Pub Date : 2026-02-03DOI: 10.1016/j.ijmm.2026.151705
Sika Dossim, Komla M Dossouvi, Amivi M Godonou, Essokedi Tchedie, Mounerou Salou, Anoumou Y Dagnra, Thierry Naas
Genomics have become crucial in addressing the public health challenges posed by antimicrobial resistance (AMR). In this study, we performed the first whole-genome sequencing (WGS) and genomic analyses of clinical Acinetobacter baumannii (A. baumannii) strains isolated at the Sylvanus Olympio University Teaching Hospital in Lomé, Togo. This prospective study, conducted from April 19 to September 02, 2019. Susceptibility profiles were obtained using the Kirby-Bauer disc diffusion method, and the nine studied carbapenem-resistant A. baumannii strains were subjected to next generation sequencing (NGS) using an Illumina platform. All isolates exhibited resistance to imipenem, ticarcillin, clavulanic acid, cefotaxime, and ciprofloxacin, but remained susceptible to colistin, tigecycline, and rifampicin. The study identified five A. baumannii ST1 strains, two ST103 strains, one ST52 strain, and one ST1153 strain. The number of AMR genes per strain ranged from six to 24, whereas the number of virulence genes per strain varied from 32 to 67. Each isolate contained at least one plasmid, with the number of plasmids per isolate ranging from one to four per isolate. The carbapenemase-producing genes blaOXA-23, blaOXA-58, blaOXA-68, blaOXA-69, blaOXA-70, blaOXA-91, and blaNDM-1 were identified, along with blaCTX-M-15 and other antibiotic resistance genes. Additionally, multidrug efflux system genes, including adeCFGHIJKLMNS, abeSJ, and amvA, and a wide array of virulence and biofilm-forming genetic determinants were found in all isolates. Eleven integrons were detected, featuring aac(3)-Ia, sat-2, and dfrA1 cassettes. Tn6018, carrying the mercury resistance gene merR and czcD (Co/Zn/Cd efflux system), and Tn2007, carrying blaOXA-23, were present in six genomes. Four Ghanaian genomes were most closely related to the A. baumannii ST1 and ST103 strains reported in this study. Furthermore, several multidrug resistance plasmids and one virulence and AMR hybrid plasmid (accession number JBFMWK020002174.1) were identified. This study provides valuable insights into clinical A. baumannii in Togo, underscoring the need for more frequent genomic studies in sub-Saharan countries to effectively monitor and combat AMR in Africa.
{"title":"Resistome, virulome and mobilome of clinical carbapenemase-producing Acinetobacter baumannii strains isolated in Togo.","authors":"Sika Dossim, Komla M Dossouvi, Amivi M Godonou, Essokedi Tchedie, Mounerou Salou, Anoumou Y Dagnra, Thierry Naas","doi":"10.1016/j.ijmm.2026.151705","DOIUrl":"https://doi.org/10.1016/j.ijmm.2026.151705","url":null,"abstract":"<p><p>Genomics have become crucial in addressing the public health challenges posed by antimicrobial resistance (AMR). In this study, we performed the first whole-genome sequencing (WGS) and genomic analyses of clinical Acinetobacter baumannii (A. baumannii) strains isolated at the Sylvanus Olympio University Teaching Hospital in Lomé, Togo. This prospective study, conducted from April 19 to September 02, 2019. Susceptibility profiles were obtained using the Kirby-Bauer disc diffusion method, and the nine studied carbapenem-resistant A. baumannii strains were subjected to next generation sequencing (NGS) using an Illumina platform. All isolates exhibited resistance to imipenem, ticarcillin, clavulanic acid, cefotaxime, and ciprofloxacin, but remained susceptible to colistin, tigecycline, and rifampicin. The study identified five A. baumannii ST1 strains, two ST103 strains, one ST52 strain, and one ST1153 strain. The number of AMR genes per strain ranged from six to 24, whereas the number of virulence genes per strain varied from 32 to 67. Each isolate contained at least one plasmid, with the number of plasmids per isolate ranging from one to four per isolate. The carbapenemase-producing genes bla<sub>OXA-23</sub>, bla<sub>OXA-58</sub>, bla<sub>OXA-68</sub>, bla<sub>OXA-69</sub>, bla<sub>OXA-70</sub>, bla<sub>OXA-91</sub>, and bla<sub>NDM-1</sub> were identified, along with bla<sub>CTX-M-15</sub> and other antibiotic resistance genes. Additionally, multidrug efflux system genes, including adeCFGHIJKLMNS, abeSJ, and amvA, and a wide array of virulence and biofilm-forming genetic determinants were found in all isolates. Eleven integrons were detected, featuring aac(3)-Ia, sat-2, and dfrA1 cassettes. Tn6018, carrying the mercury resistance gene merR and czcD (Co/Zn/Cd efflux system), and Tn2007, carrying bla<sub>OXA-23</sub>, were present in six genomes. Four Ghanaian genomes were most closely related to the A. baumannii ST1 and ST103 strains reported in this study. Furthermore, several multidrug resistance plasmids and one virulence and AMR hybrid plasmid (accession number JBFMWK020002174.1) were identified. This study provides valuable insights into clinical A. baumannii in Togo, underscoring the need for more frequent genomic studies in sub-Saharan countries to effectively monitor and combat AMR in Africa.</p>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"151705"},"PeriodicalIF":3.6,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146120298","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 : 2026-01-31DOI: 10.1016/j.ijmm.2026.151706
Jinyue Zhang, Yao Li, Tianheng Xue, Haoyu Li, Hanqi Wei, Xiaoxiao Li, Wanlian Zhang, Shihao Song
In recent years, due to the spread of antibiotic resistance, Pseudomonas aeruginosa has emerged as an ESKAPE super-resistant pathogen, posing a major threat to current therapies. Phage therapy is currently one of the most promising treatment methods. In this study, we isolated a novel strongly lytic phage HKPH_J3, which is a linear double-stranded DNA of 38008 bp with a GC content of 64.6 %, and contains no harmful genes. Phage HKPH_J3 is a member of the Casadabanvirus genus, and there are subtle genetic differences between it and homologous phages. Phenotypic analysis revealed that phage HKPH_J3 has efficient and stable lytic activity and strongly inhibits and degrades the biofilm of P. aeruginosa PAO1. Moreover, the phage HKPH_J3 significantly inhibited the cytotoxicity of P. aeruginosa PAO1, and in the G. mellonella model, phage HKPH_J3 significantly improved larval survival. In addition, we studied the phage-resistant P. aeruginosa mutant J3yd_PAO1. The infection pressure of phage HKPH_J3 causes a nonsense mutation in the type IV pili (T4P) biogenic protein PilP of P. aeruginosa PAO1, which hinders the folding of the functional domain of the PilP protein and may affect the expression of type IV pili (T4P), inhibiting the adsorption of phage HKPH_J3 and ultimately leading to phage resistance. In summary, phage HKPH_J3 has practical application value in treating drug-resistant P. aeruginosa infections. However, the development of phage resistance in bacteria hinders their application, and the resistance mechanism of bacteria is a key strategy for their survival and reproduction. And, the potential mechanism of bacteria-phage interaction is still unclear. Therefore, we investigated the phage-resistance mechanism of J3yd_PAO1, which helps to increase our understanding of phage-resistant regulation and lays the foundation for the application of phage therapy and the study of bacteria-phage evolution mechanisms.
{"title":"Characterization and antibiofilm efficacy of the Pseudomonas aeruginosa phage HKPH_J3.","authors":"Jinyue Zhang, Yao Li, Tianheng Xue, Haoyu Li, Hanqi Wei, Xiaoxiao Li, Wanlian Zhang, Shihao Song","doi":"10.1016/j.ijmm.2026.151706","DOIUrl":"https://doi.org/10.1016/j.ijmm.2026.151706","url":null,"abstract":"<p><p>In recent years, due to the spread of antibiotic resistance, Pseudomonas aeruginosa has emerged as an ESKAPE super-resistant pathogen, posing a major threat to current therapies. Phage therapy is currently one of the most promising treatment methods. In this study, we isolated a novel strongly lytic phage HKPH_J3, which is a linear double-stranded DNA of 38008 bp with a GC content of 64.6 %, and contains no harmful genes. Phage HKPH_J3 is a member of the Casadabanvirus genus, and there are subtle genetic differences between it and homologous phages. Phenotypic analysis revealed that phage HKPH_J3 has efficient and stable lytic activity and strongly inhibits and degrades the biofilm of P. aeruginosa PAO1. Moreover, the phage HKPH_J3 significantly inhibited the cytotoxicity of P. aeruginosa PAO1, and in the G. mellonella model, phage HKPH_J3 significantly improved larval survival. In addition, we studied the phage-resistant P. aeruginosa mutant J3yd_PAO1. The infection pressure of phage HKPH_J3 causes a nonsense mutation in the type IV pili (T4P) biogenic protein PilP of P. aeruginosa PAO1, which hinders the folding of the functional domain of the PilP protein and may affect the expression of type IV pili (T4P), inhibiting the adsorption of phage HKPH_J3 and ultimately leading to phage resistance. In summary, phage HKPH_J3 has practical application value in treating drug-resistant P. aeruginosa infections. However, the development of phage resistance in bacteria hinders their application, and the resistance mechanism of bacteria is a key strategy for their survival and reproduction. And, the potential mechanism of bacteria-phage interaction is still unclear. Therefore, we investigated the phage-resistance mechanism of J3yd_PAO1, which helps to increase our understanding of phage-resistant regulation and lays the foundation for the application of phage therapy and the study of bacteria-phage evolution mechanisms.</p>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"151706"},"PeriodicalIF":3.6,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146133465","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 : 2026-01-21DOI: 10.1016/j.ijmm.2026.151704
Hui Yu , Nan Wang , Changjiang Sun , Bingfeng Leng , Liping Sun , Xuming Deng , Lei Xu , Zihao Teng , Jianfeng Wang , Lin Wang
Enterotoxigenic Escherichia coli (ETEC), a predominant pathogen responsible for neonatal animal diarrhea, poses a significant threat to global health and results in considerable economic losses in animal husbandry. The pathogenicity of ETEC is primarily mediated by its adherence to intestinal epithelial cells via fimbriae adhesins and the subsequent secretion of enterotoxins. We developed a high-throughput screening platform for chorionic inhibitors. By employing semi-solid motility assays, hemagglutination inhibition assays, and cell adhesion assays, we screened a panel of natural compounds and identified Isogliquiritin (ISL) as the active compound. Subsequent validation using transmission electron microscopy and reverse transcription-polymerase chain reaction (qRT-PCR) revealed that ISL significantly inhibits the synthesis and assembly of ETEC fimbriae, thereby reducing bacterial adhesion to host cells. After assessing its safety, we demonstrated through in vivo experiments that ISL attenuates ETEC-induced diarrhea. In the Galleria mellonella larval model, ISL increased the survival rate, meanwhile in a mouse diarrhea model, ISL reduced inflammation caused by ETEC C83902 and upregulated the expression of tight junction protein (ZO-1, claudin-1, and occluding) genes. Collectively, our findings highlight that ISL is a promising natural compound for the prevention and treatment of ETEC-induced diarrhea. By targeting bacterial virulence factors rather than bacterial growth, ISL provides a novel strategy against antimicrobial resistance and offers a safer alternative for managing ETEC infections in livestock.
{"title":"Targeting fimbriae adhesin of porcine enterotoxigenic Escherichia coli by isoliquiritigenin","authors":"Hui Yu , Nan Wang , Changjiang Sun , Bingfeng Leng , Liping Sun , Xuming Deng , Lei Xu , Zihao Teng , Jianfeng Wang , Lin Wang","doi":"10.1016/j.ijmm.2026.151704","DOIUrl":"10.1016/j.ijmm.2026.151704","url":null,"abstract":"<div><div>Enterotoxigenic <em>Escherichia coli</em> (ETEC), a predominant pathogen responsible for neonatal animal diarrhea, poses a significant threat to global health and results in considerable economic losses in animal husbandry. The pathogenicity of ETEC is primarily mediated by its adherence to intestinal epithelial cells via fimbriae adhesins and the subsequent secretion of enterotoxins. We developed a high-throughput screening platform for chorionic inhibitors. By employing semi-solid motility assays, hemagglutination inhibition assays, and cell adhesion assays, we screened a panel of natural compounds and identified Isogliquiritin (ISL) as the active compound. Subsequent validation using transmission electron microscopy and reverse transcription-polymerase chain reaction (qRT-PCR) revealed that ISL significantly inhibits the synthesis and assembly of ETEC fimbriae, thereby reducing bacterial adhesion to host cells. After assessing its safety, we demonstrated through in vivo experiments that ISL attenuates ETEC-induced diarrhea. In the <em>Galleria mellonella</em> larval model, ISL increased the survival rate, meanwhile in a mouse diarrhea model, ISL reduced inflammation caused by ETEC C83902 and upregulated the expression of tight junction protein (ZO-1, claudin-1, and occluding) genes. Collectively, our findings highlight that ISL is a promising natural compound for the prevention and treatment of ETEC-induced diarrhea. By targeting bacterial virulence factors rather than bacterial growth, ISL provides a novel strategy against antimicrobial resistance and offers a safer alternative for managing ETEC infections in livestock.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151704"},"PeriodicalIF":3.6,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078369","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 : 2026-01-20DOI: 10.1016/j.ijmm.2026.151703
M. Messal , T. Störiko , J. Gerkrath , J. Michel , S. Ackermann , S.H. Tausch , V. Rickerts
This study reviews proven coccidioidomycosis cases in Germany associated with travel between 2011 and 2023 to endemic regions. We characterize clinical presentation, diagnostic practices, antifungal susceptibility, and molecular epidemiology. Fifteen human cases were confirmed by culture (12 cases) and histology (3 cases), with infections caused by Coccidioides posadasii (10 cases) and C. immitis (2 cases). Patients ranged from 23 to 82 years old, mostly without significant comorbidities. Clinical manifestations included pulmonary (6 cases), CNS (2 cases), and disseminated disease (3 cases). Serologic testing showed high sensitivity for lateral flow assays (100 %) compared to immunodiffusion (82 %). In vitro susceptibility testing indicated strong activity of amphotericin B and azole antifungals. Whole-genome sequencing revealed that most infections originated from Arizona, clustering with known clades. The findings highlight that coccidioidomycosis is rarely diagnosed in Germany but does occur in previously healthy individuals with travel to endemic regions. Importantly, antibody detection via lateral flow assay is a useful screening tool in non-endemic settings.
{"title":"Travel associated human coccidioidomycosis in Germany 2011–2023","authors":"M. Messal , T. Störiko , J. Gerkrath , J. Michel , S. Ackermann , S.H. Tausch , V. Rickerts","doi":"10.1016/j.ijmm.2026.151703","DOIUrl":"10.1016/j.ijmm.2026.151703","url":null,"abstract":"<div><div>This study reviews proven coccidioidomycosis cases in Germany associated with travel between 2011 and 2023 to endemic regions. We characterize clinical presentation, diagnostic practices, antifungal susceptibility, and molecular epidemiology. Fifteen human cases were confirmed by culture (12 cases) and histology (3 cases), with infections caused by <em>Coccidioides posadasii</em> (10 cases) and <em>C. immitis</em> (2 cases). Patients ranged from 23 to 82 years old, mostly without significant comorbidities. Clinical manifestations included pulmonary (6 cases), CNS (2 cases), and disseminated disease (3 cases). Serologic testing showed high sensitivity for lateral flow assays (100 %) compared to immunodiffusion (82 %). In vitro susceptibility testing indicated strong activity of amphotericin B and azole antifungals. Whole-genome sequencing revealed that most infections originated from Arizona, clustering with known clades. The findings highlight that coccidioidomycosis is rarely diagnosed in Germany but does occur in previously healthy individuals with travel to endemic regions. Importantly, antibody detection via lateral flow assay is a useful screening tool in non-endemic settings.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151703"},"PeriodicalIF":3.6,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078368","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}
Leptospirosis, caused by pathogenic Leptospira spp., is one of the most prevalent zoonotic diseases worldwide. While whole genome sequencing (WGS) has revealed global genetic diversity of Leptospira spp., large-scale genomic comparisons between human and animal isolates remain limited, and their epidemiological relationships are not fully understood. In this study, we performed WGS on 204 Leptospira isolates obtained from humans, dogs, and wild or feral animals in Japan between 1989 and 2021. Among these, 146 isolates of L. interrogans—the most frequently isolated Leptospira species with epidemiological relevance—were analyzed using Bayesian analysis of population structure (BAPS) and core genome multilocus sequence typing (cgMLST). These strains were classified into 30 clonal groups (CGs), including 26 novel CGs. Each CG consistently corresponded to a single serogroup, highlighting the potential of cgMLST for serogroup prediction. BAPS analysis revealed that serogroup Hebdomadis—particularly clades Li20 and Li13—predominated among human infections on islands of Okinawa Prefecture. Li20/CG486 strains were also isolated from mongooses and Ryukyu mouse, suggesting that these animals may serve as reservoirs. Li3/CG6 strains of serogroup Icterohaemorrhagiae were detected in both humans and brown rats in urban areas, underscoring the role of rats in transmission. Several canine isolates shared CGs with wildlife: Li20/CG481 with mongooses, Li20/CG486 with raccoons, Li6/CG485 with brown rats, and Li20/CG470 with large Japanese field mice, supporting environmental exposure as a likely route of canine infection. These findings demonstrate the utility of cgMLST and BAPS for high-resolution genotyping and emphasize the need for monitoring native and introduced wildlife to better understand and control leptospirosis in Japan.
{"title":"Genomic comparison of Leptospira interrogans isolated from humans, dogs, and wild and feral animals in Japan","authors":"Tetsuya Kakita , Kyosuke Takabe , Masatomo Morita , Sho Okano , Katsuya Taira , Tsuyoshi Kudeken , Haruno Taira , Hisako Kyan , So Shinya , Ryo Murata , Yukihiro Akeda , Makoto Ohnishi , Nobuo Koizumi","doi":"10.1016/j.ijmm.2026.151702","DOIUrl":"10.1016/j.ijmm.2026.151702","url":null,"abstract":"<div><div>Leptospirosis, caused by pathogenic <em>Leptospira</em> spp., is one of the most prevalent zoonotic diseases worldwide. While whole genome sequencing (WGS) has revealed global genetic diversity of <em>Leptospira</em> spp., large-scale genomic comparisons between human and animal isolates remain limited, and their epidemiological relationships are not fully understood. In this study, we performed WGS on 204 <em>Leptospira</em> isolates obtained from humans, dogs, and wild or feral animals in Japan between 1989 and 2021. Among these, 146 isolates of <em>L. interrogans</em>—the most frequently isolated <em>Leptospira</em> species with epidemiological relevance—were analyzed using Bayesian analysis of population structure (BAPS) and core genome multilocus sequence typing (cgMLST). These strains were classified into 30 clonal groups (CGs), including 26 novel CGs. Each CG consistently corresponded to a single serogroup, highlighting the potential of cgMLST for serogroup prediction. BAPS analysis revealed that serogroup Hebdomadis—particularly clades Li20 and Li13—predominated among human infections on islands of Okinawa Prefecture. Li20/CG486 strains were also isolated from mongooses and Ryukyu mouse, suggesting that these animals may serve as reservoirs. Li3/CG6 strains of serogroup Icterohaemorrhagiae were detected in both humans and brown rats in urban areas, underscoring the role of rats in transmission. Several canine isolates shared CGs with wildlife: Li20/CG481 with mongooses, Li20/CG486 with raccoons, Li6/CG485 with brown rats, and Li20/CG470 with large Japanese field mice, supporting environmental exposure as a likely route of canine infection. These findings demonstrate the utility of cgMLST and BAPS for high-resolution genotyping and emphasize the need for monitoring native and introduced wildlife to better understand and control leptospirosis in Japan.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151702"},"PeriodicalIF":3.6,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037843","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 : 2026-01-12DOI: 10.1016/j.ijmm.2026.151701
Rongjie Chen , Zhengdong Li , Dengran Li , Xiuxiu Mao , Zhe Xu
CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.
{"title":"Clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in the etiological diagnosis of community-acquired pneumonia in children","authors":"Rongjie Chen , Zhengdong Li , Dengran Li , Xiuxiu Mao , Zhe Xu","doi":"10.1016/j.ijmm.2026.151701","DOIUrl":"10.1016/j.ijmm.2026.151701","url":null,"abstract":"<div><div>CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151701"},"PeriodicalIF":3.6,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977642","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 : 2026-01-12DOI: 10.1016/j.ijmm.2026.151700
Hajnalka Juhász , Katalin Burián , Mátyás Bukva , Gabriella Terhes
Our study determined the prevalence, types of RSV, and sequence variability of the G and F genes in Hungary between 2017 and 2023. During the study, 1828 respiratory samples were collected from hospitalised pediatric patients. We confirmed the presence of RSV A in 12.74 %, RSV B in 13.85 %, and their simultaneous presence in 0.27 %. The highest RSV positivity was observed in the 2018–2019 season, while the lowest was in the 2017–2018 season. Following the SARS-CoV-2 pandemic, the RSV season has an earlier onset and longer duration than it did previously; however, an earlier onset was already detected in 2018. All RSV A isolates are classified into the A.D., while RSV B into the B.D. clades. The entire ectodomain of G protein showed a high sequence diversity, higher than in the case of B.D. strains. Mutations at position 276, adjacent to the palivizumab binding site of the F protein, could be detected. At the same time, neither K272E/N nor any other mutation is present in the palivizumab binding region in our strains. Several mutations in the nirsevimab binding region could be detected in our strains; however, none of these mutations, which would affect nirsevimab activity, were found in our isolates.
{"title":"Sequence variability of Hungarian RSV G and F proteins between 2017 and 2023: single-center study","authors":"Hajnalka Juhász , Katalin Burián , Mátyás Bukva , Gabriella Terhes","doi":"10.1016/j.ijmm.2026.151700","DOIUrl":"10.1016/j.ijmm.2026.151700","url":null,"abstract":"<div><div>Our study determined the prevalence, types of RSV, and sequence variability of the G and F genes in Hungary between 2017 and 2023. During the study, 1828 respiratory samples were collected from hospitalised pediatric patients. We confirmed the presence of RSV A in 12.74 %, RSV B in 13.85 %, and their simultaneous presence in 0.27 %. The highest RSV positivity was observed in the 2018–2019 season, while the lowest was in the 2017–2018 season. Following the SARS-CoV-2 pandemic, the RSV season has an earlier onset and longer duration than it did previously; however, an earlier onset was already detected in 2018. All RSV A isolates are classified into the A.D., while RSV B into the B.D. clades. The entire ectodomain of G protein showed a high sequence diversity, higher than in the case of B.D. strains. Mutations at position 276, adjacent to the palivizumab binding site of the F protein, could be detected. At the same time, neither K272E/N nor any other mutation is present in the palivizumab binding region in our strains. Several mutations in the nirsevimab binding region could be detected in our strains; however, none of these mutations, which would affect nirsevimab activity, were found in our isolates.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151700"},"PeriodicalIF":3.6,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977643","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 : 2025-12-23DOI: 10.1016/j.ijmm.2025.151698
Raphael Hermann , Annika Sobkowiak , Franziska Schuler , Vincent van Almsick , Alexander Mellmann , Vera Schwierzeck
Our study characterized 301 extended-spectrum beta-lactamases (ESBL) Escherichia coli isolates collected a tertiary hospital in Germany during a during an 18-month period starting from March 2021. All isolates were subjected to long-read whole genome sequencing (lrWGS) to identify resistance genes, type strains and investigate genetic relatedness. Results showed that the sequence type (ST)131 subclade B2 dominates the E. coli population. While carbapenemase genes were rare (n = 7), the most common resistance genes identified were the extended-spectrum beta-lactamase (ESBL) encoding genes blaCTX-M-15 (26.6 %), blaCTX-M-27 (18.9 %) and blaOXA-1 in combination with blaCTX-M-15 (14.6 %). About half of the isolates were categorized as nosocomial. Epidemiological evaluation and genetic analysis of bacterial isolates identified five probable cases of transmission during hospital admission. 43,7 % (55 isolates) of the E. coli ST131 isolates were detected in urine samples. 23 % of respective patients received antibiotic treatment prior to sample collection. Moreover, we used lrWGS data to investigate the antimicrobial resistance plasmids in the E. coli ST131 isolates. In total, 68 E. coli ST131 carried at least one ESBL gene on a plasmid. Of these, the blaCTX-M-27 carrying IncF plasmid was detected in 49 isolates. Taken together our study represents a detailed characterization of the ESBL E. coli population in the hospital setting and highlights the role of ST131 E. coli for hospital epidemiology.
{"title":"Epidemiology of multidrug resistant E. coli isolates from a German university hospital illustrates dominance of E. coli ST131","authors":"Raphael Hermann , Annika Sobkowiak , Franziska Schuler , Vincent van Almsick , Alexander Mellmann , Vera Schwierzeck","doi":"10.1016/j.ijmm.2025.151698","DOIUrl":"10.1016/j.ijmm.2025.151698","url":null,"abstract":"<div><div>Our study characterized 301 extended-spectrum beta-lactamases (ESBL) <em>Escherichia coli</em> isolates collected a tertiary hospital in Germany during a during an 18-month period starting from March 2021. All isolates were subjected to long-read whole genome sequencing (lrWGS) to identify resistance genes, type strains and investigate genetic relatedness. Results showed that the sequence type (ST)131 subclade B2 dominates the <em>E. coli</em> population. While carbapenemase genes were rare (n = 7), the most common resistance genes identified were the extended-spectrum beta-lactamase (ESBL) encoding genes <em>bla</em><sub>CTX-M-15</sub> (26.6 %), <em>bla</em><sub>CTX-M-27</sub> (18.9 %) and <em>bla</em><sub>OXA-1</sub> in combination with <em>bla</em><sub>CTX-M-15</sub> (14.6 %)<em>.</em> About half of the isolates were categorized as nosocomial. Epidemiological evaluation and genetic analysis of bacterial isolates identified five probable cases of transmission during hospital admission. 43,7 % (55 isolates) of the <em>E. coli</em> ST131 isolates were detected in urine samples. 23 % of respective patients received antibiotic treatment prior to sample collection. Moreover, we used lrWGS data to investigate the antimicrobial resistance plasmids in the <em>E. coli</em> ST131 isolates. In total, 68 <em>E. coli</em> ST131 carried at least one ESBL gene on a plasmid. Of these, the <em>bla</em><sub>CTX-M-27</sub> carrying <em>IncF</em> plasmid was detected in 49 isolates. Taken together our study represents a detailed characterization of the ESBL <em>E. coli</em> population in the hospital setting and highlights the role of ST131 <em>E. coli</em> for hospital epidemiology.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151698"},"PeriodicalIF":3.6,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145913841","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}
Hypervirulent Klebsiella pneumoniae (hvKp), one of the most significant pathogens in nosocomial infections, regulates the shift from long-term survival to pathogenicity via an intricate regulatory network. Nevertheless, the mechanism by which hvKp manages to uphold a variety of metabolic shifts occurring in its immediate vicinity could play a significant role in bolstering its virulence. Through the identification of DppA, a crucial component of the dipeptide (Dpp) transporter system, our findings revealed a link between DppA and the regulation of virulence and metabolism in hvKp. Significant phenotypic alterations were observed in the dppA deletion mutant, including increased biofilm formation, improved serum resistance, enhanced siderophores production, improved cell adhesion and infection, and, most crucially, in a mouse model of bloodstream infection, we demonstrated that the dppA deletion markedly increased the expression of the inflammatory mediator IL-6. Furthermore, approximately 2.5 % of the genes exhibited differential expression in the mutant, with virulence-associated genes (particularly those related to siderophores) showing substantially elevated expression levels. This study deciphers the role of DppA within the virulence and metabolic regulatory networks of hvKp, thereby establishing a foundation for future research into its pathogenic mechanisms.
{"title":"The substrate-binding protein DppA modulates the virulence of hypervirulent Klebsiella pneumoniae","authors":"Rongping Zhu , Qingzhu Zheng , Jiacheng Qiu , Yingping Cao , Xiaohong Xu","doi":"10.1016/j.ijmm.2025.151697","DOIUrl":"10.1016/j.ijmm.2025.151697","url":null,"abstract":"<div><div>Hypervirulent <em>Klebsiella pneumoniae</em> (hvKp), one of the most significant pathogens in nosocomial infections, regulates the shift from long-term survival to pathogenicity via an intricate regulatory network. Nevertheless, the mechanism by which hvKp manages to uphold a variety of metabolic shifts occurring in its immediate vicinity could play a significant role in bolstering its virulence. Through the identification of DppA, a crucial component of the dipeptide (Dpp) transporter system, our findings revealed a link between DppA and the regulation of virulence and metabolism in hvKp. Significant phenotypic alterations were observed in the <em>dppA</em> deletion mutant, including increased biofilm formation, improved serum resistance, enhanced siderophores production, improved cell adhesion and infection, and, most crucially, in a mouse model of bloodstream infection, we demonstrated that the <em>dppA</em> deletion markedly increased the expression of the inflammatory mediator IL-6. Furthermore, approximately 2.5 % of the genes exhibited differential expression in the mutant, with virulence-associated genes (particularly those related to siderophores) showing substantially elevated expression levels. This study deciphers the role of DppA within the virulence and metabolic regulatory networks of hvKp, thereby establishing a foundation for future research into its pathogenic mechanisms.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151697"},"PeriodicalIF":3.6,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798705","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 : 2025-12-16DOI: 10.1016/j.ijmm.2025.151690
Domonkos Sváb , Linda Falgenhauer , Eszter Kotogán , Trinad Chakraborty , István Tóth
Cytolethal distending toxin (CDT), a cyclomodulin and genotoxin produced by many Gram-negative bacteria including pathogenic Escherichia coli, disrupts the eukaryotic host cell cycle to facilitate bacterial colonization. In a survey of dairy cows in Hungary, 7 % of of sampled animal and farm environment isolates carried CDT-producing E. coli (CTEC). Whole genome sequencing (WGS) performed on six recent isolates and three historical CTEC strains revealed association with diverse pathotypes, including enteropathogenic- (EPEC) and necrotoxigenic- (NTEC) types, as well as several unclassified atypical strains. Four of the six strains isolated in this study carried plasmid encoding cdt-III+ NTEC, while a prophage based cdt-V allele was present in the remaining two strains which were of unknown pathotype. These isolates exhibited significant variability in their supplementary virulence genes (SVGs) content as well as in multiple prophage regions linked to virulence or fitness factors. They were phylogenetically distinct and comprised of only distantly related sequence types (STs) that include two novel STs. Several isolates also carried other genotoxic cyclomodulins such as the cytotoxic necrotizing factor (cnf), the cycle inhibiting factor (cif), and colibactin (polyketide synthase, pks) which is located on a genomic island, indicating multiple mechanisms for dysplastic damage of the eukaryotic host cells exist and highlight the role of horizontal gene transfer in the zoonotic and pathogenic potential of CTEC.
{"title":"Comparative genomic analysis of cyclomodulin-producing Escherichia coli strains of animal origin","authors":"Domonkos Sváb , Linda Falgenhauer , Eszter Kotogán , Trinad Chakraborty , István Tóth","doi":"10.1016/j.ijmm.2025.151690","DOIUrl":"10.1016/j.ijmm.2025.151690","url":null,"abstract":"<div><div>Cytolethal distending toxin (CDT), a cyclomodulin and genotoxin produced by many Gram-negative bacteria including pathogenic <em>Escherichia coli</em>, disrupts the eukaryotic host cell cycle to facilitate bacterial colonization. In a survey of dairy cows in Hungary, 7 % of of sampled animal and farm environment isolates carried CDT-producing <em>E. coli</em> (CTEC). Whole genome sequencing (WGS) performed on six recent isolates and three historical CTEC strains revealed association with diverse pathotypes, including enteropathogenic- (EPEC) and necrotoxigenic- (NTEC) types, as well as several unclassified atypical strains. Four of the six strains isolated in this study carried plasmid encoding <em>cdt-III+</em> NTEC, while a prophage based <em>cdt-V</em> allele was present in the remaining two strains which were of unknown pathotype. These isolates exhibited significant variability in their supplementary virulence genes (SVGs) content as well as in multiple prophage regions linked to virulence or fitness factors. They were phylogenetically distinct and comprised of only distantly related sequence types (STs) that include two novel STs. Several isolates also carried other genotoxic cyclomodulins such as the cytotoxic necrotizing factor (<em>cnf</em>), the cycle inhibiting factor (<em>cif</em>), and colibactin (polyketide synthase, <em>pks</em>) which is located on a genomic island, indicating multiple mechanisms for dysplastic damage of the eukaryotic host cells exist and highlight the role of horizontal gene transfer in the zoonotic and pathogenic potential of CTEC.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"322 ","pages":"Article 151690"},"PeriodicalIF":3.6,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145913863","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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