International Journal of Medical Microbiology最新文献

{"title":"Aspergillus fumigatus sensu stricto genetic diversity from cystic fibrosis patients","authors":"Aryse Martins Melo ,&nbsp;Vanice Rodrigues Poester ,&nbsp;Mariana Rodrigues Trápaga ,&nbsp;Fernando Azevedo Faria ,&nbsp;Valério Aquino ,&nbsp;Cecília Bittencourt Severo ,&nbsp;David A. Stevens ,&nbsp;Cristina Veríssimo ,&nbsp;Raquel Sabino ,&nbsp;Melissa Orzechowski Xavier","doi":"10.1016/j.ijmm.2024.151639","DOIUrl":"10.1016/j.ijmm.2024.151639","url":null,"abstract":"<div><div>We aimed to access the genetic diversity of <em>Apergillus fumigatus</em> strains obtained from cystic fibrosis (CF) patients from southern Brazil. <em>A. fumigatus</em> sensu stricto isolates from respiratory clinical specimens were genotyped by microsatellite markers and azole resistance was evaluated by azole-agar screening. Twenty-seven isolates from twenty-seven patients showed a high genetic diversity, with the differentiation of 25 different genotypes (25 unique and one common to two isolates). All isolates were susceptible to the azoles tested. We believe that prospectively monitoring <em>A. fumigatus</em> genetic diversity is essential to identify interpatient transmission and outbreaks, as is the identification of resistant strains.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142531879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Analysis and Virulence Assessment of Hypervirulent Klebsiella pneumoniae K16-ST660 in Severe Cervical Necrotizing Fasciitis","authors":"Jun Huang ,&nbsp;Jiaru Zhuang ,&nbsp;Lin Wan ,&nbsp;Yutong Liu ,&nbsp;Yiran Du ,&nbsp;Lu Zhou ,&nbsp;Renjing Hu ,&nbsp;Lanfeng Shen","doi":"10.1016/j.ijmm.2024.151635","DOIUrl":"10.1016/j.ijmm.2024.151635","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Objective&lt;/h3&gt;&lt;div&gt;To investigate the source of infection in a patient with recurrent severe neck infections caused by &lt;em&gt;Klebsiella pneumoniae&lt;/em&gt; and to analyze the virulence of isolates obtained from different sites of the patient.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;We collected preoperative neck abscess puncture fluid, intraoperative neck drainage fluid, sputum, intestinal fecal specimens, and blood samples from a patient who visited Wuxi Second People's Hospital twice between 2017 and 2018. We conducted isolation, identification, drug sensitivity tests, and string tests on the isolates. Capsule serotyping and virulence gene analysis were performed using PCR. The genetic relationship of different isolates was assessed by Multilocus Sequence Typing and virulence was evaluated using the Galleria mellonella infection model. Additionally, whole-genome sequencing was used to analyze the chromosomal and plasmid genes of one isolate.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results&lt;/h3&gt;&lt;div&gt;&lt;em&gt;Klebsiella pneumoniae&lt;/em&gt; was detected in the sputum and fecal specimens from both hospitalizations, as well as the preoperative ultrasound-guided puncture fluid and intraoperative drainage fluid from the first hospitalization, resulting in six isolates. These isolates were all K16 serotype, positive in the string test, and identified as ST660 by Multilocus Sequence Typing, indicating they belonged to the same clone. Virulence gene analysis showed that &lt;em&gt;wcaG, iucB, iroNB, rmpA, rmpA2, Aer, kfuBC, ureA, fimH, mrkD, uge&lt;/em&gt;, and &lt;em&gt;peg344&lt;/em&gt; were positive, while &lt;em&gt;allS, cf29a&lt;/em&gt;, and &lt;em&gt;Wzy_K1&lt;/em&gt; were negative. In the Galleria mellonella virulence assay, the lethality of different isolates was dose-dependent. The K16 group showed significantly higher larval mortality compared to other control groups (including K1, K2, K5, K20, and K57 groups). Genome sequencing revealed that plasmid p17388 carried numerous virulence genes and insertion sequences, particularly &lt;em&gt;ISKPN74&lt;/em&gt;, and showed high homology with other Klebsiella plasmids.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Conclusion&lt;/h3&gt;&lt;div&gt;This study is the first to report severe cervical necrotizing fasciitis caused by the K16-ST660 &lt;em&gt;Klebsiella pneumoniae&lt;/em&gt; Isolate. The high virulence of these isolates was confirmed by the Galleria mellonella virulence assay and the detection of numerous virulence genes. In-depth analysis of plasmid p17388 suggests that ISKPN74 may enhance stable integration of the plasmid into the bacterial chromosome through recombinases and transposases, thereby reducing the likelihood of plasmid loss and increasing bacterial virulence. Additionally, IS5 family insertion sequences may carry extra promoters or enhancers that, when inserted upstream of mucoviscosity-associated genes such as rmpA, may increase the transcription levels of downstream genes. This ISKPN74-mediated integration or insertion reveals a complex genetic mechanism that may contribute to the severity of infections caused by ST","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-transcribed genes SA1833-SA1832 promote persister formation by regulating the transcription of holin-like gene lrgA in methicillin-resistant Staphylococcus aureus strain N315","authors":"Shiwen Xu ,&nbsp;Jiade Zhu ,&nbsp;Yujie Li ,&nbsp;Baolin Sun","doi":"10.1016/j.ijmm.2024.151636","DOIUrl":"10.1016/j.ijmm.2024.151636","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em>, a facultative anaerobic gram-positive bacterial pathogen, has posed major threat to public health worldwide. Upon <em>S. aureus</em> infection, the host immune system is activated for clearance. However, intracellular <em>S. aureus</em>, which remains viable for an extended time, has evolved the ability to escape from immune response and extracellular antibiotics. One of possible strategies is the formation of persisters. Persistence is one of the major causes of <em>S. aureus</em> relapse infection but the underlying mechanisms remain obscure. Here, we identified two co-transcribed genes <em>SA1833-SA1832</em> that are involved in persister formation in <em>S. aureus</em>. Dysfunction of <em>SA1833</em> and/or <em>SA1832</em> significantly reduces persister formation in the presence of ceftizoxime. Additionally, we found that the expression of <em>SA1833</em> and <em>SA1832</em> under the induction of oxidative stress and SOS response is strictly regulated by the LexA-RecA pathway. Interestingly, <em>SA1833-SA1832</em> contributes to persister formation in an <em>lrgA</em>-dependent manner. Moreover, the mouse RAW264.7 macrophage infection model indicated that disrupting <em>SA1833-SA1832</em> inhibits <em>S. aureus</em> from infecting macrophages and impairs its ability to survive in the intracellular environment.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Desiccation tolerance and reduced antibiotic resistance: Key drivers in ST239-III to ST22-IV MRSA clonal replacement at a Malaysian teaching hospital","authors":"Nurul Amirah Mohamad Farook ,&nbsp;Silvia Argimón ,&nbsp;Muttaqillah Najihan Abdul Samat ,&nbsp;Sharifah Azura Salleh ,&nbsp;Sunita Sulaiman ,&nbsp;Toh Leong Tan ,&nbsp;Petrick Periyasamy ,&nbsp;Chee Lan Lau ,&nbsp;Nor Azila Muhammad Azami ,&nbsp;Raja Mohd Fadhil Raja Abd Rahman ,&nbsp;Mia Yang Ang ,&nbsp;Hui-min Neoh","doi":"10.1016/j.ijmm.2024.151638","DOIUrl":"10.1016/j.ijmm.2024.151638","url":null,"abstract":"<div><div>Molecular surveillance of methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolated from Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital revealed clonal replacement events of SCC<em>mec</em> type III-SCC<em>mercury</em> to SCC<em>mec</em> type IV strains before the year 2017; however, the reasons behind this phenomenon are still unclear. This study aimed to identify factors associated with the clonal replacement using genomic sequencing and phenotypic investigations (antibiogram profiling, growth rate and desiccation tolerance determination, survival in vancomycin sub-minimum inhibitory concentration (MIC) determination) of representative HCTM MRSA strains isolated in four-year intervals from 2005 – 2017 (n = 16). HCTM Antimicrobial Stewardship (AMS) and Infection Prevention and Control (IPC) policies were also reviewed. Phylogenetic analyses revealed the presence of 3 major MRSA lineages: ST239-III, ST22-IV and ST6-IV; MRSAs with the same STs shared similar core and accessory genomes. Majority of the ST239-III strains isolated in earlier years of the surveillance (2005, 2009 and 2013) were resistant to many antibiotics and harboured multiple AMR and virulence genes compared to ST22-IV and ST6-IV strains (isolated in 2013 and 2017). Interestingly, ST22-IV and ST6-IV MRSAs grew significantly faster and were more resistant to desiccation than ST239-III (<em>p</em> &lt; 0.05), even though the later clone survived better post-vancomycin exposure. Intriguingly, ST22-IV was outcompeted by ST239-III in broth co-cultures; though it survived better when desiccated together with ST239-III. Higher desiccation tolerance and fewer carriage of AMR genes by ST22-IV, together with reduction of antibiotic selection pressure in HCTM (due to AMS and IPC policies) during 2005 – 2017 may have provided the clone a competitive edge in replacing the previously dominant ST239-III in HCTM. This study highlights the importance of MRSA surveillance for a clearer picture of circulating clones and clonal changes. To our knowledge, this is the first genomic epidemiology study of MRSA in Malaysia, which will serve as baseline genomic data for future surveillance.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477","authors":"Frank M. Aarestrup ,&nbsp;Egon B. Hansen ,&nbsp;Happiness H. Kumburu ,&nbsp;Tutu Mzee ,&nbsp;Saria Otani","doi":"10.1016/j.ijmm.2024.151637","DOIUrl":"10.1016/j.ijmm.2024.151637","url":null,"abstract":"<div><div><em>Staphyloccous aureus</em> belonging to sequence type 5477 have recently been identified as a predominant clone causing bovine mastitis in Rwanda and Tanzania. We compared nine <em>S. aureus</em> ST5477 to 17 isolates belonging to other sequence types by their biochemical profile and ability to acidify milk and grow in minimum media containing lactose. We found that ST5477 isolates all were positive in ONPG (o-nitrophenyl-β-D-galactopyranoside) test and negative for mannitol fermentation potentially challenging the correct identification of this sequence type as <em>S. aureus.</em> In addition, ST5477 isolates were all much faster in acidifying milk and grew faster in minimal media with lactose compared to other strains suggesting an increased lactose utilization and thereby adaptation to the bovine udder environment as a possible reason for the recent successful emergence. Comparison of the <em>lac</em> gene region of the genome of a recently sequenced ST5477 and that of <em>S. aureus</em> reference genome showed that both strains contained the known <em>lac</em>ABCD genes involved in the lactose degradation, but that ST5477 had a 12 amino-acid deletion and two amino-acid differences in the <em>lac</em> gene transcription regulator, suggesting that increased transcription might play a role. In conclusion, these preliminary data suggests that improved lactose utilization and the ability to grow faster in milk may have been a key feature for the recent success of ST5477 as a bovine adapted clone.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico analysis and functional characterization of a leucine-rich repeat protein of Leptospira interrogans","authors":"João P. Gaspar ,&nbsp;Maria B. Takahashi ,&nbsp;Aline F. Teixeira ,&nbsp;Ana L.T.O. Nascimento","doi":"10.1016/j.ijmm.2024.151633","DOIUrl":"10.1016/j.ijmm.2024.151633","url":null,"abstract":"<div><p>Pathogenic spirochetes of the genus <em>Leptospira</em> are the causative agent of leptospirosis, a widely disseminated zoonosis that affects humans and animals. The ability of leptospires to quickly cross host barriers causing infection is not yet fully understood. Thus, understanding the mechanisms of pathogenicity is important to combat leptospiral infection. Outer membrane proteins are interesting targets to study as they are able to interact with host molecules. Proteins containing leucine-rich repeat (LRR) domains are characterized by the presence of multiple regions containing leucine residues and they have putative functions related to host-pathogen interactions. Hence, the present study aimed to clone and express the recombinant protein encoded by the LIC11098 gene, an LRR protein of <em>L. interrogans</em> serovar Copenhageni. <em>In silico</em> analyses predicted that the target protein is conserved among pathogenic strains of <em>Leptospira</em>, having a signal peptide and multiple LRR domains. The DNA sequence encoding the LRR protein was cloned in frame into the pAE vector, expressed without mutations in <em>Escherichia coli</em> and purified by His-tag chromatography. Circular dichroism (CD) spectrum showed that the recombinant protein was predominantly composed of β-sheets. A dose-dependent interaction was observed with cellular and plasma fibronectins, laminin and the complement system component C9, suggesting a possible role of the protein encoded by LIC11098 gene at the initial stages of infection.</p></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1438422124000377/pdfft?md5=a4c205321a10694d63ab91a1343a9a98&pid=1-s2.0-S1438422124000377-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142129008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional profiling of CHAP domain-containing peptidoglycan hydrolases of Staphylococcus aureus USA300 uncovers potential targets for anti-staphylococcal therapies","authors":"Min Wang ,&nbsp;Xiaofang Li ,&nbsp;Francis M. Cavallo ,&nbsp;Harita Yedavally ,&nbsp;Sjouke Piersma ,&nbsp;Elisa J.M. Raineri ,&nbsp;Elias Vera Murguia ,&nbsp;Jeroen Kuipers ,&nbsp;Zhenhua Zhang ,&nbsp;Jan Maarten van Dijl ,&nbsp;Girbe Buist","doi":"10.1016/j.ijmm.2024.151632","DOIUrl":"10.1016/j.ijmm.2024.151632","url":null,"abstract":"<div><p>The bacterial pathogen <em>Staphylococcus aureus</em> employs a thick cell wall for protection against physical and chemical insults. This wall requires continuous maintenance to ensure strength and barrier integrity, but also to permit bacterial growth and division. The main cell wall component is peptidoglycan. Accordingly, the bacteria produce so-called peptidoglycan hydrolases (PGHs) that cleave glycan strands to facilitate growth, cell wall remodelling, separation of divided cells and release of exported proteins into the extracellular milieu. A special class of PGHs contains so-called ‘cysteine, histidine-dependent amidohydrolase/peptidase’ (CHAP) domains. In the present study, we profiled the roles of 11 CHAP PGHs encoded by the core genome of <em>S. aureus</em> USA300 LAC. Mutant strains lacking individual CHAP PGHs were analysed for growth, cell morphology, autolysis, and invasion and replication inside human lung epithelial cells. The results show that several investigated CHAP PGHs contribute to different extents to extracellular and intracellular growth and replication of <em>S. aureus</em>, septation of dividing cells, daughter cell separation once the division process is completed, autolysis and biofilm formation. In particular, the CHAP PGHs Sle1 and SAUSA300_2253 control intracellular staphylococcal replication and the resistance to β-lactam antibiotics like oxacillin. This makes the <em>S. aureus</em> PGHs in general, and the Sle1 and SAUSA300_2253 proteins in particular, attractive targets for future prophylactic or therapeutic anti-staphylococcal interventions. Alternatively, these cell surface-exposed enzymes, or particular domains of these enzymes, could be applied in innovative anti-staphylococcal therapies.</p></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1438422124000365/pdfft?md5=262fbb700c3027a2b0c8467a74f603f3&pid=1-s2.0-S1438422124000365-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141979142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical characteristics of community-onset Clostridioides difficile infections at a tertiary hospital in mainland China: A fourteen-year (2010–2023) retrospective study","authors":"Xinrong Jiang ,&nbsp;Junyu Bian ,&nbsp;Tao Lv ,&nbsp;Lisi Zheng ,&nbsp;Yuhong Zhao ,&nbsp;Jianqin He ,&nbsp;Yunbo Chen","doi":"10.1016/j.ijmm.2024.151631","DOIUrl":"10.1016/j.ijmm.2024.151631","url":null,"abstract":"<div><h3>Background</h3><p><em>Clostridioides difficile</em> infection (CDI) is an increasingly common disease in healthcare facilities and community settings. However, there are limited reports of community-onset CDI (CO-CDI) in China.</p></div><div><h3>Methods</h3><p>We collected diarrheal stool samples from 3885 patients who went to outpatient department or emergency department in a tertiary hospital in China during 2010–2023, analyzed the correlation between patients’ basic information and the detection rate of CDI. Besides, all stool samples from 3885 outpatients included were tested by culturing. Moreover, we randomly selected 89 patients’ stools during the 14 years and isolated 126 <em>C. difficile</em> strains from them. The presence of toxin genes (<em>tcdA</em>, <em>tcdB</em>, <em>cdtA</em>, and <em>cdtB</em>) were confirmed by PCR. Toxigenic strains were typed using multilocus sequence typing (MLST). Susceptibility to 9 antimicrobials was evaluated using the E-test.</p></div><div><h3>Results</h3><p>528 of 3885 patients (13.6 %) with diarrhea were finally diagnosed as CDI. The median age of patients included was 51 years (6 months-95 years), while the median of patients with CDI was older than patients with negative results [55.5 years (6 months-93 years) <em>vs.</em> 50 years (9 months −95 years), <em>p</em> &lt; 0.001]. In winter, patients with diarrhea might be more likely to have CDI. The detection rate of CDI of patients in emergency department was much higher than those in other outpatients (20.7 % <em>vs.</em> 12.4 %, <em>p</em> &lt; 0.001), and did differ from each outpatient departments (<em>p</em> &lt; 0.05). There were 95 isolated strains detected as toxigenic <em>C. difficile</em>. Among these strains, 82 (86.3 %) had the <em>tcdA</em> and <em>tcdB</em> genes (A+B+) and 5 of these 82 strains were positive for the binary toxin genes (<em>cdtA</em> and <em>cdtB</em>) (A+B+CDT+). There were 15 different sequence types (STs) by multilocus sequence typing (MLST), while the most ST was ST-54 (23.2 %). ST types composition was relatively stable over the time span of this study. Some strains had high resistance to ciprofloxacin, clindamycin, and erythromycin. Twenty-three isolates (24.2 %) were multidrug-resistant.</p></div><div><h3>Conclusions</h3><p>Outpatients with CDI were common among patients having diarrhea during this period in our hospital. Elderly patients and patients went to emergency department may be susceptible to CDI. Based on MLST, the result revealed that the <em>C. difficile</em> isolates had high genetic diversity and maintained stability in this period. All isolates were susceptible to metronidazole and vancomycin, and nearly one quarter of all isolates had multidrug resistance.</p></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1438422124000353/pdfft?md5=3cae71e5cd569816143cb38e32858684&pid=1-s2.0-S1438422124000353-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141638298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterization of Staphylococcus argenteus from Indonesia","authors":"Indri Rooslamiati Supriadi ,&nbsp;Dewi Santosaningsih ,&nbsp;Nyoman S. Budayanti ,&nbsp;Willemien H.A. Zandijk ,&nbsp;Amber Rijfkogel ,&nbsp;Corné H.W. Klaassen ,&nbsp;Juliëtte A. Severin","doi":"10.1016/j.ijmm.2024.151629","DOIUrl":"10.1016/j.ijmm.2024.151629","url":null,"abstract":"<div><h3>Background</h3><p>In 2015, <em>Staphylococcus argenteus</em> was reported for the first time as a novel species of the <em>Staphylococcus aureus</em> complex. While <em>S. argenteus</em> has been found in many countries, its presence in Indonesia has not been reported yet. Our aim is to confirm <em>S. argenteus</em> presence in Indonesia, describe its characteristics and analyze its genomic diversity.</p></div><div><h3>Methods</h3><p>The <em>S. aureus</em> isolates used in this study were collected from patients with skin and soft tissue infections in Indonesia, between July 2009 to February 2010. Randomly selected isolates were recultured from −80 C° stocks and analyzed using matrix-assisted laser desorption/ionization – time of flight (MALDI-TOF). Isolates identified as <em>S. argenteus</em>, <em>S. roterodami</em>, or <em>S. schweitzeri</em> and <em>S. aureus</em> with a low score in the MALDI-TOF analysis were analyzed by a real-time PCR targeting the <em>nucA</em> gene able to identify true <em>S. argenteus</em>. Isolates identified as <em>S. argenteus</em> were further characterized by whole genome sequencing. Vitek®2 (bioMérieux) was used for antimicrobial susceptibility testing.</p></div><div><h3>Results</h3><p>Fifteen isolates were identified as <em>S. argenteus</em>, with the majority belonging to ST2250. Two pairs of isolates proved to be identical by core genome multilocus sequence typing analysis. Most isolates were susceptible to all antibiotics tested, except for seven isolates (46.7 %) that were resistant to benzylpenicillin, and one isolate was resistant to tetracycline (6.7 %). The presence of resistance genes <em>blaZ</em> and <em>tet(45)</em> correlated with these findings. Notably, the <em>sey</em> enterotoxin gene was prevalent in 80 % of the isolates. Other virulence factor genes were less prevalent. Plasmid replicon types in <em>S. argenteus</em> were also known to <em>S. aureus</em>.</p></div><div><h3>Conclusion</h3><p>Our study reveals the occurrence of <em>S. argenteus</em> in Indonesia. The diversity within Indonesian <em>S. argenteus</em> matches the global diversity of <em>S. argenteus.</em> Identical isolates between patients indicate potential transmission events. A lower prevalence of a broad panel of virulence factors suggests that <em>S. argenteus</em> is less virulent than <em>S. aureus.</em></p></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S143842212400033X/pdfft?md5=0e23551bcad6c03be6d39eb0b78ca47a&pid=1-s2.0-S143842212400033X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-time application of ITS and D1-D3 nanopore amplicon metagenomic sequencing in fungal infections: Enhancing fungal infection diagnostics","authors":"Seondeuk Kim ,&nbsp;Narae Kim ,&nbsp;Wan Beom Park ,&nbsp;Chang Kyung Kang ,&nbsp;Jae Hyeon Park ,&nbsp;Soon-Tae Lee ,&nbsp;Keun-Hwa Jung ,&nbsp;Kyung-Il Park ,&nbsp;Sang Kun Lee ,&nbsp;Jangsup Moon ,&nbsp;Kon Chu","doi":"10.1016/j.ijmm.2024.151630","DOIUrl":"10.1016/j.ijmm.2024.151630","url":null,"abstract":"<div><p>While fungal infections cause considerable morbidity and mortality, the performance of the current diagnostic tests for fungal infection is low. Even though fungal metagenomics or targeted next-generation sequencing have been investigated for various clinical samples, the real-time clinical utility of these methods still needs to be elucidated. In this study, we used <em>internal transcribed spacer</em> (<em>ITS</em>) and <em>D1-D3</em> ribosomal DNA nanopore amplicon metagenomic sequencing to assess its utility in patients with fungal infections. Eighty-four samples from seventy-three patients were included and categorized into ‘Fungal infection,’ ‘Fungal colonization,’ and ‘Fungal contamination’ groups based on the judgement of infectious disease specialists. In the ‘Fungal infection’ group, forty-seven initial samples were obtained from forty-seven patients. Three fungal cases detected not by the sequencing but by conventional fungal assays were excluded from the analysis. In the remaining cases, the conventional fungal assay-negative/sequencing-positive group (n=11) and conventional fungal assay-positive/sequencing-positive group (n=33) were compared. Non-<em>Candida</em> and non-<em>Aspergillus</em> fungi infections were more frequent in the conventional-negative/sequencing-positive group (p-value = 0.031). We demonstrated the presence of rare human pathogens, such as <em>Trichosporon asahii</em> and <em>Phycomyces blakesleeanus</em>. In the ‘Fungal infection’ group and ‘Fungal colonization’ group, sequencing was faster than culturing (mean difference = 4.92 days, p-value &lt; 0.001/ mean difference = 4.67, p-value &lt;0.001). Compared to the conventional diagnostic methods including culture, nanopore amplicon sequencing showed a shorter turnaround time and a higher detection rate for uncommon fungal pathogens.</p></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1438422124000341/pdfft?md5=c8f82b8db17e2d758359b6a89455570a&pid=1-s2.0-S1438422124000341-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141638299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}