scholarly journals Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adriana Maria Sanabria ◽  
Jessin Janice ◽  
Erik Hjerde ◽  
Gunnar Skov Simonsen ◽  
Anne-Merethe Hanssen
Keyword(s):  
Staphylococcus Aureus ◽  
Blood Culture ◽  
Virulence Genes ◽  
Sequence Data ◽  
Joint Infection ◽  
Clinical Samples ◽  
Virulence Determinants ◽  
Periprosthetic Tissue ◽  
Shotgun Metagenomics ◽  
Genome Coverage

AbstractShotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.

scholarly journals Shotgun-Metagenomics Based Prediction Of Antibiotic Resistance And Virulence Determinants In Staphylococcus Aureus From Prosthetic Joint Tissue On Blood Culture Bottles

2021 ◽  
Author(s):  
Adriana Maria Sanabria ◽  
Jessin Janice ◽  
Erik Hjerde ◽  
Gunnar Skov Simonsen ◽  
Anne-Merethe Hanssen
Keyword(s):  
Staphylococcus Aureus ◽  
Blood Culture ◽  
Virulence Genes ◽  
Sequence Data ◽  
Joint Infection ◽  
Clinical Samples ◽  
Shotgun Metagenomics ◽  
Joint Tissue ◽  
Genome Coverage ◽  
Prosthetic Joint

Abstract Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with prosthetic joint tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known prosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209x. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis had a significant impact on the results. Read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.

scholarly journals Prevalence of Methicillin Resistant and Virulence Determinants in Clinical Isolates of Staphylococcus aureus

2018 ◽  
Vol 10 (1) ◽  
pp. 108-115
Author(s):  
Manjunath Chavadi ◽  
Rahul Narasanna ◽  
Ashajyothi Chavan ◽  
Ajay Kumar Oli ◽  
Chandrakanth Kelmani. R
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Morphology ◽  
Methicillin Resistance ◽  
Protein A ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Virulence Determinants ◽  
Methicillin Resistant ◽  
Alternative Medicines ◽  
Mrsa Strains

Introduction:Methicillin-resistantStaphylococcus aureus(MRSA) is the major threat that is a result of the uncontrolled use of antibiotics causing a huge loss in health, so understanding their prevalence is necessary as a public health measure.Objective:The aim of this study was to determine the prevalence of methicillin-resistant MRSA and virulence determinant among associatedS. aureusfrom the clinical samples obtained from various hospital and health care centers of the Gulbarga region in India.Materials and Methods:All the collected samples were subjected for the screening ofS. aureusand were further characterized by conventional and molecular methods including their antibiotic profiling. Further, the response of methicillin antibiotic on cell morphology was studied using scanning electron microscopy.Results:A total 126S. aureuswas isolated from the clinical samples which showed, 100% resistant to penicillin, 55.5% to oxacillin, 75.3% to ampicillin, 70.6% to streptomycin, 66.6% to gentamicin, 8.7% to vancomycin and 6.3% to teicoplanin. The selected MRSA strains were found to possessmecA(gene coding for penicillin-binding protein 2A) andfemA(factor essential for methicillin resistance)genetic determinants in their genome with virulence determinants such as Coagulase (coa) and the X region of the protein A (spa)gene. Further, the methicillin response in resistantS. aureusshowed to be enlarged and malformed on cell morphology.Conclusion:The molecular typing of clinical isolates ofS. aureusin this study was highly virulent and also resistant to methicillin; this will assist health professionals to control, exploration of alternative medicines and new approaches to combat Staphylococcal infections more efficiently by using targeted therapy.

scholarly journals Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Phelim Bradley ◽  
N. Claire Gordon ◽  
Timothy M. Walker ◽  
Laura Dunn ◽  
Simon Heys ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Mycobacterium Tuberculosis ◽  
Sequence Data ◽  
Error Rates ◽  
Graph Representation ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Independent Validation ◽  
Validation Set ◽  
Sensitivity Specificity

Abstract The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package (‘Mykrobe predictor’) that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.

scholarly journals Optimal Periprosthetic Tissue Specimen Number for Diagnosis of Prosthetic Joint Infection

2016 ◽  
Vol 55 (1) ◽  
pp. 234-243 ◽  
Author(s):  
Trisha N. Peel ◽  
Tim Spelman ◽  
Brenda L. Dylla ◽  
John G. Hughes ◽  
Kerryl E. Greenwood-Quaintance ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Blood Culture ◽  
Prosthetic Joint Infection ◽  
Joint Infection ◽  
Revision Arthroplasty ◽  
Periprosthetic Tissue ◽  
Culture Bottle ◽  
Culture Techniques ◽  
Prosthetic Joint ◽  
Tissue Specimens

ABSTRACTWe recently demonstrated improved sensitivity of prosthetic joint infection (PJI) diagnosis using an automated blood culture bottle system for periprosthetic tissue culture [T. N. Peel et al., mBio 7(1):e01776-15, 2016,https://doi.org/10.1128/mBio.01776-15]. This study builds on the prior research by examining the optimal number of periprosthetic tissue specimens required for accurate PJI diagnosis. Current guidelines recommend five to six, which is impractical. We applied Bayesian latent class modeling techniques for estimating diagnostic test properties of conventional culture techniques (aerobic and anaerobic agars and thioglycolate broth) compared to inoculation into blood culture bottles. Conventional, frequentist receiver operating characteristic curve analysis was conducted as a sensitivity analysis. The study was conducted at Mayo Clinic, Rochester, MN, from August 2013 through April 2014 and included 499 consecutive patients undergoing revision arthroplasty from whom 1,437 periprosthetic tissue samples were collected and processed. For conventional periprosthetic tissue culture techniques, the greatest accuracy was observed when four specimens were obtained (91%; 95% credible interval, 77 to 100%), whereas when using inoculation of periprosthetic tissues into blood culture bottles, the greatest accuracy of diagnosis was observed when three specimens were cultured (92%; 95% credible intervals, 79 to 100%). Results of this study show that the greatest accuracy of PJI diagnosis is obtained when three periprosthetic tissue specimens are obtained and inoculated into blood culture bottles or four periprosthetic tissue specimens are obtained and cultured using standard plate and broth cultures. Increasing the number of specimens to five or more, per current recommendations, does not improve accuracy of PJI diagnosis.

scholarly journals Improved Diagnosis of Prosthetic Joint Infection by Culturing Periprosthetic Tissue Specimens in Blood Culture Bottles

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Trisha N. Peel ◽  
Brenda L. Dylla ◽  
John G. Hughes ◽  
David T. Lynch ◽  
Kerryl E. Greenwood-Quaintance ◽  
...  
Keyword(s):  
Blood Culture ◽  
Prosthetic Joint Infection ◽  
Joint Infection ◽  
Revision Arthroplasty ◽  
Broth Culture ◽  
Periprosthetic Tissue ◽  
Tissue Samples ◽  
Prosthetic Joint ◽  
Prosthetic Joint Infections ◽  
Tissue Specimens

ABSTRACTDespite known low sensitivity, culture of periprosthetic tissue specimens on agars and in broths is routine. Culture of periprosthetic tissue samples in blood culture bottles (BCBs) is potentially more convenient, but it has been evaluated in a limited way and has not been widely adopted. The aim of this study was to compare the sensitivity and specificity of inoculation of periprosthetic tissue specimens into blood culture bottles with standard agar and thioglycolate broth culture, applying Bayesian latent class modeling (LCM) in addition to applying the Infectious Diseases Society of America (IDSA) criteria for prosthetic joint infection. This prospective cohort study was conducted over a 9-month period (August 2013 to April 2014) at the Mayo Clinic, Rochester, MN, and included all consecutive patients undergoing revision arthroplasty. Overall, 369 subjects were studied; 117 (32%) met IDSA criteria for prosthetic joint infection, and 82% had late chronic infection. Applying LCM, inoculation of tissues into BCBs was associated with a 47% improvement in sensitivity compared to the sensitivity of conventional agar and broth cultures (92.1 versus 62.6%, respectively); this magnitude of change was similar when IDSA criteria were applied (60.7 versus 44.4%, respectively;P= 0.003). The time to microorganism detection was shorter with BCBs than with standard media (P< 0.0001), with aerobic and anaerobic BCBs yielding positive results within a median of 21 and 23 h, respectively. Results of our study demonstrate that the semiautomated method of periprosthetic tissue culture in blood culture bottles is more sensitive than and as specific as agar and thioglycolate broth cultures and yields results faster.IMPORTANCEProsthetic joint infections are a devastating complication of arthroplasty surgery. Despite this, current microbiological techniques to detect and diagnose infections are imperfect. This study examined a new approach to diagnosing infections, through the inoculation of tissue samples from around the prosthetic joint into blood culture bottles. This study demonstrated that, compared to current laboratory practices, this new technique increased the detection of infection. These findings are important for patient care to allow timely and accurate diagnosis of infection.

scholarly journals Association between agr group, genetic background, virulence factors and disease types of Staphylococcus aureus isolated from Chinese children

2020 ◽  
Author(s):  
Yan Xu ◽  
Suyun Qian ◽  
Kaihu Yao ◽  
Fang Dong ◽  
Wenqi Song ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genetic Background ◽  
Virulence Genes ◽  
Critical Role ◽  
Group Iv ◽  
Type I ◽  
Virulence Determinants ◽  
Accessory Gene ◽  
Group Iii ◽  
Group I

Abstract Background Staphylococcus aureus (S. aureus) accessory gene regulator (agr) system plays a critical role in staphylococcal pathogenesis. Our study aimed to investigate the relationship between agr group, the genetic background, virulence genes and disease types distribution of S. aureus isolated from different clinical sources among Chinese children.Methods S. aureus strains were isolated from Beijing Children’s hospital from October 2017 to October 2019. Isolates were typed by multilocus sequence typing (MLST), staphylococcal protein A (spa), agr, and staphylococcal cassette chromosome mec (SCCmec) typing (for methicillin-resistant S. aureus [MRSA] isolates). Furthermore, all isolates were tested for the presence of 19 selected virulence genes.Results A total of 191 non-repetitive S. aureus clinical isolates were collected and the agr type I was the most prevalent (84.8%). S. aureus isolates were divided into 33 sequence types (STs), 20 clonal complexes (CCs) and 59 spa types, ST59 (39.8%) and t437 (37.7%) were the predominant types. CC59, CC25, CC22, CC951, CC8, and CC398 isolates possessed agr group I; CC15 isolates harbored agr group II; CC30 strains were characterized as agr group III, and CC121 harbored agr group IV. Of the 19 virulence genes, the tst gene was more prevalent among agr group III compared to other groups (p = 0.006); eta and etb genes were more prevalent among agr group IV than other groups (p = 0.003 and 0.001, respectively); nearly all strains that harbored the lukS/F-PV gene (98.3%) belonged to agr group I (p = 0.004); the frequencies of bbp and ebpS genes belonged to agr group I were statistically lower than that of other groups (p < 0.001). Among 161 diagnoses, the frequency of strains from cellulitis patient harbored agr group III was higher than that of other groups (p = 0.046), and one strain isolated from staphylococcal scalded skin syndrome (SSSS) patient, which was identified as agr type IV (p = 0.021).Conclusions The results indicated that the S. aureus agr type was linked to the genetic background. Besides, a possible relationship between the agr group, several virulence determinants, and specific disease types was observed.

scholarly journals Comparison of Diagnostic Accuracy of Periprosthetic Tissue Culture in Blood Culture Bottles to That of Prosthesis Sonication Fluid Culture for Diagnosis of Prosthetic Joint Infection (PJI) by Use of Bayesian Latent Class Modeling and IDSA PJI Criteria for Classification

2018 ◽  
Vol 56 (6) ◽  
pp. e00319-18 ◽  
Author(s):  
Qun Yan ◽  
Melissa J. Karau ◽  
Kerryl E. Greenwood-Quaintance ◽  
Jayawant N. Mandrekar ◽  
Douglas R. Osmon ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Blood Culture ◽  
Gold Standard ◽  
Latent Class ◽  
Joint Infection ◽  
Periprosthetic Tissue ◽  
Prosthetic Joint ◽  
Latent Class Modeling ◽  
Sonication Culture ◽  
Fluid Culture

ABSTRACT We have previously demonstrated that culturing periprosthetic tissue in blood culture bottles (BCBs) improves sensitivity compared to conventional agar and broth culture methods for diagnosis of prosthetic joint infection (PJI). We have also shown that prosthesis sonication culture improves sensitivity compared to periprosthetic tissue culture using conventional agar and broth methods. The purpose of this study was to compare the diagnostic accuracy of tissue culture in BCBs (subsequently referred to as tissue culture) to prosthesis sonication culture (subsequently referred to as sonicate fluid culture). We studied 229 subjects who underwent arthroplasty revision or resection surgery between March 2016 and October 2017 at Mayo Clinic in Rochester, Minnesota. Using the Infectious Diseases Society of America (IDSA) PJI diagnostic criteria (omitting culture criteria) as the gold standard, the sensitivity of tissue culture was similar to that of the sonicate fluid culture (66.4% versus 73.1%, P = 0.07) but was significantly lower than that of the two tests combined (66.4% versus 76.9%, P < 0.001). Using Bayesian latent class modeling, which assumes no gold standard for PJI diagnosis, the sensitivity of tissue culture was slightly lower than that of sonicate fluid culture (86.3% versus 88.7%) and much lower than that of the two tests combined (86.3% versus 99.1%). In conclusion, tissue culture in BCBs reached sensitivity similar to that of prosthesis sonicate fluid culture for diagnosis of PJI, but the two tests combined had the highest sensitivity without compromising specificity. The combination of tissue culture in BCBs and sonicate fluid culture is recommended to achieve the highest level of microbiological diagnosis of PJI.

Detection of New Virulence Genes in mecA-positive Staphylococcus aureus Isolated From Clinical Samples

2017 ◽  
Vol 25 (6) ◽  
pp. 310-313 ◽  
Author(s):  
Morteza Eshaghi ◽  
Meysam Hasannejad Bibalan ◽  
Abazar Pournajaf ◽  
Mehrdad Gholami ◽  
Malihe Talebi
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Genes ◽  
Clinical Samples

scholarly journals Screening of virulence genes in Staphylococcus aureus isolates from rabbits

2015 ◽  
Vol 23 (3) ◽  
pp. 185 ◽  
Author(s):  
David Viana Martín ◽  
Laura Selva ◽  
Mariola Penadés ◽  
Juan Manuel Corpa
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Factors ◽  
Multilocus Sequence Typing ◽  
Virulence Genes ◽  
Bacterial Virulence ◽  
Virulence Determinants ◽  
Different Ages

<p><em>Staphylococcus aureus</em> is a versatile pathogen able to cause disease in both humans and animals. In rabbits, this bacterium infects animals of different ages, producing several purulent lesions. The ability of <em>S. aureus</em> to cause disease depends on a combination of virulence factors. The aim of this study was therefore to investigate the distribution of bacterial virulence determinants in 69 <em>S. aureus</em> isolates from rabbits. Some virulence factors (7 adhesins, 1 toxin and 1 protease) were positive in all rabbit <em>S. aureus</em> isolates analysed, while others (1 adhesin and 10 toxins) were always negative. The remaining virulence factors were more variable among isolates. An association between genotype and the different profiles of virulence factors was observed, but not with the type of lesion (P&lt;0.05). One strain of each genotype was further analysed by multilocus sequence typing, generating ST121, ST96 and ST2951, determining a greater number of enterotoxins in ST121 isolates compared to ST96 and ST2951 isolates, which could justify the different pathogenicity between strains. </p>

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