Annals of Clinical Microbiology and Antimicrobials最新文献

{"title":"Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals.","authors":"Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li","doi":"10.1186/s12941-024-00766-4","DOIUrl":"10.1186/s12941-024-00766-4","url":null,"abstract":"<p><strong>Background: </strong>Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with bla_OXA-23 gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread.</p><p><strong>Methods: </strong>We conducted a retrospective study of CRAB patients at three teaching hospitals from 2019 to 2022. We identified bacterial isolates, collected clinical data, and performed antimicrobial susceptibility testing. Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around bla_OXA-23. Phylogenetic tree was constructed to analyze the genetic relationship of isolates.</p><p><strong>Results: </strong>A total of 92 non-repetitive CRAB isolates were collected, with sputum samples accounting for the majority (94.57%, n = 87) of samples. These were distributed into ST2, with ST2 identified to have the highest prevalence of infection, accounting for 99.99% (n = 91) of all isolates. The major resistance genes identified were bla_OXA-23, bla_OXA-66, bla_OXA-51, and bla_ADC. Also, 92 CRAB strains showed high levels of resistance to common clinical antibiotics, but not minocycline. Meanwhile, most of the isolates carried virulence genes such as various ompA, csuA, csuB, csuC, csuD, abaI, abaR, lpxC, lpxA, and bmfRS. Single nucleotide polymorphism (SNP) analyses further indicated that the bacterial genome was progressively polymorphic with time. We analyzed the environment of the bla_OXA-23 gene and found that CRAB accumulated in the context of prominent environmental antibiotic exposure and had longer survival times in the antibiotic environment, resulting in the tendency of bacteria to develop greater antibiotic resistance.</p><p><strong>Conclusions: </strong>We find that CRAB is prevalent within the ICU and is progressively resistant to antibiotics over time. Enhanced clinical understanding and timely management of CRAB infections will be crucial to minimize or even eliminate the spread of CRAB within the ICU setting.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"2"},"PeriodicalIF":4.6,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142977080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence and molecular characteristics of colistin-resistant isolates among carbapenem-resistant Klebsiella pneumoniae in Central South China: a multicenter study.","authors":"Zijuan Jian, Yanjun Liu, Zhiqian Wang, Peilin Liu, Jiahui Wang, Qun Yan, Wenen Liu","doi":"10.1186/s12941-024-00769-1","DOIUrl":"10.1186/s12941-024-00769-1","url":null,"abstract":"<p><strong>Background: </strong>The emergence of colistin resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant public health concern, as colistin has been the last resort for treating such infections. This study aimed to investigate the prevalence and molecular characteristics of colistin-resistant CRKP isolates in Central South China.</p><p><strong>Methods: </strong>CRKP isolates from twelve hospitals in Central South China were screened for colistin resistance using broth microdilution. The epidemiological characteristics, virulome, resistome, plasmid replicons and two-component systems associated with colistin resistance of colistin-resistant isolates were explored by whole-genome sequencing. The mgrB gene and the relative expression of the pmrC and pmrK genes were analyzed by polymerase chain reaction (PCR) and real-time quantitative PCR, respectively. The bacterial virulence was evaluated through a Galleria mellonella larvae infection model.</p><p><strong>Results: </strong>Of the 429 nonduplicate CRKP isolates, 26 (6.1%) were colistin-resistant and they included eight clonal clusters. Six distinct sequence type (ST)-capsule loci (KL) types were identified: ST11-KL64, ST11-KL47, ST963-KL16, ST307-KL102, ST751-KL64 and ST5254-KL47. 88.5% (23/26) of them were found to carry at least one carbapenemase gene, including bla_KPC-2 (65.4%, 17/26) and bla_NDM-1 (7.7%, 2/26), as well as coharbouring bla_KPC-2 and bla_NDM-1 (15.4%, 4/26). Diverse mutations of colistin resistance-related genes were observed, with mgrB inactivation by insertions and the T157P deleterious mutation in pmrB being detected in 57.7% and 42.3% of the colistin-resistant isolates, respectively. In addition, a novel deleterious mutation, R248P, in the crrB gene was found in two ST11 isolates. 88.5% of the 26 isolates presented an increase in pmrK transcription, and 69.2% of them had an overexpression of the pmrC gene. All the 16 ST11-KL64 isolates and one ST751-KL64 isolate (65.4%, 17/26) carried at least two hypervirulence biomarkers and showed high virulence in vivo.</p><p><strong>Conclusions: </strong>This study highlights the presence of different colistin resistance mechanisms in isolates belonging to the same clone and identified multiple clonal transmission clusters in colistin resistant isolates, including the globally high-risk ST11 and ST307 clones, of which a significant proportion exhibited high virulence. Consequently, it is crucial to enforce measures to prevent the ongoing spread of colistin resistance.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"1"},"PeriodicalIF":4.6,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and metagenomic predicted antimicrobial resistance in pediatric critically ill patients with infectious diseases in a single center of Zhejiang.","authors":"Nan Zhang, Xiaojing Zhang, Yuxin Guo, Yafeng Zheng, Wei Gai, Zihao Yang","doi":"10.1186/s12941-024-00767-3","DOIUrl":"10.1186/s12941-024-00767-3","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance (AMR) poses a significant threat to pediatric health; therefore, precise identification of pathogens as well as AMR is imperative. This study aimed at comprehending antibiotic resistance patterns among critically ill children with infectious diseases admitted to pediatric intensive care unit (PICU) and to clarify the impact of drug-resistant bacteria on the prognosis of children.</p><p><strong>Methods: </strong>This study retrospectively collected clinical data, identified pathogens and AMR from 113 children's who performed metagenomic next-generation sequencing for pathogen and antibiotic resistance genes identification, and compared the clinical characteristic difference and prognostic effects between children with and without AMR detected.</p><p><strong>Results: </strong>Based on the presence or absence of AMR test results, the 113 patients were divided into Antimicrobial resistance test positive group (AMRT+, n = 44) and Antimicrobial resistance test negative group (AMRT-, n = 69). Immunocompromised patients (50% vs. 28.99%, P = 0.0242) and patients with underlying diseases (70.45% vs. 40.58%, P = 0.0019) were more likely to develop resistance to antibiotics. Children in the AMRT + group showed significantly increased C-reaction protein, score of pediatric sequential organ failure assessment and pediatric risk of mortality of children and longer hospital stay and ICU stay in the AMRT + group compared to the AMRT+- group (P < 0.05). Detection rate of Gram-negative bacteria was significantly higher in the AMRT + group rather than Gram-positive bacteria (n = 45 vs. 31), in contrast to the AMRT- group (n = 10 vs. 36). Cephalosporins, β-lactams/β-Lactamase inhibitors, carbapenems and sulfonamides emerged as the most common types of drug resistance in children. Resistance rates to these antibiotics exhibited considerable variation across common pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii.</p><p><strong>Conclusions: </strong>The development of drug resistance in bacteria will significantly affect the prognosis of patients. The significant differences in drug resistance of common pathogenic bacteria indicate that identification of drug resistance is important for the rational use of antibiotics and patient prognosis.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"107"},"PeriodicalIF":4.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus.","authors":"Linzy Elton, Alan Williams, Shanom Ali, Jelena Heaphy, Vicky Pang, Liam Commins, Conor O'Brien, Özge Yetiş, Estelle Caine, Imogen Ward, Monika Muzslay, Samuel Yui, Kush Karia, Ellinor Shore, Sylvia Rofael, Damien J F Mack, Timothy D McHugh, Emmanuel Q Wey","doi":"10.1186/s12941-024-00762-8","DOIUrl":"10.1186/s12941-024-00762-8","url":null,"abstract":"<p><strong>Introduction: </strong>Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.</p><p><strong>Methods: </strong>25 isolates were cultured from clinical patient samples or swabs, that tested positive for OXA-48-like variants using the NG-Test® CARBA-5 test and whole genome sequenced (WGS) using Oxford Nanopore Technologies (ONT). 158 swabs and 52 wastewater samples were collected from the ward environment. 60 isolates (matching clinical isolate genera; Klebsiella, Enterobacter, Citrobacter and Escherichia) were isolated from the environmental samples using selective agar. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.</p><p><strong>Results: </strong>21/25 (84%) clinical isolates had > 1 bla_OXA gene and 19/25 (76%) harboured > 1 bla_NDM gene. Enterobacterales were most commonly isolated from environmental wastewater samples 27/52 (51.9%), then stick swabs 5/43 (11.6%) and sponge swabs 5/115 (4.3%). 11/60 (18%) environmental isolates harboured > 1 bla_OXA gene and 1.9% (1/60) harboured bla_NDM-1. bla_OXA genes were found in 2/36 (5.5%) metagenomic environmental samples.</p><p><strong>Conclusions: </strong>Potential for putative patient-patient and patient-ward transmission was shown. Metagenomic sampling needs optimization to improve sensitivity.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"108"},"PeriodicalIF":4.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Liver abscesses secondary to a non-O1/non-O139 Vibrio cholerae bacteremia acquired in a non-coastal area: a case report.","authors":"Coen Veenstra, Marion Kolader, Sébastien Matamoros, Kim Sigaloff","doi":"10.1186/s12941-024-00764-6","DOIUrl":"10.1186/s12941-024-00764-6","url":null,"abstract":"<p><p>Non-O1/non-O139 Vibrio cholerae (NOVC) strains are a distinct group of Vibrio cholerae that do not cause epidemic cholera. NOVC infections usually cause mild forms of gastroenteritis, and rarely severe (extra)intestinal infections, mostly affecting immunocompromised patients. Here, we describe the clinical course of a patient with NOVC bacteremia causing multiple liver abscesses, after drinking from a freshwater well in a non-coastal area. This case highlights the potential of a V. cholerae strain, that is phylogenetically distinct from the current pandemic cholera strain, to cause severe extra-intestinal infections, including liver abscesses.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"109"},"PeriodicalIF":4.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drug susceptibility testing of Nocardia spp. using the disk diffusion method.","authors":"Clémence Prudhomme, Brune Joannard, Gérard Lina, Eleonore De Launay, Oana Dumitrescu, Elisabeth Hodille","doi":"10.1186/s12941-024-00768-2","DOIUrl":"10.1186/s12941-024-00768-2","url":null,"abstract":"<p><strong>Background: </strong>Drug susceptibility testing (DST) for Nocardia spp. is essential to initiate effective antibiotic therapy. Currently, the only recommended technique is the determination of minimum inhibitory concentrations (MICs) by microdilution. This method can be tedious to perform, despite the availability of ready-to-use plates. Herein, the aim was to determine the critical inhibition diameters specific to Nocardia spp.</p><p><strong>Methods: </strong>MICs of 134 Nocardia isolates were determined by microdilution. Interpretative categories (Susceptible/Intermediate/Resistant) were determined using Clinical and Laboratory Standards Institute breakpoints. In parallel, disk diffusion DST was performed. Receiver-operating-characteristic (ROC) curves were constructed to determine the inhibition diameter value that best discriminated between susceptible and non-susceptible strains (intermediate/resistant). The category agreement (CA), the rate of major (maj) and very major (vmj) discrepancies between microdilution and disk diffusion method was calculated.</p><p><strong>Results: </strong>For tobramycin, the critical diameter of 19 mm (diameter ≤ 19 mm = resistant strain; diameter > 19 mm = susceptible strain) provided a CA of 98.5%, 0.0% vmj, and 2.9% maj discrepancies, reaching strictly the acceptable performance criteria defined by the U.S. Food and Drug Administration (FDA). For amikacin, the critical diameter of 25 mm (diameter ≤ 25 mm = resistant strain; diameter > 25 mm = susceptible strain) provided a CA of 98.5%, 0.0% vmj, and 1.5% maj discrepancies. For imipenem, excluding N. farcinica and N. cyriacigeorgica, the critical diameter of 29 mm (diameter ≤ 29 mm = resistant strain; diameter > 29 mm = susceptible strain), provided a CA of 98.6%, 0.0% vmj, and 0.0% maj discrepancies. Despite an estimated vmj rate 0.0%, the 95%-confident-interval exceeded the FDA criteria due to an insufficient number of amikacin/imipenem-resistant strains. For other tested antibiotics (ciprofloxacin, moxifloxacin, amoxicillin-clavulanate, ceftriaxone, cotrimoxazole, linezolid), the FDA criteria were not reached.</p><p><strong>Conclusions: </strong>Although the FDA criteria were mostly unmet, disk diffusion DST was suitable to accurately categorize Nocardia isolates into interpretative categories for the aminoglycosides and imipenem only, excluding species N. farcinica and N. cyriacigeorgica.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"105"},"PeriodicalIF":4.6,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meningitis due to Gemella sp. in a patient with severe ENT conditions: case report and review of the literature.","authors":"Ilyès Benhalima, Lola Jacquemont, Laurine Milière, Alina Tone, Nicolas Ettahar, Gisèle Dewulf, Edith Mazars","doi":"10.1186/s12941-024-00765-5","DOIUrl":"10.1186/s12941-024-00765-5","url":null,"abstract":"<p><p>In June 2022, a 73-year-old man with a history of laryngeal and esophageal carcinoma was admitted to the emergency unit with sudden fever, confusion, and general condition deterioration. Initial assessments showed a fever of 38.5 °C, elevated C-reactive protein (CRP) at 209 mg/L, and a neutrophil count of 10.4 G/L, with negative results for urine analysis, blood cultures, and multiple infectious pathogens, including Legionella pneumophila, pneumococcal antigen, and SARS-CoV-2. Computed tomography (CT) scans revealed no significant infectious focus.Empirical treatment with Ceftriaxone and Ciprofloxacin was initiated. Despite treatment, the patient's condition remained unchanged, and a lumbar puncture revealed turbid cerebrospinal fluid (CSF) with 14,300 white blood cells (WBC)/mm³, predominantly neutrophils, elevated proteins, and decreased glucose. Gram staining suggested Neisseria meningitidis, but further testing was necessary. Antibiotic therapy was switched to Cefotaxime and Dexamethasone, and the patient was transferred to the Tropical and Infectious Disease Unit.Multiplex PCR assays and additional CSF tests were negative for common pathogens. Sequencing of 16S ribosomal RNA identified Gemella sp. The patient's condition improved with continued Cefotaxime treatment, and he recovered without neurological sequelae. Subsequent dental CT revealed poor dental hygiene but no signs of osteo-meningeal breach or bone lysis.A literature review identified 22 reported cases of central nervous system (CNS) infections caused by various Gemella species from 1980 to 2022. Of these, 59% presented with meningitis, and 41% had additional encephalitis or brain abscesses. Complete recovery occurred in 77% of cases, with 9% resulting in neurological damage and another 9% in fatal outcomes. Relapses occurred in 14% of the cases. The review highlighted that CNS infections by Gemella spp. primarily affect immunocompromised adults with ENT (ear nose throat) or neurological breaches, although some cases involved healthy individuals.This case underscores the diagnostic challenges posed by uncommon pathogens like Gemella and highlights the utility of molecular microbiology in identifying causative agents, thus guiding appropriate treatment. The patient's history of ENT and esophageal cancers, along with recent radiotherapy and chemotherapy, likely contributed to the infection's development. The case emphasizes the importance of thorough investigation in febrile confusion cases and the potential role of Gemella spp. in CNS infections.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"106"},"PeriodicalIF":4.6,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transmission cluster of cefiderocol-non-susceptible carbapenem-resistant Acinetobacter baumannii in cefiderocol-naïve individuals.","authors":"Claudia Alteri, Antonio Teri, Maria Francesca Liporace, Antonio Muscatello, Leonardo Terranova, Margherita Carnevale Schianca, Federica Salari, Beatrice Silvia Orena, Flaminia Gentiloni Silverj, Mara Bernazzani, Simona Biscarini, Giulia Renisi, Lisa Cariani, Caterina Matinato, Ciro Canetta, Alessandra Bandera, Annapaola Callegaro","doi":"10.1186/s12941-024-00763-7","DOIUrl":"10.1186/s12941-024-00763-7","url":null,"abstract":"<p><strong>Background: </strong>During prolonged FDC therapy, the emergence of FDC non-susceptibility in CRAB has been reported. Here, we report a transmission cluster of FDC-non-susceptible CRAB in four patients, all naïve to FDC treatment, characterized by a premature stop codon and amino acid deletion in the PirA protein.</p><p><strong>Methods: </strong>CRAB strains obtained from patients admitted in a single medicine ward of the IRCCS Fondazione Ospedale Maggiore Policlinico between March and July 2024 were analyzed by WGS and antimicrobial susceptibility testing. Phylogenetic analysis was used to assess their genetic relatedness.</p><p><strong>Results: </strong>Between March and July 2024, an outbreak of 33 CRAB was observed among hospitalized patients in a single ward at IRCCS. Genomic analysis, available in 29 cases, revealed that 24 isolates belonged to ST208/1806, 4 to ST369, and one to ST195/1816 (according to the Oxford scheme). FDC susceptibility was affected only in the four ST369 isolates (Kirby-Bauer disk diffusion diameter: 13 mm; UMIC^® method MIC: 4 mg/L), all characterized by a premature stop codon followed by a 52 amino acid deletion located between the amino acids 377 and 428 of the siderophore-drug receptor PirA. No other relevant mutations were detected in the iron-uptake genes. Core-genome ML tree including ST369 reference strains revealed that the four ST369 isolates were highly related and formed a distinct cluster (SNP distance: 3 [IQR: 1-6]). Of note, the four isolates were collected from four FDC-naïve individuals, two experiencing a CRAB-mediated infection.</p><p><strong>Conclusions: </strong>Our findings alert about the circulation of clones carrying modified siderophore-drug receptors without evidence of previous FDC treatment and support the importance of testing FDC susceptibility appropriately before its administration.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"104"},"PeriodicalIF":4.6,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11607823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis.","authors":"Cristina Elías-López, Montserrat Muñoz-Rosa, Julia Guzmán-Puche, Elena Pérez-Nadales, Eduardo Chicano-Galvez, Luis Martínez-Martínez","doi":"10.1186/s12941-024-00761-9","DOIUrl":"10.1186/s12941-024-00761-9","url":null,"abstract":"<p><strong>Background: </strong>The permeability of the outer membrane barrier modulates the susceptibility of microorganisms to antimicrobial agents. Loss or structural alterations of porins contribute to decreased antibiotic concentration of multiple antimicrobial agents. Precise definition of porin profiles is of critical importance to understand the role of porins in antimicrobial resistance. The objectives of this study are to compare the expression patterns of major outer membrane proteins (OMP) of clinical isolates of Klebsiella pneumoniae obtained with Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF/MS), with those obtained with sodium-dodecyl-sulphate polyacrylamide gel electrophoresis (SDS-PAGE), and to correlate porin expression patterns with the sequences of porins genes defined with whole genome sequencing (WGS).</p><p><strong>Methods: </strong>The OMP profiles of 26 clinical isolates of K. pneumoniae and of strain ATCC 13883 (wild-type) and ATCC 700603 (producing SHV-18) have been determined using both SDS-PAGE and MALDI-TOF/MS. SDS-PAGE was performed using both homemade and commercial gels, and protein bands were identified by liquid chromatography coupled to mass spectrometry. A rapid extraction method was used to analyse OMPs by MALDI-TOF/MS. The sequences of porin genes were obtained by WGS and mutations were defined by BLAST.</p><p><strong>Results: </strong>Same results were obtained for all strains either using SDS-PAGE or MALDI-TOF/MS. SDS-PAGE showed protein bands of ~ 35, ~36, and ~ 37 kDa, identified as OmpA, OmpK36 and OmpK35, respectively. By MALDI-TOF/MS, peaks at ~ 35,700 (OmpA), ~ 37,000 (OmpK35), and ~ 38,000 (OmpK36) m/z were detected. ompK35 was intact in nine wild-type isolates and was truncated in 13 isolates, but OmpK35 was not observed in 3 isolates without mutations in ompK35. One point mutation was detected in another isolate and multiple mutations were detected in the remaining isolate. ompK36 was truncated in two isolates lacking this protein and presented one point mutation (n = 1) or multiple mutations in the remaining isolates.</p><p><strong>Conclusion: </strong>MALDI-TOF/MS was reliable for porin detection, but because of the complex regulation of porin genes, WGS cannot always anticipate protein expression, as observed with SDS-PAGE and MALDI-TOF/MS.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"103"},"PeriodicalIF":4.6,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergence of carbapenem resistance in persistent Shewanella algae bacteremia: the role of pdsS G547W mutation in adaptive subpopulation dynamics.","authors":"Yao-Ting Huang, Po-Yu Liu","doi":"10.1186/s12941-024-00759-3","DOIUrl":"10.1186/s12941-024-00759-3","url":null,"abstract":"<p><p>This study elucidates the in vivo genetic mechanisms contributing to the emerging resistance to carbapenem in Shewanella algae through a lens of adaptive microbial evolution. Leveraging PacBio amplification-free sequencing, we tracked the evolution of β-lactam resistance in clinical isolates from a persistent S. algae bacteremia case amidst antimicrobial therapy. Our investigation spotlighted a recurrent G547W mutation in the sensor histidine kinase (pdsS), which was associated with the overexpression of an OmpA-like protein (pdsO) within a proteobacteria-specific sortase system. Intriguingly, we observed a recurrent switch between wild-type and G547W alleles, revealing an adaptive expansion and contraction of underlying cell subpopulations in response to β-lactam exposure. Comparative transcriptome analyses further demonstrated the overexpression of genes pivotal for membrane integrity, biofilm formation, immune evasion, and β-lactamase activation in resistant samples. This underscores the pre-existence of resistant cells at minuscule frequencies even without antibiotic pressure, potentially explaining the within-host emergence of resistance during antibiotic treatments. Our findings provide pivotal insights into the dynamic genetic adaptations of S. algae under therapeutic pressures, unmasking intricate resistance mechanisms and highlighting the critical role of subpopulation dynamics in treatment outcomes.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"102"},"PeriodicalIF":4.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11580497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}