Access microbiology最新文献

{"title":"Erysipelothrix rhusiopathiae-associated bloodstream infection in a patient with systemic lupus erythematosus: a case report and literature review.","authors":"Calvin Ka-Fung Lo, Cole Schonhofer, Neil Mina, Shazia Masud, Patrick Ho Pun Wong, Michael G Chapman","doi":"10.1099/acmi.0.000881.v3","DOIUrl":"10.1099/acmi.0.000881.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Systemic human infections caused by <i>Erysipelothrix rhusiopathiae</i> have been increasingly reported especially within immunocompromised hosts and those with significant occupational exposure to livestock and aquatic animals. We report a case of <i>E. rhusiopathiae</i> bacteraemia in a patient with systemic lupus erythematosus (SLE) and present a literature review on clinical outcomes and microbiologic diagnosis for this organism. <b>Casepresentation.</b> A 43-year-old female patient was reporting a 1-month history of intermittent fevers. She recently increased her immunosuppression medication for her underlying SLE on the advice of her rheumatologist. The patient sustained a finger laceration from butchering cattle meat 2 weeks after the onset of her initial symptoms, with worsening index finger swelling and increased febrile episodes. Two weeks post-injury, multiple blood cultures were drawn, and each isolated Gram-positive bacilli. Given her recurrent intermittent fevers, there was a concern for ongoing infection, and therefore, intravenous vancomycin was started with prompt referral to an outpatient parenteral antibiotic therapy clinic. The Gram-positive bacillus was confirmed as <i>E. rhusiopathiae</i> via matrix-assisted laser desorption/ionization-time of flight analysis. Given intrinsic resistance to vancomycin, vancomycin was switched to intravenous ceftriaxone as targeted antimicrobial therapy for 2 weeks. Reassuringly, there was no echocardiographic evidence of infective endocarditis, warranting the prolonged treatment course. Post-treatment, she remained symptom-free with the resolution of joint symptoms and fevers. <b>Conclusion.</b> Our report illustrates a case of <i>E. rhusiopathiae</i> bacteraemia from an immunodeficient host, with prompt microbiologic diagnosis and intervention with appropriate antimicrobial coverage. Literature reflects the rarity of this infection, predilections to specific susceptible hosts and the importance of raising awareness of zoonotic infections.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence.","authors":"Deisy G Carneiro, Pedro Marcus P Vidigal, Túlio Morgan, Maria Cristina D Vanetti","doi":"10.1099/acmi.0.000828.v3","DOIUrl":"10.1099/acmi.0.000828.v3","url":null,"abstract":"<p><p><i>Salmonella enterica</i> serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. <i>Salmonella</i> Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The <i>Salmonella</i> pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many <i>Salmonella</i> serotypes, and <i>Salmonella</i> Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of <i>Salmonella</i> Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve <i>Salmonella</i> pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to <i>Salmon_118970_sal3</i> and <i>Gifsy-2</i>. The genome also contains two CRISPR systems. Comparative genome analysis with <i>Salmonella</i> Enteritidis ATCC 13076, <i>Salmonella</i> Typhimurium ATCC 13311, and <i>Salmonella</i> Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among <i>Salmonella</i> Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in <i>Salmonella</i> Enteritidis PT4 578.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salmonella Weltevreden lung abscess and empyema without preceding gastrointestinal symptoms: an emerging pathogen in Australia?","authors":"Victoria Grey, Ernest Tee, Lauren Phillips, Gino Micalizzi, Mark Armstrong","doi":"10.1099/acmi.0.000635.v3","DOIUrl":"10.1099/acmi.0.000635.v3","url":null,"abstract":"<p><p>Non-typhoidal <i>Salmonella</i> lung infections are rare and are usually confined to immunocompromised hosts. Previous case reports have found that usually patients have either gastroenteritis or bacteraemia in addition to pulmonary involvement. We present the first known reported case of a <i>Salmonella</i> Weltevreden lung abscess and empyema in an immunocompetent patient without gastroenteritis. Despite the use of antimicrobials active against the pathogen, the patient needed surgical intervention to achieve adequate source control. While <i>S</i>. Weltevreden has previously been associated with returned travellers, especially from Southeast Asia, its incidence in Queensland is now increasing. Therefore, it is important for clinicians to be aware of its potential severity as well as the range of presentations.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corynebacterium amycolatum peritonitis in a patient undergoing peritoneal dialysis: case report and literature review.","authors":"Fatima Zahra Adil, Imane Aragon, Elmostafa Benaissa, Yassine Ben Lahlou, Fatna Bssaibis, Adil Maleb, Mariama Chadli, Mostafa Elouennass","doi":"10.1099/acmi.0.000880.v3","DOIUrl":"10.1099/acmi.0.000880.v3","url":null,"abstract":"<p><p>Peritoneal dialysis is a blood purification technique used in cases of end-stage chronic kidney failure, based on the filtering capabilities of the peritoneum. Infections, often caused by poor asepsis during catheter manipulation, are generally attributed to <i>Staphylococcus epidermidis</i> and <i>Staphylococcus aureus. Corynebacterium</i>, usually considered non-pathogenic, is rarely involved in these infections. We present a case of peritonitis due to <i>Corynebacterium amycolatum</i> in a patient undergoing peritoneal dialysis. The diagnosis was made based on cytobacteriological examination of the dialysate fluid, which on two occasions showed high levels of white blood cells with a predominance of neutrophilic polymorphonuclear and a monomorphic appearance of colonies on agar medium, whose identification by biochemical tests and antibiotic sensitivity study confirmed the presence of <i>C. amycolatum</i>. The patient was successfully treated with vancomycin, resulting in symptom resolution and sterilization of the dialysate fluid. Although rare, the involvement of <i>Corynebacterium</i> species underscores the importance of confirming its pathogenicity. Further studies are needed to better understand the epidemiology of these infections and guide future treatments. This case also highlights the need for a rigorous approach to confirming the pathogenicity of <i>Corynebacterium</i> despite its traditional classification as a contaminant.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bloodstream infections in cancer patients in central India: pathogens and trends of antimicrobial resistance over a 5-year period.","authors":"Sonali Choudhari, Ruchita Gawande, Jerestin Watchmaker, Pooja Bamnote, Pradeep Mishra, Pankaj Dwivedi","doi":"10.1099/acmi.0.000673.v5","DOIUrl":"https://doi.org/10.1099/acmi.0.000673.v5","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; Bloodstream infection (BSI) is a common complication with a high fatality rate in cancer patients. There are notable variations in the epidemiology of BSI over time and among different countries. Infections due to multidrug-resistant organisms (MDROs) such as extended-spectrum beta-lactamases (ESBLs) and carbapenem-resistant &lt;i&gt;Enterobacteriaceae&lt;/i&gt; (CRE) are increasing. This may lead to inadequate empirical antibiotic therapy, increasing the antimicrobial resistance (AMR) problem and unfavourable outcomes in these immunocompromised patients. There is paucity of data pertaining to AMR in such vulnerable patients from developing countries such as India. The aim of this study was to investigate the distribution of the bacterial pathogens causing BSI and the AMR trend in cancer patients in central India. &lt;b&gt;Methodology.&lt;/b&gt; This single-centre retrospective observational study was conducted in a tertiary care cancer hospital. Patients with solid organ and haematological malignancies, both adults and paediatric, who had blood cultures sent to the microbiology laboratory from January 2018 to December 2022 were included. Blood cultures were processed using the BacT/ALERT 3D system (bioMérieux, France), and the identification of the bacteria and their antimicrobial susceptibility (AST) was performed using the Vitek 2 compact system (bioMérieux, France). Electronic medical records and microbiology lab records were used to retrieve the demographic and microbiological data. Microsoft Excel (RRID:SCR_016137) was used to enter and tabulate the data. Statistical analysis was performed using SPSS version 29 (RRID:SCR_002865). &lt;b&gt;Results.&lt;/b&gt; A total of 687 isolates from 524 patients were studied. Gram-negative bacteria (64%) were the commonest cause of BSI in the studied patients, followed by Gram-positive cocci (25%) and fungal isolates (9%). Ten cases were polymicrobial. &lt;i&gt;Escherichia coli&lt;/i&gt; (&lt;i&gt;n&lt;/i&gt;=140) was the most common among the isolated pathogens, followed by &lt;i&gt;Klebsiella&lt;/i&gt; species (&lt;i&gt;n&lt;/i&gt;=103), &lt;i&gt;Pseudomonas&lt;/i&gt; species (&lt;i&gt;n&lt;/i&gt;=102), and coagulase-negative staphylococci (CONS) (&lt;i&gt;n&lt;/i&gt;=92). Among the 140 isolates of &lt;i&gt;E. coli&lt;/i&gt;, 66% were extended-spectrum β-lactamase (ESBL) producers and 26% were resistant to carbapenem. Among the 103 isolated &lt;i&gt;Klebsiella&lt;/i&gt; species, 50% were carbapenem resistant and 36% were ESBL producers. Among enterobacterales, the CRE rate was 34%. Carbapenem resistance was seen in 25% of &lt;i&gt;Pseudomonas&lt;/i&gt; species and 53% of &lt;i&gt;Acinetobacter&lt;/i&gt; species isolates. &lt;i&gt;Klebsiella&lt;/i&gt; species were the most resistant pathogens isolated. CONS comprised 56% of all Gram-positive isolates, followed by &lt;i&gt;Staphylococcus aureus&lt;/i&gt; (36%), enterococci species (11%), and streptococci species (3%). Methicillin resistance was 60% in CONS and 64% in &lt;i&gt;S. aureus&lt;/i&gt;. One vancomycin-resistant enterococcus was isolated. Non-&lt;i&gt;albicans Candida&lt;/i&gt; was the most common fungal pathogen. The sensitivity ","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meropenem-resistant Burkholderia pseudomallei: a concerning single case in Australia with no prior meropenem exposure.","authors":"Pirathaban Sivabalan, Ferris Satyaputra, Ian Gassiep, Brian Forde, Jaimie Frazer, Matthew Glover, Buenafe Adams, Robert Norton","doi":"10.1099/acmi.0.000619.v4","DOIUrl":"10.1099/acmi.0.000619.v4","url":null,"abstract":"<p><p>We report a case of cutaneous melioidosis in a 54-year-old male with a meropenem-resistant sub-population. He was empirically treated with episodic doxycycline and trimethoprim-sulfamethoxazole; however, the abscess re-accumulated. The patient had no prior exposure to meropenem. A sub-population of the isolate was meropenem resistant with an MIC >32 µg ml^-1 and the identification was re-confirmed as <i>Burkholderia pseudomallei</i>. Whole-genome sequencing with ARDaP analysis only revealed a resistance determinant to doxycycline and did not reveal a resistance determinant to meropenem. Furthermore, no carbapenemases were detected through multiple bioinformatics tools. To date, this is the first reported case in Australia of a <i>B. pseudomallei</i> isolate resistant to meropenem without previous carbapenem exposure.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriological profile of community peritonitis operated in a Moroccan Hospital.","authors":"Samia Bazhar, Elmostafa Benaissa, Fatima Ziad, Leila Laamara, Yassine Ben Lahlou, Mariama Chadli, Mostafa Elouennass","doi":"10.1099/acmi.0.000816.v5","DOIUrl":"https://doi.org/10.1099/acmi.0.000816.v5","url":null,"abstract":"<p><p><b>Introduction.</b> Peritonitis is characterized by acute inflammation of the peritoneum, often resulting from digestive organ perforation or intra-abdominal septic focus. It may be of either infectious or non-infectious origin. The bacteria involved are those of the digestive flora (<i>Enterobacteriaceae</i> and anaerobes), while Gram-positive cocci and yeasts can be isolated in nosocomial infections. Our study aims to isolate and identify the germs involved in community-acquired peritonitis in order to assess their susceptibility to the antibiotics available in our country. <b>Methods.</b> This is a retrospective study of the bacteriological profile of community peritonitis in Rabat Morocco. A total of 150 adult patients with peritonitis were admitted and samples were collected intraoperatively for bacteriological examination between 1 July 2022 and 30 April 2023. <b>Results.</b> Among the 150 patients, 101 (67.8%) were males and 49 (32.2%) were females, with a sex ratio (M/F) of 2 : 1. The mean age of the patients was 40.5 years±20.12. The distribution of bacteria was dominated by <i>Escherichia coli</i> (44%). Overall, 70% of <i>E. coli</i> isolated exhibited resistance to ampicillin, whereas no resistance to ampicillin has been reported for <i>Enterococcus</i>. <b>Discussion.</b> In the present study, we were interested in the bacteriological profile of community peritonitis in order to adapt the antibiotic therapy to our bacterial ecology. Our findings indicate a concerning trend of increasing resistance among <i>E. coli</i> to the commonly used amoxicillin/clavulanic acid combination in our clinical setting. <b>Conclusion.</b> Consequently, there is a need to reassess the empiric antibiotic prescribed for the management of community-acquired peritonitis.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete sequences of pIJ101-based Streptomyces-Escherichia coli shuttle vectors.","authors":"Katelyn V Brown, S Eric Nybo","doi":"10.1099/acmi.0.000893.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000893.v3","url":null,"abstract":"<p><p>High-copy-number plasmids are indispensable tools for gene overexpression studies in prokaryotes to engineer pathways or probe phenotypes of interest. The development of genetic tools for the industrially relevant Actinobacteria is of special interest, given their utility in producing keratolytic enzymes and biologically active natural products. Within the Actinobacteria, <i>Streptomyces-Escherichia coli</i> shuttle vectors based on the SCP2* and pIJ101 incompatibility groups are widely employed for molecular cloning and gene expression studies. Here, the sequences of two commonly used pIJ101-based <i>Streptomyces-E. coli</i> shuttle vectors, pEM4 and pUWL201, were determined using next-generation sequencing. These plasmids drive the expression of heterologous genes using the constitutive <i>ermE*p</i> promoter. pEM4 was found to be 8.3 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the <i>lacZɑ</i> fragment, a ColE1 origin of replication and the <i>Streptomyces</i> pIJ101 origin of replication. pUWL201 was found to be 6.78 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the <i>lacZɑ</i> fragment, a ColE1 origin of replication and the <i>Streptomyces</i> pIJ101 origin of replication. Interestingly, the sequences for both pEM4 and pUWL201 exceed their previously reported size by 1.1 and 0.4 kbp, respectively. This report updates the literature with the corrected sequences for these shuttle vectors, ensuring their compatibility with modern synthetic biology cloning methodologies.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11498179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental sampling for the detection of capripox viruses and peste des petits ruminants virus in households and livestock markets in Plateau State, Nigeria.","authors":"Emma Brown, David Ehizibolo, Banenat B Dogonyaro, Yiltawe Wungak, Olumuyiwa Oyekan, Adeyinka Adedeji, Sandra Ijeoma, Rebecca Atai, Moses Oguche, Mark Samson, Fabrizio Rosso, Anna B Ludi, Georgina Limon, Andrew E Shaw, Claire Colenutt, Simon Gubbins","doi":"10.1099/acmi.0.000872.v3","DOIUrl":"10.1099/acmi.0.000872.v3","url":null,"abstract":"<p><p>Multiple transboundary animal diseases (TADs) circulate in Plateau State, Nigeria, where livestock keeping is common and contributes to both the physical and socio-economic well-being of a large proportion of the population. In this study, we explored the potential for environmental sampling to detect viruses causing TADs circulating in the region. Electrostatic dust cloths were used to swab areas of the environment likely to have contact with secretions and excretions from infected animals. Samples were collected monthly from five households, one transhumance site and one livestock market in two local government areas in Plateau State between March and October 2021. These were tested for the presence of peste des petits ruminants virus (PPRV) and capripox viruses using real-time PCR. Of the 458 samples collected, 2.4% (<i>n</i> = 11) were positive for PPRV RNA and 1.3 % (<i>n</i> = 6) were positive for capripox virus DNA. A capripox differentiation assay showed that these samples were positive for sheep pox virus (<i>n</i> = 2), goat pox virus (<i>n</i> = 2) and lumpy skin disease virus (<i>n</i> = 2). Our results demonstrate that environmental sampling could be used as part of TAD surveillance in the area. Environmental swabs require little technical knowledge to collect and can be used to detect multiple viruses from a single sample.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.","authors":"","doi":"10.1099/acmi.0.000894.v3","DOIUrl":"10.1099/acmi.0.000894.v3","url":null,"abstract":"<p><p>Fluoroquinolone-resistant <i>Escherichia coli</i> sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are published in the literature, none of which are from Australia. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains sequenced using Oxford Nanopore Technologies and Illumina. Using <i>in silico</i> genotyping, we found that all strains were multi-drug resistant, including resistances to fluoroquinolones and cephalosporins. <i>In vitro</i> antibiotic susceptibility testing mostly correlated with individual genotypes. The exception was MS8320, which had additional <i>in vitro</i> resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a <i>bla</i> _TEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular locus switch. Phenotypic confirmation of differing capsules in Australian ST1193 strains, coupled with genetic analysis revealing insertions downstream of the capsular locus, underscored the genetic distinctions between K5 and K1 capsule encoding strains. This study provides five new reference ST1193 genomes from Australia. These include the earliest complete K5-capsule ST1193 genomes on record (collected 2007), alongside our reference genome (MS10858), a clinical isolate obtained early during the ST1193 expansion and representative of the predominant K1-associated clade. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}