetic variants with the development of VRE-BSI.
Results
The multilocus sequence typing (MLST) sequence types (ST) ST80 and ST117 were the most prevalent STs among VRE-BSI and VRE-COL isolates (ST80: 133 [55 %]; ST117: 98 [41 %]). ST80 was significantly more prevalent in VRE-BSI isolates compared to VRE-COL isolates (75 [63 %] vs. 58 [48 %], p = 0.027). Only fms21 (pilA), a gene of pili gene cluster 1 (PCG-1), coding for a cell-wall-anchored protein involved in adhesive processes, was significantly more prevalent in the VRE-BSI group. GWAS identified no associations of genes or variants with VRE-BSI.
Conclusion
Using comparative genomics and GWAS, we could not identify a distinct virulence profile for the development of VRE-BSI.
{"title":"Virulome and genome-wide association study of vancomycin-resistant Enterococcus faecium from bloodstream infections versus colonization isolates","authors":"Christian W. Böing , Julia S. Schneider , Neele J. Froböse , Annette Jurke , Stefanie Kampmeier , Alexander Mellmann","doi":"10.1016/j.ijmm.2025.151683","DOIUrl":"10.1016/j.ijmm.2025.151683","url":null,"abstract":"<div><h3>Introduction</h3><div>Vancomycin-resistant <em>Enterococcus faecium</em> (VREfm) are multidrug-resistant pathogens that cause severe nosocomial infections. The knowledge of virulence profiles of VREfm for the development of invasive infections is still limited. The aim of this study was to analyse gene profiles and genetic variants of VREfm and their association with the development of VREfm bloodstream infections (VRE-BSI).</div></div><div><h3>Methods</h3><div>One-hundred twenty randomly selected VRE-BSI isolates from a state-wide surveillance study in the German state of North Rhine-Westphalia were included in the analysis and matched with one-hundred twenty VREfm colonization (VRE-COL) isolates from a tertiary hospital in North Rhine-Westphalia. All isolates were subjected to whole genome sequencing (WGS) and analysed for the presence or absence of known or putative virulence genes of <em>E. faecium</em>. A genome-wide association study (GWAS) approach was conducted to identify potential associations of genes and genetic variants with the development of VRE-BSI.</div></div><div><h3>Results</h3><div>The multilocus sequence typing (MLST) sequence types (ST) ST80 and ST117 were the most prevalent STs among VRE-BSI and VRE-COL isolates (ST80: 133 [55 %]; ST117: 98 [41 %]). ST80 was significantly more prevalent in VRE-BSI isolates compared to VRE-COL isolates (75 [63 %] vs. 58 [48 %], p = 0.027). Only <em>fms21</em> (<em>pilA</em>), a gene of pili gene cluster 1 (PCG-1), coding for a cell-wall-anchored protein involved in adhesive processes, was significantly more prevalent in the VRE-BSI group. GWAS identified no associations of genes or variants with VRE-BSI.</div></div><div><h3>Conclusion</h3><div>Using comparative genomics and GWAS, we could not identify a distinct virulence profile for the development of VRE-BSI.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151683"},"PeriodicalIF":3.6,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145558397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In 2017, a large outbreak of Legionnaires' disease, involving 58 patients, occurred in a public bath facility in Hiroshima Prefecture, Japan. We analyzed 94 Legionella pneumophila strains isolated from patients and the public bath facility using molecular typing methods, including Pulsed-Field Gel Electrophoresis, sequence-based typing, multi-locus variable number tandem repeat analysis, and Whole-Genome Sequencing (WGS). Genotypes obtained using these molecular epidemiological typing methods were highly correlated with each other. L. pneumophila strains of various genotypes were isolated from the public bath facility, of which only ST2398 and ST2399 were isolated from patients. ST2398 and ST2399, isolated from patients, bath water, and swabs, derived from one common circulating system at the bath facility out of seven were found to be novel genotypes and a highly clonal genetic lineage by single nucleotide variant (SNV) analysis based on WGS. The result of haplotype network analysis based on SNVs showed that ST2398 and ST2399 differed only approximately 30–42 SNVs, and some environmental strains that differed by only 0–3 SNVs from patient strains were isolated. These results demonstrated that this outbreak was caused by L. pneumophila assigned to the ST2398 and ST2399 clades. We found that at least three patients were co-infected with different clusters of L. pneumophila serogroup 1. Our results show that several strains must be isolated from a single sample to consider the accumulation of mutations in water and co-infection when investigating outbreaks.
{"title":"A large outbreak investigation of Legionnaires’ disease associated with a public bath facility in Hiroshima, Japan, using PFGE, SBT, MLVA, and whole-genome sequencing","authors":"Takahiro Hiratsuka , Noriko Nakanishi , Hiroko Akita , Kanako Masuda , Shoko Komatsu , Ryohei Nomoto , Junko Amemura-Maekawa","doi":"10.1016/j.ijmm.2025.151680","DOIUrl":"10.1016/j.ijmm.2025.151680","url":null,"abstract":"<div><div>In 2017, a large outbreak of Legionnaires' disease, involving 58 patients, occurred in a public bath facility in Hiroshima Prefecture, Japan. We analyzed 94 <em>Legionella pneumophila</em> strains isolated from patients and the public bath facility using molecular typing methods, including Pulsed-Field Gel Electrophoresis, sequence-based typing, multi-locus variable number tandem repeat analysis, and Whole-Genome Sequencing (WGS). Genotypes obtained using these molecular epidemiological typing methods were highly correlated with each other. <em>L. pneumophila</em> strains of various genotypes were isolated from the public bath facility, of which only ST2398 and ST2399 were isolated from patients. ST2398 and ST2399, isolated from patients, bath water, and swabs, derived from one common circulating system at the bath facility out of seven were found to be novel genotypes and a highly clonal genetic lineage by single nucleotide variant (SNV) analysis based on WGS. The result of haplotype network analysis based on SNVs showed that ST2398 and ST2399 differed only approximately 30–42 SNVs, and some environmental strains that differed by only 0–3 SNVs from patient strains were isolated. These results demonstrated that this outbreak was caused by <em>L. pneumophila</em> assigned to the ST2398 and ST2399 clades. We found that at least three patients were co-infected with different clusters of <em>L. pneumophila</em> serogroup 1. Our results show that several strains must be isolated from a single sample to consider the accumulation of mutations in water and co-infection when investigating outbreaks.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151680"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-28DOI: 10.1016/j.ijmm.2025.151682
Yong-An Shi , Hang Kim Nguyen , Pei-Jane Tsai , Cheng-Hsun Chiu , Chuan Chiang-Ni
Group A Streptococcus (GAS) isolates with spontaneous mutations in covR and covS are frequently identified in patients with necrotizing fasciitis and toxic shock syndrome. CovR/CovS is a two-component regulator system, and the phosphorylation of CovR is solely modulated by CovS. Nonetheless, the phenotype of the ∆covS mutant and the ∆covR mutant is not entirely identical. It has been shown that the expression of SpeB protease is only detected in the ∆covR mutant, and the ∆covR mutant causes more severe local lesions than the ∆covS mutant in the mouse infection model. SpeB-mediated gasdermin A cleavage triggers keratinocyte death, resulting in sizeable lesion size but preventing invasive skin infection by GAS. This study, therefore, elucidated whether SpeB is a key factor related to trigger keratinocyte death after the ∆covR mutant infection. Although the ∆covR mutant caused more keratinocyte deaths than the ∆covS mutant, this difference was not contributed by SpeB but mediated by streptolysin S (SLS). Moreover, SLS in the ∆covR mutant contributed to increased macrophage cell death and elevated IL-1β levels. Similar to the SpeB expression profile, SLS was upregulated in the ∆covR mutant but repressed in the ∆covS mutant. In a mouse subcutaneous infection model, the SLS-deficient ∆covR mutant exhibited reduced lesion size and mortality compared to the ∆covR mutant, suggesting that SLS repression does not contribute to GAS immune evasion or invasive skin infection. This finding may help explain the differential presentations after ∆covR mutant and ∆covS mutant infection and why clinical GAS isolates more frequently harbor spontaneous mutations in covS rather than in covR.
{"title":"Differential expression profile of streptolysin S in the covR and covS mutants of group A Streptococcus is a mediator of keratinocyte death and aggressive local infection","authors":"Yong-An Shi , Hang Kim Nguyen , Pei-Jane Tsai , Cheng-Hsun Chiu , Chuan Chiang-Ni","doi":"10.1016/j.ijmm.2025.151682","DOIUrl":"10.1016/j.ijmm.2025.151682","url":null,"abstract":"<div><div>Group A <em>Streptococcus</em> (GAS) isolates with spontaneous mutations in <em>covR</em> and <em>covS</em> are frequently identified in patients with necrotizing fasciitis and toxic shock syndrome. CovR/CovS is a two-component regulator system, and the phosphorylation of CovR is solely modulated by CovS. Nonetheless, the phenotype of the ∆<em>covS</em> mutant and the ∆<em>covR</em> mutant is not entirely identical. It has been shown that the expression of SpeB protease is only detected in the ∆<em>covR</em> mutant, and the ∆<em>covR</em> mutant causes more severe local lesions than the ∆<em>covS</em> mutant in the mouse infection model. SpeB-mediated gasdermin A cleavage triggers keratinocyte death, resulting in sizeable lesion size but preventing invasive skin infection by GAS. This study, therefore, elucidated whether SpeB is a key factor related to trigger keratinocyte death after the ∆<em>covR</em> mutant infection. Although the ∆<em>covR</em> mutant caused more keratinocyte deaths than the ∆<em>covS</em> mutant, this difference was not contributed by SpeB but mediated by streptolysin S (SLS). Moreover, SLS in the ∆<em>covR</em> mutant contributed to increased macrophage cell death and elevated IL-1β levels. Similar to the SpeB expression profile, SLS was upregulated in the ∆<em>covR</em> mutant but repressed in the ∆<em>covS</em> mutant. In a mouse subcutaneous infection model, the SLS-deficient ∆<em>covR</em> mutant exhibited reduced lesion size and mortality compared to the ∆<em>covR</em> mutant, suggesting that SLS repression does not contribute to GAS immune evasion or invasive skin infection. This finding may help explain the differential presentations after ∆<em>covR</em> mutant and ∆<em>covS</em> mutant infection and why clinical GAS isolates more frequently harbor spontaneous mutations in <em>covS</em> rather than in <em>covR</em>.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151682"},"PeriodicalIF":3.6,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145424653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-26DOI: 10.1016/j.ijmm.2025.151681
Francesca McDonagh , Aneta Kovarova , Anna Tumeo , Andy O’Connor , Niamh McEvoy , Aneesa Mangalam Lonappan , Kasthuri Venkateswaran , Elaine K. Murray , Brian Hallahan , Georgios Miliotis
Objectives
This study aims to generate the first complete genome of Pantoea septica and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of P. septica, clarifying features relevant to opportunistic infection in vulnerable cohorts.
Methods
P. septica GABEPS69 was an opportunistic coloniser isolated from the saliva of a patient prescribed the antipsychotic clozapine, leading to a dysbiotic oral microbiome. A hybrid sequencing approach yielded a closed genome comprising a 4.1 Mb chromosome and six plasmids. Phenotypic susceptibility was determined by disk-diffusion and minimum inhibitory concentration (MIC) assays. Its chromosomal and plasmidic content was bioinformatically analysed alongside all canonical GenBank available P. septica genomes and the type strains of taxonomic neighbours Pantoea piersonii and "Pantoea latae", with focus on virulence-factors (VFs), antimicrobial-resistance-genes (ARGs), metal-resistance-genes (MRGs) and biosynthetic gene clusters.
Results
GABEPS69 exhibited a narrow resistance spectrum, displaying resistance to the third-generation cephalosporin cefpodoxime. Plasmid pGABEPS69_1 harboured an aerobactin pathogenicity island homologue; a locus implicated in enhanced virulence, that was also identified across most other P. septica genomes and in the closely related human-pathogen Pantoea piersonii. A conserved chromosomal class-A β-lactamase homologue was also identified. Additionally, a universal presence of bioactive thiopeptide biosynthetic-gene-clusters was observed in P. septica genomes, suggesting a potential role in microbiome modulation.
Conclusion
This study presents a first complete genome of P. septica, revealing its genomic architecture, resistance, and virulence potential. Detailed plasmid analysis and comparative genomics enhance our understanding of the species clinical relevance and microbiome-modulating capacity. These findings motivate surveillance of transient oral microbiota in at-risk populations, including patients receiving clozapine.
{"title":"Complete genome and comparative genomic analysis of cefpodoxime resistant Pantoea septica strain GABEPS69 isolated from saliva of a patient diagnosed with treatment resistant schizophrenia","authors":"Francesca McDonagh , Aneta Kovarova , Anna Tumeo , Andy O’Connor , Niamh McEvoy , Aneesa Mangalam Lonappan , Kasthuri Venkateswaran , Elaine K. Murray , Brian Hallahan , Georgios Miliotis","doi":"10.1016/j.ijmm.2025.151681","DOIUrl":"10.1016/j.ijmm.2025.151681","url":null,"abstract":"<div><h3>Objectives</h3><div>This study aims to generate the first complete genome of <em>Pantoea septica</em> and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of <em>P. septica,</em> clarifying features relevant to opportunistic infection in vulnerable cohorts<em>.</em></div></div><div><h3>Methods</h3><div><em>P. septica</em> GABEPS69 was an opportunistic coloniser isolated from the saliva of a patient prescribed the antipsychotic clozapine, leading to a dysbiotic oral microbiome. A hybrid sequencing approach yielded a closed genome comprising a 4.1 Mb chromosome and six plasmids. Phenotypic susceptibility was determined by disk-diffusion and minimum inhibitory concentration (MIC) assays. Its chromosomal and plasmidic content was bioinformatically analysed alongside all canonical GenBank available <em>P. septica</em> genomes and the type strains of taxonomic neighbours <em>Pantoea piersonii</em> and \"<em>Pantoea latae</em>\", with focus on virulence-factors (VFs), antimicrobial-resistance-genes (ARGs), metal-resistance-genes (MRGs) and biosynthetic gene clusters.</div></div><div><h3>Results</h3><div>GABEPS69 exhibited a narrow resistance spectrum, displaying resistance to the third-generation cephalosporin cefpodoxime. Plasmid pGABEPS69_1 harboured an aerobactin pathogenicity island homologue; a locus implicated in enhanced virulence, that was also identified across most other <em>P. septica</em> genomes and in the closely related human-pathogen <em>Pantoea piersonii</em>. A conserved chromosomal class-A β-lactamase homologue was also identified. Additionally, a universal presence of bioactive thiopeptide biosynthetic-gene-clusters was observed in <em>P. septica</em> genomes, suggesting a potential role in microbiome modulation.</div></div><div><h3>Conclusion</h3><div>This study presents a first complete genome of <em>P. septica</em>, revealing its genomic architecture, resistance, and virulence potential. Detailed plasmid analysis and comparative genomics enhance our understanding of the species clinical relevance and microbiome-modulating capacity. These findings motivate surveillance of transient oral microbiota in at-risk populations, including patients receiving clozapine.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151681"},"PeriodicalIF":3.6,"publicationDate":"2025-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145453578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-15DOI: 10.1016/j.ijmm.2025.151679
Shereen O. Abd Algaffar , Annelies Verbon , Kimberly Eadie , Deborah Horst-Kreft , Sami A. Khalid , Wendy W.J. van de Sande
Mycetoma is a neglected tropical disease characterized by large tumorous lesions. It can be caused by fungi (eumycetoma) or bacteria (actinomycetoma). The hallmark of mycetoma is the formation of grains by the causative agent. Grains can only be formed in vivo; therefore, in vivo models are crucial to studying mycetoma. In vivo, grain models have been developed in the invertebrate Galleria mellonella for eumycetoma, but not for actinomycetoma. Here, we aimed to develop the first actinomycetoma grain model in G. mellonella larvae. Actinomadura madurae strains DSM43236 and DSM44005 were used to infect G. mellonella larvae. Larval survival was monitored over 10 days. Grain formation was studied histologically and compared to grains in human tissues. The efficacy of trimethoprim-sulfamethoxazole and amikacin, the current standard treatment for actinomycetoma, was determined. A. madurae infection decreased the survival of G. mellonella larvae in a concentration-dependent manner. Grains were formed within 24 h post-infection. After 72 h these grains became melanised. No significantly enhanced survival was noted with trimethoprim-sulfamethoxazole, amikacin, or a combination thereof. In this model, the melanised A. madurae grains did differ from human grains, most likely due to the immune system of G. mellonella. The lack of therapeutic efficacy could be caused by this melanin or the fact that A. madurae grains, in general, are less susceptible to these drugs. More research will be needed to address this question.
{"title":"The development of an Actinomadura madurae grain model in Galleria mellonella larvae","authors":"Shereen O. Abd Algaffar , Annelies Verbon , Kimberly Eadie , Deborah Horst-Kreft , Sami A. Khalid , Wendy W.J. van de Sande","doi":"10.1016/j.ijmm.2025.151679","DOIUrl":"10.1016/j.ijmm.2025.151679","url":null,"abstract":"<div><div>Mycetoma is a neglected tropical disease characterized by large tumorous lesions. It can be caused by fungi (eumycetoma) or bacteria (actinomycetoma). The hallmark of mycetoma is the formation of grains by the causative agent. Grains can only be formed <em>in vivo;</em> therefore, <em>in vivo</em> models are crucial to studying mycetoma<em>. In vivo,</em> grain models have been developed in the invertebrate <em>Galleria mellonella</em> for eumycetoma, but not for actinomycetoma. Here, we aimed to develop the first actinomycetoma grain model in <em>G. mellonella</em> larvae. <em>Actinomadura madurae</em> strains DSM43236 and DSM44005 were used to infect <em>G. mellonella</em> larvae. Larval survival was monitored over 10 days. Grain formation was studied histologically and compared to grains in human tissues. The efficacy of trimethoprim-sulfamethoxazole and amikacin, the current standard treatment for actinomycetoma, was determined. <em>A. madurae</em> infection decreased the survival of <em>G. mellonella</em> larvae in a concentration-dependent manner. Grains were formed within 24 h post-infection. After 72 h these grains became melanised. No significantly enhanced survival was noted with trimethoprim-sulfamethoxazole, amikacin, or a combination thereof. In this model, the melanised <em>A. madurae</em> grains did differ from human grains, most likely due to the immune system of <em>G. mellonella</em>. The lack of therapeutic efficacy could be caused by this melanin or the fact that <em>A. madurae</em> grains, in general, are less susceptible to these drugs. More research will be needed to address this question.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151679"},"PeriodicalIF":3.6,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.ijmm.2025.151676
Leonie H. Aldejohann , Joerg Steinmann , Tamara Ruegamer , Ronny Martin , Nadja Thielemann , Grit Walther , Oliver Kurzai , Alexander M. Aldejohann
Background
COVID-19-associated-pulmonary-aspergillosis (CAPA) is a severe superinfection mostly affecting critically ill COVID-19 patients. Early diagnosis and clinical management of CAPA remain major clinical challenges.
Here, we evaluated different approaches to classify culture-positive CAPA at its peak season, assessed incidence and mortality, identified risk factors and analysed clinical and laboratory CAPA-management of three German tertiary care hospitals.
Methods
A retrospective multi-center analysis was performed. Inclusion criteria were SARS-CoV-2-positivity, Aspergillus-culture-positivity of lower respiratory tract specimen and ARDS. Cases were primarily classified according to ECMM/ISHAM-criteria. Species-ID was confirmed by each center. Susceptibility was assessed by EUCAST-microdilution or VIPcheck-screening. Statistical analysis revealed mortality affecting factors.
Results
95 culture-positive CAPA cases were classified as possible (36/95) or probable (59/95) by ECMM/ISHAM; 54 probable cases matched 2 or 3 additional classifications. Incidence rates were higher in ICU (2020/21: 1.56 %/2.13 % non-ICU vs. 5.14 %/6.77 % ICU). A. fumigatus was the most abundant species (93 %; (88/95)). Most patients received steroids to treat COVID-19-ARDS and required respiratory support (steroids: 71 % (67/95); intubated patients 52 % (49/95); ECMO (48 % (46/95)). Retrospective evaluation showed adherence to ECMM/ISHAM antifungal therapy guideline in 71 % (67/95). Case fatality rate was 60 % (57/95). A significant association between GM indices > 3 in respiratory fluid or nicotine abuse (p = 0.035 FE, OR=0.252, 95 % CI=0.066–0.986) and mortality was observed in univariate analysis. Convalescent plasma therapy was significantly associated with mortality reduction in uni- and multivariate analysis (p = 0.020).
Conclusion
Our data reveal regional differences in prevalence, diagnosis, and treatment of culture-positive CAPA in Germany. We could identify new factors affecting survival or mortality.
{"title":"Culture-positive COVID-19-associated pulmonary aspergillosis (CAPA) in Germany","authors":"Leonie H. Aldejohann , Joerg Steinmann , Tamara Ruegamer , Ronny Martin , Nadja Thielemann , Grit Walther , Oliver Kurzai , Alexander M. Aldejohann","doi":"10.1016/j.ijmm.2025.151676","DOIUrl":"10.1016/j.ijmm.2025.151676","url":null,"abstract":"<div><h3>Background</h3><div>COVID-19-associated-pulmonary-aspergillosis (CAPA) is a severe superinfection mostly affecting critically ill COVID-19 patients. Early diagnosis and clinical management of CAPA remain major clinical challenges.</div><div>Here, we evaluated different approaches to classify culture-positive CAPA at its peak season, assessed incidence and mortality, identified risk factors and analysed clinical and laboratory CAPA-management of three German tertiary care hospitals.</div></div><div><h3>Methods</h3><div>A retrospective multi-center analysis was performed. Inclusion criteria were SARS-CoV-2-positivity, <em>Aspergillus</em>-culture-positivity of lower respiratory tract specimen and ARDS. Cases were primarily classified according to ECMM/ISHAM-criteria. Species-ID was confirmed by each center. Susceptibility was assessed by EUCAST-microdilution or VIPcheck-screening. Statistical analysis revealed mortality affecting factors.</div></div><div><h3>Results</h3><div>95 culture-positive CAPA cases were classified as possible (36/95) or probable (59/95) by ECMM/ISHAM; 54 probable cases matched 2 or 3 additional classifications. Incidence rates were higher in ICU (2020/21: 1.56 %/2.13 % non-ICU vs. 5.14 %/6.77 % ICU). <em>A. fumigatus</em> was the most abundant species (93 %; (88/95)). Most patients received steroids to treat COVID-19-ARDS and required respiratory support (steroids: 71 % (67/95); intubated patients 52 % (49/95); ECMO (48 % (46/95)). Retrospective evaluation showed adherence to ECMM/ISHAM antifungal therapy guideline in 71 % (67/95). Case fatality rate was 60 % (57/95). A significant association between GM indices > 3 in respiratory fluid or nicotine abuse (p = 0.035 FE, OR=0.252, 95 % CI=0.066–0.986) and mortality was observed in univariate analysis. Convalescent plasma therapy was significantly associated with mortality reduction in uni- and multivariate analysis (p = 0.020).</div></div><div><h3>Conclusion</h3><div>Our data reveal regional differences in prevalence, diagnosis, and treatment of culture-positive CAPA in Germany. We could identify new factors affecting survival or mortality.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151676"},"PeriodicalIF":3.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-21DOI: 10.1016/j.ijmm.2025.151675
Deng Hui , Zhu Bin , Zhang Shiyu , Zhang Bin , Dilihumar Zaire , Gao Ruihan , Liu Shuting , Zhou Xin , Zhou Shunchang , Xiong Jian , Yang Xuecheng , Feng Xuemei , Lu Yinping , Zheng Xin , Wang Baoju
Hepatitis B virus (HBV) infection seems to be related to gut microbiota. This study aims to explore the effects of HBV infection on gut microbiota and possible immunological mechanisms using the Chinese woodchuck model. Nine adult woodchucks were randomly divided into Cyclosporine A (CsA) or Control group. Animals were orally treated with CsA and saline for 2 weeks before WHV inoculation, and continued until 8 weeks after that. Blood CsA concentrations were tested at 2 weeks after administration and before discontinuation. Quantitative PCR was used to detect serum WHV DNA. Flow cytometry was used to detect T cell immune response. Feces were collected for 16S rRNA sequencing. The result shows CsA oral administration can reach effective blood drug concentration in woodchucks and successfully prolong WHV replication. After 2 weeks of oral treatment, there was no significant difference in the gut microbiota between the two groups. At the clearance period of serum WHV, the relative abundance of Prevotella and Prevotella genera in the phylum Bacteroidetes significantly increased, while the relative abundance of Firmicutes significantly decreased. Meanwhile, the CD107a degranulation of CD4-T cells in peripheral blood showed a decreasing trend, while there was no significant difference in the frequency of PD-1+ CD4-T cells. In Conclusion, oral administration of CsA can significantly prolong the replication time of WHV in Chinese woodchucks. The gut microbiota of Chinese woodchuck undergoes significant changes during serum WHV clearance, which implies the Chinese woodchuck model can be used to study the interaction between HBV infection and gut microbiota.
{"title":"The impact of HBV infection on gut microbiota using Chinese woodchuck model with woodchuck hepatitis virus (WHV) infection","authors":"Deng Hui , Zhu Bin , Zhang Shiyu , Zhang Bin , Dilihumar Zaire , Gao Ruihan , Liu Shuting , Zhou Xin , Zhou Shunchang , Xiong Jian , Yang Xuecheng , Feng Xuemei , Lu Yinping , Zheng Xin , Wang Baoju","doi":"10.1016/j.ijmm.2025.151675","DOIUrl":"10.1016/j.ijmm.2025.151675","url":null,"abstract":"<div><div>Hepatitis B virus (HBV) infection seems to be related to gut microbiota. This study aims to explore the effects of HBV infection on gut microbiota and possible immunological mechanisms using the Chinese woodchuck model. Nine adult woodchucks were randomly divided into Cyclosporine A (CsA) or Control group. Animals were orally treated with CsA and saline for 2 weeks before WHV inoculation, and continued until 8 weeks after that. Blood CsA concentrations were tested at 2 weeks after administration and before discontinuation. Quantitative PCR was used to detect serum WHV DNA. Flow cytometry was used to detect T cell immune response. Feces were collected for 16S rRNA sequencing. The result shows CsA oral administration can reach effective blood drug concentration in woodchucks and successfully prolong WHV replication. After 2 weeks of oral treatment, there was no significant difference in the gut microbiota between the two groups. At the clearance period of serum WHV, the relative abundance of Prevotella and Prevotella genera in the phylum Bacteroidetes significantly increased, while the relative abundance of Firmicutes significantly decreased. Meanwhile, the CD107a degranulation of CD4-T cells in peripheral blood showed a decreasing trend, while there was no significant difference in the frequency of PD-1+ CD4-T cells. In Conclusion, oral administration of CsA can significantly prolong the replication time of WHV in Chinese woodchucks. The gut microbiota of Chinese woodchuck undergoes significant changes during serum WHV clearance, which implies the Chinese woodchuck model can be used to study the interaction between HBV infection and gut microbiota.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"321 ","pages":"Article 151675"},"PeriodicalIF":3.6,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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