Journal of medical microbiology最新文献

{"title":"MARGINAL NOTES, February 2023. Picking through the rubble.","authors":"Timothy J J Inglis","doi":"10.1099/jmm.0.001679","DOIUrl":"https://doi.org/10.1099/jmm.0.001679","url":null,"abstract":"","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9412647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The foundations of aetiology: a common language for infection science.","authors":"Timothy J J Inglis","doi":"10.1099/jmm.0.001637","DOIUrl":"https://doi.org/10.1099/jmm.0.001637","url":null,"abstract":"<p><p>With the adoption of <i>infection science</i> as an umbrella term for the disciplines that inform our ideas of infection, there is a need for a common language that links infection's constituent parts. This paper develops a conceptual framework for infection science from the major themes used to understand causal relationships in infectious diseases. The paper proposes using the four main themes from the <i>Principia Aetiologica</i> to classify infection knowledge into four corresponding domains: Clinical microbiology, Public health microbiology, Mechanisms of microbial disease and Antimicrobial countermeasures. This epistemology of infection gives form and process to a revised infection ontology and an infectious disease heuristic. Application of the proposed epistemology has immediate practical implications for organization of journal content, promotion of inter-disciplinary collaboration, identification of emerging priority themes, and integration of cross-disciplinary areas such as One Health topics and antimicrobial resistance. Starting with these foundations, we can build a coherent narrative around the idea of infection that shapes the practice of infection science.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9475180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishing breakpoints for amoxicillin/clavulanate and ampicillin/sulbactam for rapid antimicrobial susceptibility testing directly from positive blood culture bottles.","authors":"Elisabeth König,&nbsp;Juliane Iser,&nbsp;Tanja Zechner-Sammer,&nbsp;Herwig Friedl,&nbsp;Robert Krause,&nbsp;Thomas Valentin,&nbsp;Eva Leitner,&nbsp;Ivo Steinmetz,&nbsp;Ines Zollner-Schwetz","doi":"10.1099/jmm.0.001672","DOIUrl":"https://doi.org/10.1099/jmm.0.001672","url":null,"abstract":"<p><p><b>Introduction.</b> In 2018, EUCAST released guidelines on rapid antimicrobial susceptibility testing (RAST) directly from positive blood culture bottles for selected bacterial species and antimicrobial agents, but not for the commonly used agents amoxicillin/clavulanate (AMC) and ampicillin/sulbactam (SAM).<b>Hypothesis/Gap statement</b>. This work addresses the <i>Enterobacterales</i> RAST capability gap for betalactam/betalactamase inhibitor combinations.<b>Aim.</b> We aimed to determine RAST breakpoints for AMC and SAM for <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> after 4 and 6 h of incubation directly from positive blood cultures.<b>Methodology.</b> Blood culture bottles were spiked with clinical isolates of <i>E. coli</i> (<i>n</i>=89) and <i>K. pneumoniae</i> (<i>n</i>=81). RAST was performed according to EUCAST guidelines and zones were read after 4 and 6 h. Breakpoints were defined to avoid very major errors.<b>Results.</b> The proportion of readable zone diameters after 4 h of incubation were 90.8 % in <i>E. coli</i> and 85.8 % in <i>K. pneumoniae</i> isolates. After 6 h of incubation all zone diameters could be read. The proposed breakpoints for <i>E. coli</i> after 6 h of incubation were ≥16 mm S (susceptible), 14-15 mm ATU (area of technical uncertainty) and <14 mm R (resistant) for AMC; ≥15 mm S, 12-14 mm ATU and <12 mm R for SAM; for <i>K. pneumoniae</i> these were ≥16 mm S, 14-15 mm ATU and <14 mm R for AMC; ≥13 mm S, 12 mm ATU, <12 mm R for SAM. Applying our newly set breakpoints, major errors were infrequent (2.6 %).<b>Conclusion.</b> We propose novel AMC and SAM breakpoints for RAST directly from positive blood cultures for reading after 4 and 6 h of incubation.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9173827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poor accuracy of single serological IgM tests in children with suspected acute <i>Mycoplasma pneumoniae</i> infection in Guangzhou, China.","authors":"Qiu-Ying Peng,&nbsp;Liang Zhang,&nbsp;Hua Deng,&nbsp;Yu-Ming Ye,&nbsp;Rui-Lin Huang,&nbsp;Yao-Qiong Liang,&nbsp;Su-Shi Feng,&nbsp;Juan Li,&nbsp;Xue-Qun Luo,&nbsp;Yan-Li Peng","doi":"10.1099/jmm.0.001673","DOIUrl":"https://doi.org/10.1099/jmm.0.001673","url":null,"abstract":"<p><p><b>Introduction.</b> Early and accurate diagnosis of <i>Mycoplasma pneumoniae</i> (<i>MP</i>) infection of children with pneumonia is at the core of treatment in clinical practice.<b>Gap Statement.</b> Serological immunoglobulin M (IgM) tests for <i>MP</i> infection of children in south China have been rarely described.<b>Aim.</b> To assess the diagnostic performance and clinical application of serodiagnosis of <i>MP</i> infection in paediatric pneumonia patients.<b>Methodology.</b> Serum samples from 144 children diagnosed with <i>MP</i> pneumonia were subjected to a particle agglutination (PA)-based IgM assay. Meanwhile, we used an established suspension array as the reference standard method for the detection of <i>MP</i> DNA in bronchoalveolar lavage fluid (BALF) from all patients to assess the reliability of serological assays.<b>Results.</b> When running immunological testing in single serum samples, 80.6 %(79/98) of cases were diagnosed with <i>MP</i> infection, whereas only 55 (56.1 %) cases were positive in <i>MP</i> DNA analysis. Furthermore, single serum tests for IgM during acute <i>MP</i> infection resulted in 85.5 % (47/55) sensitivity and 25.6 % (11/43) specificity. Nevertheless, immunological testing and <i>MP</i> DNA analysis yielded the same results when paired sera were available for <i>MP</i> IgM antibody testing.<b>Conclusion.</b> Paired serological IgM assays are necessary for the determination of an acute <i>MP</i> infection, whereas single serological IgM testing is unreliable. Moreover, even a short interval of two <i>MP</i> serological tests works well.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9491419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JMM Profile: Sindbis virus, a cause of febrile illness and arthralgia.","authors":"Sophie Harding,&nbsp;Sanam Sewgobind,&nbsp;Nicholas Johnson","doi":"10.1099/jmm.0.001674","DOIUrl":"https://doi.org/10.1099/jmm.0.001674","url":null,"abstract":"<p><p>Sindbis virus (SINV) is the causative agent of a febrile infection commonly called Ockelbo disease, Pogosta disease or Karelian fever in northern Europe. Finland, Sweden, Russia and South Africa experience periodic SINV outbreaks. SINV is classified within the family Togaviridae and genus Alphavirus. Symptoms of SINV infection in humans include joint inflammation and pain, fever, rash and fatigue. In some cases, joint symptoms can persist for years after recovery from the initial infection. Clinical signs of SINV infection are rarely reported in animals, although infection in horses has been documented. There is no specific treatment or vaccination. The virus is transmitted by mosquitoes, particularly those belonging to the <i>Culex</i> genus, but <i>Aedes, Culiseta</i> or <i>Mansonia</i> species may also act as vectors. Wild birds act as amplifying hosts and are implicated in the long-distance spread of the virus.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9158568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergence of carbapenem-resistant <i>Pseudomonas alcaligenes</i> and <i>Pseudomonas paralcaligenes</i> clinical isolates with plasmids harbouring <i>bla</i> _IMP-1 in Japan.","authors":"Emi Ono,&nbsp;Mari Tohya,&nbsp;Tatsuya Tada,&nbsp;Tomomi Hishinuma,&nbsp;Shin Watanabe,&nbsp;Kyoko Kuwahara-Arai,&nbsp;Teruo Kirikae","doi":"10.1099/jmm.0.001684","DOIUrl":"https://doi.org/10.1099/jmm.0.001684","url":null,"abstract":"<p><p><b>Introduction.</b> The emergence of carbapenem-resistant <i>Pseudomonas</i> species producing metallo-β-lactamase (MBL) has become a serious medical problem worldwide. IMP-type MBL was firstly detected in 1991 in Japan. Since then, it has become one of the most prevalent types of MBLs.<b>Hypothesis/Gap statement.</b> Avirulent species of <i>Pseudomonas</i>, such as <i>Pseudomonas alcaligenes</i>, function as reservoirs of drug resistance-associated genes encoding carbapenemases in clinical settings.<b>Methodology.</b> Active surveillance for carbapenem-resistant Gram-negative pathogens was conducted in 2019 at a hospital in Tokyo, Japan. Of the 543 samples screened for carbapenem-resistant isolates, 2 were species of <i>Pseudomonas</i>. One was from a stool sample from a medical staff member, and the other was from a stool sample from a hospitalized patient.<b>Results.</b> Whole-genome sequencing showed that the former isolate was a strain of <i>P. alcaligenes</i>, and the latter was a strain of <i>Pseudomonas paralcaligenes</i>, a species close to <i>P. alcaligenes</i>. Both isolates were resistant to all carbapenems and harboured <i>bla</i> _IMP-1 genes encoding IMP-1 MBL, which conferred resistance to carbapenems. The <i>bla</i> _IMP-1 genes of <i>P. alcaligenes</i> and <i>P. paralcaligenes</i> were located on the plasmids, pMRCP2, 323125 bp in size, and pMRCP1333, 16592 bp in size, respectively. The sequence of 82 % of pMRCP2 was 92 % similar to the sequence of a plasmid of <i>P. aeruginosa</i> PA83, whereas the sequence of 79 % of pMRCP1333 was >95 % similar to the sequence of a plasmid of <i>Achromobacter xylosoxidans</i> FDAARGOS 162. The genomic environments surrounding the <i>bla</i> _IMP-1 of pMRCP2 and pMRCP1333 differed completely from each other.<b>Conclusions.</b> These results indicate that the two isolates acquired <i>bla</i> _IMP-1 from different sources and that <i>P. alcaligenes</i> and <i>P. paralcaligenes</i> function as vectors and reservoirs of carbapenem-resistant genes in hospitals.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9541907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Japanese encephalitis in India: current situation and future needs.","authors":"Nikunja Kumar Das,&nbsp;Sameena Khan,&nbsp;Shital Algule,&nbsp;Sahjid Sadrudin Mukhida","doi":"10.1099/jmm.0.001677","DOIUrl":"https://doi.org/10.1099/jmm.0.001677","url":null,"abstract":"","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9710110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Legionellapneumophila</i> induces methylomic changes in ten-eleven translocation to ensure bacterial reproduction in human lung epithelial cells.","authors":"Sherry A Guirgis,&nbsp;Khalil A El-Halfawy,&nbsp;Mai Alalem,&nbsp;Hany Khalil","doi":"10.1099/jmm.0.001676","DOIUrl":"https://doi.org/10.1099/jmm.0.001676","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Legionella pneumophila</i> is a Gram-negative flagellated bacteria that can infect human lungs and cause a severe form of pneumonia named Legionnaires' disease.<b>Hypothesis.</b> We hypothesize that <i>L. pneumophila</i> infection induces methylomic changes in methylcytosine dioxygenases, ten-eleven translocation (TET) genes, and controls DNA methylation following infection.<b>Aim.</b> In the current research, we sought to further investigate DNA methylation changes in human lung epithelial cells upon <i>L. pneumophila</i> infection and determine how methylation inhibitor agents disturb <i>L. pneumophila</i> reproduction.<b>Methodology.</b> A549 cell line was used in <i>L. pneumophila</i> infection and inhibitors' treatment, including 5<i>-</i>azacytidine (5-AZA) and (-)-epigallocatechin-3-O-gallate (EGCG).<b>Results.</b> Interestingly, DNA methylation analysis of infected A549 using sodium bisulfite PCR and the methylation-sensitive HpaII enzyme showed potential methylation activity within the promoter regions of ten-eleven translocation (TET) genes located on CpG/397-8 and CpG/385-6 of TET1 and TET3, respectively. Such methylation changes in TET effectors decreased their expression profile following infection, indicated by quantitative real-time PCR (RT-qPCR), immunoblotting and flow cytometry. Furthermore, pre-treatment of A549 cells with 5-AZA or EGCG significantly decreased the bacterial reproduction characterized by the expression of <i>L. pneumophila</i> 16S ribosomal RNA and the c.f.u. ml^-1 of bacterial particles. Moreover, both methylation inhibitors showed potent inhibition of methionine synthase (MS) expression, which was further confirmed by the docking analysis of inhibitor ligands and crystal structure of MS protein.<b>Conclusion.</b> These data provide evidence for the methylomic changes in the promoter region of TET1 and TET3 by <i>L. pneumophila</i> infection in the A549 cell line and suggest the anti-bacterial properties of 5-AZA and EGCG, as methylation inhibitors, are due to targeting the epigenetic effector methionine synthase.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9136977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 in outdoor air following the third wave lockdown release, Portugal, 2021.","authors":"Priscilla Gomes da Silva,&nbsp;Maria São José Nascimento,&nbsp;Sofia I V Sousa,&nbsp;João R Mesquita","doi":"10.1099/jmm.0.001659","DOIUrl":"https://doi.org/10.1099/jmm.0.001659","url":null,"abstract":"<p><p>Aiming to contribute with more data on the presence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in outdoor environments, we performed air sampling in outdoor terraces from restaurants in three major cities of Portugal in April 2021, following the third wave lockdown release in the country. Air samples (<i>n</i>=19) were collected in 19 restaurant terraces during lunch time. Each air sample was collected using a Coriolis Compact air sampler, followed by RNA extraction and real-time quantitative PCR for the detection of viral RNA. Viral viability was also assessed through RNAse pre-treatment of samples. Only one of the 19 air samples was positive for SARS-CoV-2 RNA, with 7337 gene copies m^-3 for the genomic region N2, with no viable virus in this sample. The low number of positive samples found in this study is not surprising, as sampling took place in outdoor settings where air circulation is optimal, and aerosols are rapidly dispersed by the air currents. These results are consistent with previous reports stating that transmission of SARS-CoV-2 in outdoor spaces is low, although current evidence shows an association of exposures in settings where drinking and eating is possible on-site with an increased risk in acquiring SARS-CoV-2 infection. Moreover, the minimal infectious dose for SARS-CoV-2 still needs to be determined so that the real risk of infection in different environments can be accurately established.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10703449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence of cat-to-human transmission of <i>Staphylococcus felis</i>.","authors":"Gregorius J Sips,&nbsp;Marloes A M van Dijk,&nbsp;Mireille van Westreenen,&nbsp;Linda van der Graaf-van Bloois,&nbsp;Birgitta Duim,&nbsp;Els M Broens","doi":"10.1099/jmm.0.001661","DOIUrl":"https://doi.org/10.1099/jmm.0.001661","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Staphylococcus felis</i> is a coagulase-negative staphylococcal species that is commonly isolated from healthy cats. Like other commensal staphylococci, <i>S. felis</i> can cause opportunistic infections, e.g. otitis externa, skin and urinary tract infections, in cats.<b>Gap Statement.</b> Several studies have reported within-household transmission between humans and pets and human infections caused by coagulase-positive staphylococci. However, human infections with coagulase-negative staphylococci of zoonotic origin are relatively rare.<b>Methodology.</b> Culture of a surgical site infection in a 58-year-old woman who underwent a laminectomy revealed dominant growth of <i>S. felis</i>. The three cats owned by the patient were sampled to investigate potential within-household transmission. <i>S. felis</i> isolates were sequenced to investigate the relatedness of the isolates and to look for virulence factors and host specific genes.<b>Results.</b> All cats were colonized with <i>S. felis</i>. Comparative genomics of the isolates showed that each cat was colonized with a distinct genotype. The patient's isolate clustered with isolates of one of the cats. Sequence analysis of the studied isolates together with 29 publicly available <i>S. felis</i> genomes detected putative virulence factors that can be crucial in potential interspecies transmission.<b>Conclusion.</b> The current case is the first reported human infection caused by <i>S. felis</i> and highlights the zoonotic potential of this bacterial species. Evidence of cat-to-human transmission was shown by comparative genomics of isolates from the patient with isolates of her cats.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10703450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}