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Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE, Walker H, Hawkins PA, Tran T, McGee L, Beall BW. Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences. BMC Genomics 2017; 18:621. [PMID: 28810827 PMCID: PMC5558719 DOI: 10.1186/s12864-017-4017-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type). This study evaluates the prediction performance for previously uncharacterized (new) PBP types and the probability of encountering new PBP types, both of which impact the overall prediction accuracy. RESULTS The MM and RF methods were used to predict MICs of 4309 previously reported pneumococcal isolates in 2 datasets and the results were compared to the known broth microdilution MICs to 6 β-lactams. Based on a method that specifically evaluated predictions for new PBP types, the RF results were more accurate than MM results for new PBP types and showed percent essential agreement (MICs agree within ±1 dilution) >97%, percent category agreement (interpretive results agree) >93%, major discrepancy (sensitive isolate predicted as resistant) rate < 1.2%, and very major discrepancy (resistant isolate predicted as sensitive) rate < 1.4% for all 6 β-lactams. The identification of new PBP types over time was well approximated by a diminishingly increasing curve (Pearson's r = 0.99) and minimally impacted overall MIC prediction performance. CONCLUSIONS MIC prediction using the RF method could be an accurate alternative of phenotypic susceptibility testing even in the presence of previously uncharacterized PBP types.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA.
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Robert E Gertz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Hollis Walker
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Paulina A Hawkins
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Theresa Tran
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Bernard W Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329, USA
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Hawkins PA, Akpaka PE, Nurse-Lucas M, Gladstone R, Bentley SD, Breiman RF, McGee L, Swanston WH. Antimicrobial resistance determinants and susceptibility profiles of pneumococcal isolates recovered in Trinidad and Tobago. J Glob Antimicrob Resist 2017; 11:148-151. [PMID: 28818574 PMCID: PMC5711790 DOI: 10.1016/j.jgar.2017.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/28/2017] [Accepted: 08/05/2017] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES In Latin America and the Caribbean, pneumococcal infections are estimated to account for 12000-18000 deaths, 327000 pneumonia cases, 4000 meningitis cases and 1229 sepsis cases each year in children under five years old. Pneumococcal antimicrobial resistance has evolved into a worldwide health problem in the last few decades. This study aimed to determine the antimicrobial susceptibility profiles of pneumococcal isolates collected in Trinidad and Tobago and their associated genetic determinants. METHODS Whole-genome sequences were obtained from 98 pneumococcal isolates recovered at several regional hospitals, including 83 invasive and 15 non-invasive strains, recovered before (n=25) and after (n=73) introduction of pneumococcal conjugate vaccines (PCVs). A bioinformatics pipeline was used to identify core genomic and accessory elements conferring antimicrobial resistance phenotypes, including β-lactam non-susceptibility. RESULTS AND DISCUSSION Forty-one isolates (41.8%) were predicted as resistant to at least one antimicrobial class, including 13 (13.3%) resistant to at least three classes. The most common serotypes associated with antimicrobial resistance were 23F (n=10), 19F (n=8), 6B (n=6) and 14 (n=5). The most common serotypes associated with penicillin non-susceptibility were 19F (n=7) and 14 (n=5). Thirty-nine isolates (39.8%) were positive for PI-1 or PI-2 type pili: 30 (76.9%) were PI-1+, 4 (10.3%) were PI-2+ and 5 (12.8%) were positive for both PI-1 and PI-2. Of the 13 multidrug-resistant isolates, 10 belonged to globally distributed clones PMEN3 and PMEN14 and were isolated in the post-PCV period, suggesting clonal expansion.
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Affiliation(s)
- Paulina A Hawkins
- Emory University, Atlanta, GA, USA; US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA.
| | - Patrick E Akpaka
- The University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | | | | | | | - Lesley McGee
- US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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Hawkins P, Mercado E, Chochua S, Castillo ME, Reyes I, Chaparro E, Gladstone R, Bentley SD, Breiman RF, Metcalf BJ, Beall B, Ochoa TJ, McGee L. Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing. Int J Med Microbiol 2017; 307:415-421. [PMID: 28756964 PMCID: PMC5615106 DOI: 10.1016/j.ijmm.2017.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/20/2017] [Accepted: 07/18/2017] [Indexed: 11/22/2022] Open
Abstract
Before PCV7 introduction, invasive pneumococcal disease (IPD) was responsible for approximately 12,000–18,000 deaths annually among children <5 years in Latin America. In Peru, PCV7 was introduced in 2009. We used whole genome sequencing to deduce key features of invasive strains collected in Lima, Peru from 2006 to 2011. We sequenced 212 IPD isolates from 16 hospitals in Lima pre (2006–2009; n = 133) and post (2010–2011; n = 79) PCV7 introduction; 130 (61.3%) isolates were from children ≤ 5 years old. CDC’s Streptococcus lab bioinformatics pipeline revealed serotypes, sequence types (STs), pilus genes, PBP types and other resistance determinants. During the pre-PCV7 period, serotype 14 was the most common serotype (24.8%), followed by 6 B (20.3%), 19F (10.5%), and 23F (6.8%). Post-PCV7, the proportion of PCV7 serotype 6 B decreased significantly (to 6.3%), while 19F (16.3%), 14 (15.0%), 23F (7.5%), and 19A (7.5%) were the most common serotypes; only serotypes 3 and 10A increased significantly. Overall, 82% (n = 173) of all isolates carried at least one resistance determinant, including 72 (34%) isolates that carried resistance determinants against 3 or more antimicrobial classes; of these 72 isolates, 56 (78%) belonged to a PCV7 serotype. Eighty-two STs were identified, with 53 of them organized in 14 clonal complexes. ST frequencies were distributed differently pre and post-PCV7 introduction, with only 18 of the 57 STs identified in years 2006–2009 isolates also observed in years 2010–2011 isolates. The apparent expansion of a 19F/ST1421 lineage with predicted β-lactam resistance (PBP type 13:16:20) and carrying resistance determinants against four additional antimicrobial classes was observed.
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Affiliation(s)
- Paulina Hawkins
- Emory University, Atlanta, USA; Centers for Disease Control and Prevention, Atlanta, USA.
| | - Erik Mercado
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sopio Chochua
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Maria E Castillo
- Universidad Peruana Cayetano Heredia, Lima, Peru; Instituto Nacional de Salud del Niño, Lima, Peru
| | | | - Eduardo Chaparro
- Universidad Peruana Cayetano Heredia, Lima, Peru; Hospital Cayetano Heredia, Lima, Peru
| | | | | | | | | | - Bernard Beall
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
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Pfaller MA, Mendes RE, Flamm RK, Jones RN, Sader HS. Ceftaroline Activity Against Multidrug-Resistant Streptococcus pneumoniae from U.S. Medical Centers (2014) and Molecular Characterization of a Single Ceftaroline Nonsusceptible Isolate. Microb Drug Resist 2017; 23:571-579. [PMID: 27918694 DOI: 10.1089/mdr.2016.0258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae isolates (2,614) were collected from patients at 135 U.S. Medical Centers during 2014. Isolates were evaluated for multidrug resistance to penicillin, ceftriaxone, erythromycin, tetracycline, trimethoprim-sulfamethoxazole, and levofloxacin. A single isolate (853008) demonstrated a ceftaroline nonsusceptible minimal inhibitory concentration (MIC) value, and it was subjected to molecular characterization. Ceftaroline (MIC50/90, ≤0.015/0.12 μg/ml) was eightfold more potent than ceftriaxone (MIC50/90, ≤0.06/1 μg/ml) against all isolates. For multidrug-resistant (MDR) isolates (28.8% of tested strains), ceftaroline (MIC50/90, 0.06/0.25 μg/ml; 99.9% susceptible) was the most active agent tested, being eightfold more active than ceftriaxone (MIC50/90, 0.25/2 μg/ml; 81.5% susceptible at MIC, ≤1 μg/ml) and 16-fold more active than penicillin (MIC50/90, 0.25/4 μg/ml; 78.5% susceptible at MIC, ≤2 μg/ml). Isolate 853008 was a single locus variant of sequence type 377 and serotype 35B. It had multiple substitutions in the penicillin-binding proteins (PBPs), mainly PBP2x, when compared with reference sequences from the R6 strain. Isolate 853008 showed 31 amino acid alterations in MurM. The in vitro data presented here confirm that ceftaroline potency against S. pneumoniae to be higher than other β-lactams, including against those isolates demonstrating ceftriaxone nonsusceptible and MDR phenotypes.
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Affiliation(s)
- Michael A Pfaller
- 1 JMI Laboratories , North Liberty, Iowa
- 2 University of Iowa , Iowa City, Iowa
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105
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Eyre DW, De Silva D, Cole K, Peters J, Cole MJ, Grad YH, Demczuk W, Martin I, Mulvey MR, Crook DW, Walker AS, Peto TEA, Paul J. WGS to predict antibiotic MICs for Neisseria gonorrhoeae. J Antimicrob Chemother 2017; 72:1937-1947. [PMID: 28333355 PMCID: PMC5890716 DOI: 10.1093/jac/dkx067] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 11/26/2022] Open
Abstract
Background Tracking the spread of antimicrobial-resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes. Objectives We investigate whether WGS and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of MICs in N. gonorrhoeae. Methods WGS was used to identify previously reported potential resistance determinants in 681 N. gonorrhoeae isolates, from England, the USA and Canada, with phenotypes for cefixime, penicillin, azithromycin, ciprofloxacin and tetracycline determined as part of national surveillance programmes. Multivariate linear regression models were used to identify genetic predictors of MIC. Model performance was assessed using leave-one-out cross-validation. Results Overall 1785/3380 (53%) MIC values were predicted to the nearest doubling dilution and 3147 (93%) within ±1 doubling dilution and 3314 (98%) within ±2 doubling dilutions. MIC prediction performance was similar across the five antimicrobials tested. Prediction models included the majority of previously reported resistance determinants. Applying EUCAST breakpoints to MIC predictions, the overall very major error (VME; phenotypically resistant, WGS-prediction susceptible) rate was 21/1577 (1.3%, 95% CI 0.8%-2.0%) and the major error (ME; phenotypically susceptible, WGS-prediction resistant) rate was 20/1186 (1.7%, 1.0%-2.6%). VME rates met regulatory thresholds for all antimicrobials except cefixime and ME rates for all antimicrobials except tetracycline. Country of testing was a strongly significant predictor of MIC for all five antimicrobials. Conclusions We demonstrate a WGS-based MIC prediction approach that allows reliable MIC prediction for five gonorrhoea antimicrobials. Our approach should allow reasonably precise prediction of MICs for a range of bacterial species.
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Affiliation(s)
- David W. Eyre
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Dilrini De Silva
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Kevin Cole
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
- National Infection Service, Public Health England, UK
| | - Joanna Peters
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
- National Infection Service, Public Health England, UK
| | - Michelle J. Cole
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, London, UK
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
- National Infection Service, Public Health England, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Tim E. A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - John Paul
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
- National Infection Service, Public Health England, UK
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Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN, Clarke SC. Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microb Genom 2017; 3:e000119. [PMID: 29026652 PMCID: PMC5628697 DOI: 10.1099/mgen.0.000119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 11/18/2022] Open
Abstract
Serotype replacement has been reported in carriage and disease after pneumococcal conjugate vaccine (PCV) introductions in the UK and globally. We previously described concurrent expansion and decline of sequence types associated with serotype replacement over 5 years following PCV introductions in the UK. Here we use whole-genome sequencing to fully characterise the population structure of pneumococcal isolates collected over seven winters encompassing PCV7 and PCV13 introductions in the UK, investigating the importance of lineages in serotype replacement. We analysed 672 pneumococcal genomes from colonised children of 4 years old or less. The temporal prevalence of 20 lineages, defined by hierarchical Bayesian analysis of population structure (BAPS), was assessed in the context of serotype replacement. Multiple serotypes were detected in the primary winter of sampling within three vaccine-type (VT) lineages BAPS4, BAPS10 and BAPS11, in which serotype replacement were observed. In contrast, serotype replacement was not seen in the remaining three VT lineages (BAPS1, BAPS13 and BAPS14), that expressed a single serotype (6B, 6A and 3, respectively) in the primary winter. One lineage, BAPS1 serotype 6B was undetectable in the population towards the end of the study period. The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population. This observation could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere. It could further indicate whether any antibiotic resistance associated with the lineages is likely to be affected by replacement.
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Affiliation(s)
- Rebecca A. Gladstone
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Vanessa Devine
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - David Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Johanna M. Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stephen D. Bentley
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Saul N. Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- NIHR Wellcome Trust Clinical Research, Manchester Royal Infirmary, Grafton St, Manchester M13 9WL, UK
| | - Stuart C. Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
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Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing. J Clin Microbiol 2017; 55:2334-2347. [PMID: 28490492 PMCID: PMC5527411 DOI: 10.1128/jcm.00462-17] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/08/2017] [Indexed: 01/08/2023] Open
Abstract
Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.
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Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci. Antimicrob Agents Chemother 2017; 61:AAC.02646-16. [PMID: 28193649 PMCID: PMC5404556 DOI: 10.1128/aac.02646-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/20/2022] Open
Abstract
The identification of commensal streptococci species is an everlasting problem due to their ability to genetically transform. A new challenge in this respect is the recent description of Streptococcus pseudopneumoniae as a new species, which was distinguished from closely related pathogenic S. pneumoniae and commensal S. mitis by a variety of physiological and molecular biological tests. Forty-one atypical S. pneumoniae isolates have been collected at the German National Reference Center for Streptococci (GNRCS). Multilocus sequence typing (MLST) confirmed 35 isolates as the species S. pseudopneumoniae. A comparison with the pbp2x sequences from 120 commensal streptococci isolated from different continents revealed that pbp2x is distinct among penicillin-susceptible S. pseudopneumoniae isolates. Four penicillin-binding protein x (PBPx) alleles of penicillin-sensitive S. mitis account for most of the diverse sequence blocks in resistant S. pseudopneumoniae, S. pneumoniae, and S. mitis, and S. infantis and S. oralis sequences were found in S. pneumoniae from Japan. PBP2x genes of the family of mosaic genes related to pbp2x in the S. pneumoniae clone Spain23F-1 were observed in S. oralis and S. infantis as well, confirming its global distribution. Thirty-eight sites were altered within the PBP2x transpeptidase domains of penicillin-resistant strains, excluding another 37 sites present in the reference genes of sensitive strains. Specific mutational patterns were detected depending on the parental sequence blocks, in agreement with distinct mutational pathways during the development of beta-lactam resistance. The majority of the mutations clustered around the active site, whereas others are likely to affect stability or interactions with the C-terminal domain or partner proteins.
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Sierra JM, Fusté E, Rabanal F, Vinuesa T, Viñas M. An overview of antimicrobial peptides and the latest advances in their development. Expert Opin Biol Ther 2017; 17:663-676. [PMID: 28368216 DOI: 10.1080/14712598.2017.1315402] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The recent dramatic increase in the incidence of antimicrobial resistance has been recognized by organizations such as the United Nations and World Health Organization as well as the governments of the USA and several European countries. A relatively new weapon in the fight against severe infections caused by multi-drug resistant bacteria is antimicrobial peptides (AMPs). These include colistin, currently regarded as the last line of antimicrobial therapy against multi-drug resistant microorganisms. Areas covered: Here, the authors provide an overview of the current research on AMPs. The focus is AMPs currently being developed for the treatment of recalcitrant bacterial infections, the synergies of AMPs and antibiotics, and the activity of AMPs against biofilm. This review also includes a brief introduction into the use of AMPs in infections caused by Mycobacterium, fungi, and parasites. Expert opinion: In research into new antimicrobials, AMPs are gaining increasing attention. While many are natural and are produced by a wide variety of organisms, others are being newly designed and chemically synthesized in the laboratory to achieve novel antimicrobial agents. The same strategy to fight infections in nature is thus being effectively exploited to safeguard human and animal health.
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Affiliation(s)
- Josep M Sierra
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Ester Fusté
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain.,b Dept. Public Health, Mental Health and Perinatal Nursing. School of nursing , University of Barcelona , Barcelona , Spain
| | - Francesc Rabanal
- c Department of Organic Chemistry, Faculty of Chemistry , University of Barcelona , Barcelona , Spain
| | - Teresa Vinuesa
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Miguel Viñas
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain.,d Departament of Biomedicine , Cooperativa de Ensino Superior Politécnico e Universitário, IINFACTS , Gandra , Portugal
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Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. Clin Microbiol Infect 2017; 23:574.e7-574.e14. [PMID: 28257899 DOI: 10.1016/j.cmi.2017.02.021] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/15/2017] [Accepted: 02/18/2017] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Our objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS). METHODS For 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions with broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing β-lactams. Conventional serotyping was compared to WGS-based assignments for 302 isolates. RESULTS All 28 isolates with reduced susceptibility to β-lactam antibiotics harboured one of 19 rare PBP2x types. Resistances to erythromycin/clindamycin (808/1975 isolates, 41.0%), erythromycin (235/1975, 11.9%) and lincosamide/streptogramin A/pleuromutilins (56/1975, 2.8%) were predicted by the presence of erm-methylase, mef and lsa determinants, respectively (41 of 56 lsa gene-positive isolates also contained lnu, erm and/or mef genes). Presence of both erm and lsa determinants (25 isolates) predicted non-susceptibility to quinupristin/dalfopristin. Most isolates (1680/1975, 85.1%) were tet gene-positive, although 41/1565 (2.6%) tetM-positive isolates were tetracycline-susceptible. All 53 fluoroquinolone-resistant isolates contained ParC and/or GyrA substitutions. Resistances to rifampin (eight isolates), trimethoprim, chloramphenicol and vancomycin (two isolates each) were predicted by the pipeline. Resistance to macrolides/lincosamides without pipeline prediction was rare and correlated to divergent resistance genes or rRNA A2062G substitution. A selection of 267 isolates assigned WGS-based serotypes were also conventionally serotyped. Of these, 246 (92.1%) were in agreement, with the remaining 21 (7.8%) conventionally non-serotypeable. For 32 of 1975 isolates (1.6%), WGS-based serotypes could not be assigned. CONCLUSION The WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.
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Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. Sci Rep 2017; 7:42808. [PMID: 28205635 PMCID: PMC5311915 DOI: 10.1038/srep42808] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/16/2017] [Indexed: 12/14/2022] Open
Abstract
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the ‘distance to resistance’. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings.
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