Journal of medical microbiology最新文献

{"title":"Characterization of the follicular fluid microbiota based on culturomics and sequencing analysis.","authors":"Wenting Wei,&nbsp;Yazhou Zhou,&nbsp;Haiyang Zuo,&nbsp;Min Li,&nbsp;Zhiyuan Pan,&nbsp;Bin Liu,&nbsp;Lu Wang,&nbsp;Yafang Tan,&nbsp;Ruifu Yang,&nbsp;Wei Shang,&nbsp;Yujing Bi,&nbsp;Weizhou Wang","doi":"10.1099/jmm.0.001741","DOIUrl":"https://doi.org/10.1099/jmm.0.001741","url":null,"abstract":"<p><p><b>Introduction.</b> The human oocyte microenvironment is follicular fluid, which is important for follicle growth, ovulation and maturation of the oocyte. The micro-organisms present in follicular fluid could be a predictor of <i>in vitro</i> fertilization outcomes.<b>Hypothesis/Gap Statement.</b> Women with follicular fluid colonized with micro-organisms can be asymptomatic, but the presence of some genera in the follicular fluid correlates with <i>in vitro</i> fertilization.<b>Aim.</b> To confirm the existence of micro-organisms in follicular fluid, and to profile the micro-organisms present in follicular fluid sampled from women undergoing <i>in vitro</i> fertilization with different outcomes.<b>Methodology.</b> Women undergoing <i>in vitro</i> fertilization (<i>n</i>=163) were divided into different subgroups according to their <i>in vitro</i> fertilization outcomes. Their follicular fluid samples were collected, and among them, 157 samples were analysed by 16S rDNA sequencing, and 19 samples were analysed using culturomics.<b>Results.</b> The culturomics results suggested that the 19 follicular fluid samples were not sterile. The isolation rates for <i>Streptococcus</i>, <i>Finegoldia</i> and <i>Peptoniphilus</i> were >50 % in the 19 samples. Linear discriminant analysis effect size analysis showed differential bacteria abundance according to the pregnancy rate, the rate of normal fertilization, the rate of high-quality embryos and the rate of available oocytes. The sequencing results showed that micro-organisms could be detected in all 157 samples. <i>Pseudomonas</i>, <i>Lactobacillus</i>, <i>Comamonas</i>, <i>Streptococcus</i> and <i>Acinetobacter</i> were detected in all of the samples, but with a wide range of relative abundance. <i>Pseudomonas</i>, <i>Lactobacillus</i>, <i>Ralstonia</i> and <i>Vibrio</i> constituted a notable fraction of the microbiota.<b>Conclusions.</b> Follicular fluid is not sterile. Micro-organisms in follicular fluid could be a predictor of <i>in vitro</i> fertilization outcomes.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10352618","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 characterisation of antimicrobial resistant <i>Escherichia coli</i> from dairy calves.","authors":"Merning Mwenifumbo,&nbsp;Adrian L Cookson,&nbsp;Shengguo Zhao,&nbsp;Ahmed Fayaz,&nbsp;Jackie Benschop,&nbsp;Sara A Burgess","doi":"10.1099/jmm.0.001742","DOIUrl":"10.1099/jmm.0.001742","url":null,"abstract":"<p><p><b>Introduction.</b> Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) <i>Escherichia coli</i>.<b>Gap statement.</b> <i>E. coli</i> strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.<b>Aim.</b> To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant <i>E. coli</i> isolated from calves located on dairy farms that feed waste-milk to their replacement calves.<b>Methodology.</b> Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant <i>E. coli</i>. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant <i>E. coli</i>.<b>Results.</b> Fifty-eight percent (23/40) of calves harboured antimicrobial resistant <i>E. coli</i>: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing <i>E. coli</i>. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic <i>E. coli</i> lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.<b>Conclusion.</b> Our study identified a high incidence of tetracycline and streptomycin-resistant <i>E. coli</i> in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10352619","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":"A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types.","authors":"Xuebo Li,&nbsp;Xuelian Yuan,&nbsp;Xiumin Zhu,&nbsp;Changjun Li,&nbsp;Lei Ji,&nbsp;Kebo Lv,&nbsp;Geng Tian,&nbsp;Kang Ning,&nbsp;Jialiang Yang","doi":"10.1099/jmm.0.001744","DOIUrl":"https://doi.org/10.1099/jmm.0.001744","url":null,"abstract":"<p><p><b>Background.</b> Local recurrence and distant metastasis are the main causes of death in patients with cancer. Only considering species abundance changes when identifying markers of recurrence and metastasis in patients hinders finding solutions.<b>Hypothesis.</b> Consideration of microbial abundance changes and microbial interactions facilitates the identification of microbial markers of tumour recurrence and metastasis.<b>Aim.</b> This study aims to simultaneously consider microbial abundance changes and microbial interactions to identify microbial markers of recurrence and metastasis in multiple cancer types.<b>Method.</b> One thousand one hundred and six non-RM (patients without recurrence and metastasis within 3 years after initial surgery) tissue samples and 912 RM (patients with recurrence or metastasis within 3 years after initial surgery) tissue samples representing 11 cancer types were collected from The Cancer Genome Atlas (TCGA).<b>Results.</b> Tumour tissue bacterial composition differed significantly among 11 cancers. Among them, the tissue microbiome of four cancers, head and neck squamous cell carcinoma (HNSC), lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD) and uterine corpus endometrial carcinoma (UCEC), showed relatively good performance in predicting recurrence and metastasis in patients, with areas under the receiver operating characteristic curve (AUCs) of 0.78, 0.74, 0.91 and 0.93, respectively. Considering both species abundance changes and microbial interactions for the four cancers, a combination of nine genera (<i>Niastella</i>, <i>Schlesneria</i>, <i>Thioalkalivibrio</i>, <i>Phaeobacter</i>, <i>Sphaerotilus</i>, <i>Thiomonas</i>, <i>Lawsonia</i>, <i>Actinobacillus</i> and <i>Spiroplasma</i>) performed best in predicting patient survival.<b>Conclusion.</b> Taken together, our results imply that comprehensive consideration of microbial abundance changes and microbial interactions is helpful for mining bacterial markers that carry prognostic information.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10435557","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":"Molecular characterization and genotyping of isolates from cancer patients with <i>Clostridioides difficile</i> infection or asymptomatic colonization.","authors":"Daniel de-la-Rosa-Martinez,&nbsp;Miriam Bobadilla Del Valle,&nbsp;Veronica Esteban-Kenel,&nbsp;Paola Zinser Peniche,&nbsp;Alfredo Ponce De León Garduño,&nbsp;Patricia Cornejo Juárez,&nbsp;María Nancy Sánchez Cruz,&nbsp;Adrian Camacho-Ortiz,&nbsp;Diana Vilar-Compte","doi":"10.1099/jmm.0.001748","DOIUrl":"https://doi.org/10.1099/jmm.0.001748","url":null,"abstract":"<p><p><b>Introduction.</b> Cancer patients with <i>Clostridioides difficile</i> infection (CDI) are at a higher risk for adverse outcomes. In addition, a high prevalence of <i>Clostridioides difficile</i> asymptomatic colonization (CDAC) has been reported in this vulnerable population.<b>Gap Statement.</b> The molecular characteristics and potential role of CDAC in healthcare-related transmission in the cancer population have been poorly explored.<b>Aim.</b> We aimed to compare the molecular and genotypic characteristics of <i>C. difficile</i> isolates from cancer patients with CDAC and CDI.<b>Method.</b> We conducted a prospective cohort study of cancer patients with CDAC or CDI from a referral centre. Molecular characterization, typification and <i>tcdC</i> gene expression of isolates were performed.<b>Results.</b> The hospital-onset and community-onset healthcare facility-associated CDI rates were 4.5 cases/10 000 patient-days and 1.4 cases/1 000 admissions during the study period. Fifty-one <i>C. difficile</i> strains were isolated: 37 (72 %) and 14 (28 %) from patients with CDI or CDAC, respectively. All isolates from symptomatic patients were <i>tcdA+/tcdB+</i>, and four (10 %) were <i>ctdA+/ctdB+</i>. In the CDAC group, 10 (71 %) isolates were toxigenic, and none were <i>ctdA+/ctdB</i>+. The Δ18 in-frame <i>tcdC</i> deletion and two transition mutations were found in five isolates. After bacterial typing, 60 % of toxigenic isolates from asymptomatic carriers were clonal to those from patients with <i>C. difficile</i>-associated diarrhoea. No NAP1/027/BI strains were detected.<b>Conclusions.</b> We found a clonal association between <i>C. difficile</i> isolates from patients with CDAC and CDI. Studies are needed to evaluate the potential role of asymptomatic carriers in the dynamics of nosocomial transmission to support infection control measures and reduce the burden of CDI in high-risk groups.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10135953","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":"Utility of in-house and commercial PCR assay in diagnosis of Covid-19 associated mucormycoss in an emergency setting in a tertiary care center.","authors":"Mragnayani Pandey,&nbsp;Janya Sachdev,&nbsp;Renu Kumari Yadav,&nbsp;Neha Sharad,&nbsp;Anupam Kanodia,&nbsp;Jaya Biswas,&nbsp;R Sruti Janani,&nbsp;Sonakshi Gupta,&nbsp;Gagandeep Singh,&nbsp;Meera Ekka,&nbsp;Bhaskar Rana,&nbsp;Sudesh Gourav,&nbsp;Alok Thakar,&nbsp;Ashutosh Biswas,&nbsp;Kapil Sikka,&nbsp;Purva Mathur,&nbsp;Neelam Pushker,&nbsp;Viveka P Jyotsna,&nbsp;Rakesh Kumar,&nbsp;Manish Soneja,&nbsp;Naveet Wig,&nbsp;M V Padma Srivastava,&nbsp;Immaculata Xess","doi":"10.1099/jmm.0.001745","DOIUrl":"https://doi.org/10.1099/jmm.0.001745","url":null,"abstract":"<p><p><b>Introduction.</b> Invasive mucormycosis (IM) is a potentially fatal infection caused by fungi of the order <i>Mucorales</i>. Histopathology, culture, and radiology are the mainstays of diagnosis, but they are not sufficiently sensitive, resulting in delayed diagnosis and intervention. Recent studies have shown that PCR-based techniques can be a promising way to diagnose IM.<b>Hypothesis/Gap Statement.</b> Early diagnosis of fungal infections using molecular diagnostic techniques can improve patient outcomes, especially in invasive mucormycosis.<b>Aim.</b> The aim of this study was to evaluate the utility of our in-house mould-specific real time PCR assay (qPCR) in comparison with the commercially available real time PCR (<i>MucorGenius</i> PCR), for the early diagnosis of mucormycosis in tissue samples from patients with suspicion of invasive mucormycosis (IM). This in-house assay can detect and distinguish three clinically relevant mould species, e.g. <i>Aspergillus</i> spp., <i>Mucorales</i> and <i>Fusarium</i> spp. in a single reaction with only one pair of primers, without the need for sequencing.<b>Methodology.</b> We enrolled 313 tissue samples from 193 patients with suspected IM in this prospective study. All cases were classified using EORTC/MSGERC guidelines. All samples were tested using traditional methods, in-house qPCR, and MucorGenius PCR.<b>Results.</b> Using direct microscopy as a gold standard, the overall sensitivity and specificity of in-house qPCR for detection of IM was 92.46% and 80% respectively, while that of the MucorGenius PCR was 66.67% and 90% respectively. However, co-infection of IM and IA adversely affected the performance of MucorGenius PCR in detection of IM.The in-house PCR detected <i>Aspergillus</i> spp. in 14 cases and <i>Fusarium</i> spp<i>.</i> in 4 cases which showed clinical and radiological features of fungal sinusitis. The in-house qPCR also performed better in detecting possible cases of IM. This aids early diagnosis and appropriate treatment to improve patient outcomes.<b>Conclusion.</b> Because the in-house PCR is not only sensitive and specific, but also entirely based on SYBR Green for detection of targets, it is less expensive than probe-based assays and can be used on a regular basis for the diagnosis of IM in resource-constrained settings. It can be used to distinguish between mucormycosis and fungal sinusitis caused by <i>Aspergillus</i> and <i>Fusarium</i> in high-risk patients, as well as to accurately detect <i>Mucorales</i> in fungal co-infection cases.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10238054","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":"Serum levels of type I interferon (IFN-I) is associated with the severity of COVID-19.","authors":"Yuting Sun,&nbsp;Gang Wang,&nbsp;Rongshuai Wang,&nbsp;Liang Ren,&nbsp;Zilin Yuan,&nbsp;Yueping Liu,&nbsp;Yuzhang Wu,&nbsp;Rong Chen,&nbsp;Yongwen Chen,&nbsp;Bo Diao","doi":"10.1099/jmm.0.001694","DOIUrl":"https://doi.org/10.1099/jmm.0.001694","url":null,"abstract":"<p><p><b>Introduction.</b> Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, coronavirus disease 2019 (COVID-19) has threatened global public health. Immune damage mechanisms are essential guidelines for clinical treatment and immune prevention.<b>Hypothesis.</b> The dysregulated type I interferon (IFN-I) responses, lymphocytopenia and hypercytokinemia during SARS-CoV-2 infection have been reported. However, whether there is a correlation between levels of IFN-I and the severity of COVID-19 has not been reported yet.<b>Aim.</b> To investigate the source of IFN-I and detect the exact roles of them in the pathogenesis of COVID-19.<b>Methodology.</b> Here ELISA was used to detect serum IFN-I (IFN-α and IFN-β) for 137 cases with laboratory-confirmed COVID-19 admitted into one hospital in Wuhan from December 2019 to March 2020, and the relationships between IFN-α/β concentrations and patients' clinical parameters were conducted by statistical analysis.<b>Results.</b> Both IFN-α and IFN-β concentrations dramatically increased in COVID-19 patients, especially in old patients (>80 years) and severe cases. Statistical analysis demonstrated that serum IFN-α/β concentrations were negatively correlated with the counts of total CD3<b>+</b>T<b>,</b> CD4⁺ and CD8⁺T cells, especially in critically ill cases. Moreover, serum IFN-α levels were positively correlated to IL-6 and TNF-α. Finally, immunofluorescent double staining showed that IFN-α and IFN-β are major secretions from macrophages and dendritic cells (DCs) in lymph nodes from COVID-19 autopsies.<b>Conclusion.</b> These results demonstrate that macrophages and DCs are the main origination of IFN-I, and <b>s</b>erum levels of IFN-I are positively associated with lymphopenia and cytokine storm, suggesting that IFN-α/β deteriorated the severity of COVID-19. Anti-interferon or IFN-I signalling block drugs are needed to treat ICU patients.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9920248","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":"Molecular strategy for the direct detection and identification of the most common fungal community in cerumen specimens by multiplex PCR.","authors":"Ahmad Jabrodini,&nbsp;Maryam Sohrabizdeh,&nbsp;Shima Aboutalebian,&nbsp;Seyed Basir Hashemi,&nbsp;Kamiar Zomorodian,&nbsp;Arefeh Alirezaie,&nbsp;Mona Rasti Jahromi,&nbsp;Seyedeh Neda Shamsdin,&nbsp;Marjan Motamedi","doi":"10.1099/jmm.0.001746","DOIUrl":"https://doi.org/10.1099/jmm.0.001746","url":null,"abstract":"<p><p><b>Introduction.</b> Otomycosis is a superficial fungal infection that is responsible for approximately 9-27 % of otitis externa. However, fungal communities in otomycosis are varied, but <i>Aspergillus</i> spp. and <i>Candida</i> spp. are the most common causes of this infection.<b>Hypothesis Statement.</b> The multiplex PCR assay is postulated to be able to directly detect more than one fungal genus in cerumen specimens.<b>Aim.</b> This study aimed to develop and evaluate the role of the multiplex PCR assay in detecting the most common genus of fungi that cause otomycosis directly from the cerumen specimens.<b>Methodology.</b> To detect <i>Candida</i> and <i>Aspergillus</i>/<i>Penicillium</i> genera, three pairs of primers, including pan-fungal, pan-<i>Candida</i>, and pan-<i>Aspergillus/Penicillium</i>, were used in a multiplex PCR. In order to evaluate the performance and reproducibility of the multiplex PCR. the cerumen of 140 patients suspected of otomycosis were investigated.<b>Results.</b> Pan-<i>Candida</i> and pan-<i>Aspergillus/Penicillium</i> primers were designed to amplify the ITS1-5.8S-ITS2 region and the β-tubulin gene, respectively. In the multiplex PCR assay, 64 (47.40 %) and 118 (87.40 %) specimens were positive with pan-<i>Candida</i> and pan-<i>Aspergillus/Penicillium</i> primers, respectively. Double amplicon bands of <i>Candida</i> and <i>Aspergillus</i> were obtained in 51 (37.77 %) specimens. In the culture method, yeast (<i>n</i>=18, 13.33 %) and mould (<i>n</i>=117, 86.66 %) were isolated from 135 cerumen specimens. The sensitivity, specificity, and positive and negative predictive values of the multiplex PCR assays using culture method results as the gold standard were determined to be 94, 33, 97, and 22 %, respectively.<b>Conclusion.</b> In our study, multiplex PCR assays enabled simultaneous detection of two common genera of the causative agent of otomycosis in a cerumen specimen. Regarding the high sensitivity of the first step of the multiplex PCR assay, this assay may be used for the direct detection of <i>Candida</i> and <i>Aspergillus</i> genera in other clinical specimens.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10071697","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":"Covenant between pharmacists and clinicians on the appropriateness of antimicrobial therapy.","authors":"Maria Khan,&nbsp;Saba Khan","doi":"10.1099/jmm.0.001727","DOIUrl":"https://doi.org/10.1099/jmm.0.001727","url":null,"abstract":"","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220340","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":"MARGINAL NOTES, June 2023 - running on empty.","authors":"T J J Inglis","doi":"10.1099/jmm.0.001735","DOIUrl":"https://doi.org/10.1099/jmm.0.001735","url":null,"abstract":"","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9893400","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 rare <i>Salmonella enterica</i> serovar Isangi: genomic characterization of the antimicrobial resistance, virulence potential and epidemiology of Brazilian strains in comparison to global isolates.","authors":"Felipe Pinheiro Vilela,&nbsp;Dália Dos Prazeres Rodrigues,&nbsp;Marc William Allard,&nbsp;Juliana Pfrimer Falcão","doi":"10.1099/jmm.0.001736","DOIUrl":"https://doi.org/10.1099/jmm.0.001736","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Salmonella enterica</i> serovar Isangi (<i>S</i>. Isangi) is a rare non-typhoidal serovar, related to invasive nosocomial infections in various countries and to increasing antimicrobial resistance rates.<b>Gap statement.</b> Despite existing reports on <i>S</i>. Isangi, there is a lack of information of specific traits regarding this serovar, which could be improved through genomic analyses.<b>Aim.</b> Our goals were to characterize the antimicrobial resistance, virulence potential and genomic relatedness of 11 <i>S</i>. Isangi strains from Brazil in comparison to 185 genomes of global isolates using whole-genome sequencing (WGS) data.<b>Methodology.</b> Phenotypic resistance was determined by disc-diffusion. The search for resistance genes, plasmids, prophages, <i>Salmonella</i> pathogenicity islands (SPIs) and virulence genes, plus multi-locus sequence typing (MLST) and core-genome MLST (cgMLST) were performed using WGS.<b>Results.</b> Brazilian <i>S</i>. Isangi strains showed phenotypic resistance to nalidixic acid, ciprofloxacin and streptomycin, and harboured antimicrobial resistance [<i>qnrB19</i>, <i>aac(6')-Iaa</i>, <i>mdsAB</i>] and heavy metal tolerance (<i>arsD, golST</i>) genes. Col(pHAD28) and IncFII(S) plasmids, virulence genes related to adherence, macrophage induction, magnesium uptake, regulation and type III secretion systems, 12 SPIs and eight prophages were detected. The 185 additional global genomes analysed harboured resistance genes against 11 classes of antimicrobial compounds, 22 types of plasmids, 32 prophages, 14 SPIs, and additional virulence genes related to serum resistance, stress adaptation and toxins. Sequence type (ST)216 was assigned to genomes from Brazil and other countries, while ST335 was the most frequent ST, especially among South African genomes. cgMLST showed that Brazilian genomes were more closely related to genomes from European and African countries, the USA and Taiwan, while the majority of South African genomes were more closely related among each other.<b>Conclusion.</b> The presence of <i>S</i>. Isangi strains from Brazil and different countries showing a close genomic correlation, antimicrobial resistance profiles to drugs used in human therapy and a large number of virulence determinants reinforced the need for stronger initiatives to monitor rare non-typhoidal <i>Salmonella</i> serovars such as <i>S</i>. Isangi in order to prevent its dissemination among human and non-human sources.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9844264","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}