scholarly journals Equations To Predict Antimicrobial MICs in Neisseria gonorrhoeae Using Molecular Antimicrobial Resistance Determinants

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
Walter Demczuk ◽  
Irene Martin ◽  
Pam Sawatzky ◽  
Vanessa Allen ◽  
Brigitte Lefebvre ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Training Data ◽  
Sequencing Analysis ◽  
Regression Equations ◽  
Validation Data ◽  
Data Set ◽  
Content Type ◽  
Resistance Determinants ◽  
Extended Spectrum

ABSTRACT The emergence of Neisseria gonorrhoeae strains that are resistant to azithromycin and extended-spectrum cephalosporins represents a public health threat, that of untreatable gonorrhea infections. Multivariate regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to the overall antimicrobial MICs for ceftriaxone, cefixime, azithromycin, tetracycline, ciprofloxacin, and penicillin. A training data set consisting of 1,280 N. gonorrhoeae strains was used to generate regression equations which were then applied to validation data sets of Canadian (n = 1,095) and international (n = 431) strains. The predicted MICs for extended-spectrum cephalosporins (ceftriaxone and cefixime) were fully explained by 5 amino acid substitutions in PenA, A311V, A501P/T/V, N513Y, A517G, and G543S; the presence of a disrupted mtrR promoter; and the PorB G120 and PonA L421P mutations. The correlation of predicted MICs within one doubling dilution to phenotypically determined MICs of the Canadian validation data set was 95.0% for ceftriaxone, 95.6% for cefixime, 91.4% for azithromycin, 98.2% for tetracycline, 90.4% for ciprofloxacin, and 92.3% for penicillin, with an overall sensitivity of 99.9% and specificity of 97.1%. The correlations of predicted MIC values to the phenotypically determined MICs were similar to those from phenotype MIC-only comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular data will facilitate the transition to whole-genome sequencing analysis from phenotypic testing and can fill the surveillance gap in an era of increased reliance on nucleic acid assay testing (NAAT) diagnostics to better monitor the dynamics of N. gonorrhoeae.

scholarly journals Linear regression equations to predict β-lactam, macrolide, lincosamide and fluoroquinolone minimum inhibitory concentrations from molecular antimicrobial resistance determinants in Streptococcus pneumoniae

2021 ◽  
Author(s):  
Walter Demczuk ◽  
Irene Martin ◽  
Averil Griffith ◽  
Brigitte Lefebvre ◽  
Allison McGeer ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Antimicrobial Resistance ◽  
Linear Regression ◽  
Training Data ◽  
Data Sets ◽  
Sequencing Analysis ◽  
Regression Equations ◽  
Validation Data ◽  
Resistance Determinants ◽  
Multiple Variable

Antimicrobial resistance in Streptococcus pneumoniae represents a threat to public health and monitoring the dissemination of resistant strains is essential to guiding health policy. Multiple-variable linear regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to antimicrobial minimum inhibitory concentration (MIC) for penicillin, ceftriaxone, erythromycin, clarithromycin, clindamycin, levofloxacin, and trimethoprim/sulfamethoxazole. Training data sets consisting of Canadian S. pneumoniae isolated from 1995 to 2019 were used to generate multiple-variable linear regression equations for each antimicrobial. The regression equations were then applied to validation data sets of Canadian (n=439) and USA (n=607 and n=747) isolates. The MIC for β-lactam antimicrobials were fully explained by amino acid substitutions in motif regions of the penicillin binding proteins PBP1a, PPB2b, and PBP2x. Accuracy of predicted MICs within one doubling dilution to phenotypically determined MICs for penicillin was 97.4%, ceftriaxone 98.2%; erythromycin 94.8%; clarithromycin 96.6%; clindamycin 98.2%; levofloxacin 100%; and trimethoprim/sulfamethoxazole 98.8%; with an overall sensitivity of 95.8% and specificity of 98.0%. Accuracy of predicted MICs to the phenotypically determined MICs was similar to phenotype-only MIC comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular determinants will facilitate the transition from routine phenotypic testing to whole genome sequencing analysis and can fill the surveillance gap in an era of increased reliance on nucleic acid assay diagnostics to better monitor the dynamics of S. pneumoniae .

scholarly journals Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

2017 ◽  
Vol 55 (5) ◽  
pp. 1454-1468 ◽  
Author(s):  
W. Demczuk ◽  
S. Sidhu ◽  
M. Unemo ◽  
D. M. Whiley ◽  
V. G. Allen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Dna Sequences ◽  
Diversity Index ◽  
23S Rrna ◽  
Content Type ◽  
Typing Scheme ◽  
Resistance Determinants ◽  
Index Value ◽  
User Friendly

ABSTRACTA curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants inNeisseria gonorrhoeaewas developed and is publicly accessible (https://ngstar.canada.ca). TheN. gonorrhoeaeSequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA,mtrR,porB,ponA,gyrA,parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entirepenAsequence, combining the historical nomenclature forpenAtypes I to XXXVIII with novel nucleotide sequence designations; the fullmtrRsequence and a portion of its promoter region; portions ofponA,porB,gyrA, andparC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n= 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n= 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n= 100; 13.0%), ST-42 and ST-91 (n= 45; 5.9%), ST-64 (n= 44; 5.72%), and ST-139 (n= 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n= 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n= 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n= 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n= 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistantN. gonorrhoeaestrains.

scholarly journals Cerebrospinal Fluid Treponema pallidum Particle Agglutination Assay for Neurosyphilis Diagnosis

2017 ◽  
Vol 55 (6) ◽  
pp. 1865-1870 ◽  
Author(s):  
Christina M. Marra ◽  
Clare L. Maxwell ◽  
Shelia B. Dunaway ◽  
Sharon K. Sahi ◽  
Lauren C. Tantalo
Keyword(s):  
Cerebrospinal Fluid ◽  
Vision Loss ◽  
Treponema Pallidum ◽  
Training Data ◽  
Validation Data ◽  
Data Set ◽  
Convenience Sample ◽  
Content Type ◽  
Agglutination Assay ◽  
Particle Agglutination

ABSTRACT Limited data suggest that the cerebrospinal fluid Treponema pallidum particle agglutination assay (CSF-TPPA) is sensitive and a CSF Treponema pallidum hemagglutination assay (CSF-TPHA) titer of ≥1:640 is specific for neurosyphilis diagnosis. CSF-TPPA reactivity and titer were determined for a convenience sample of 191 CSF samples from individuals enrolled in a study of CSF abnormalities in syphilis (training data set). The sensitivity of a reactive test and the specificity for reactivity at serial higher CSF dilutions were determined. Subsequently, CSF-TPPA reactivity at a 1:640 dilution was determined for all available samples from study participants enrolled after the last training sample was collected (validation data set, n = 380). Neurosyphilis was defined as (i) a reactive CSF Venereal Disease Research Laboratory test (CSF-VDRL), (ii) detection of T. pallidum in CSF by reverse transcriptase PCR, or (iii) new vision loss or hearing loss. In the training data set, the diagnostic sensitivities of a reactive CSF fluorescent treponemal antibody absorption test (CSF-FTA-ABS) and a reactive CSF-TPPA did not differ significantly (67 to 98% versus 76 to 95%). The specificity of a CSF-TPPA titer of ≥1:640 was significantly higher than that of lower dilutions and was not significantly different from that of CSF-VDRL. In the validation data set, the diagnostic specificity of a CSF-TPPA titer of ≥1:640 was high and did not differ significantly from that of CSF-VDRL (93 to 94% versus 90 to 91%). Ten CSF samples with a nonreactive CSF-VDRL had a CSF-TPPA titer of ≥1:640. If a CSF-TPPA titer of ≥1:640 was used in addition to a reactive CSF-VDRL, the number of neurosyphilis diagnoses would have increased from 47 to 57 (21.3%). A CSF-TPPA titer cutoff of ≥1:640 may be useful in identifying patients with neurosyphilis when CSF-VDRL is nonreactive.

scholarly journals Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

2016 ◽  
Vol 60 (5) ◽  
pp. 2972-2980 ◽  
Author(s):  
Masato Akiba ◽  
Tsuyoshi Sekizuka ◽  
Akifumi Yamashita ◽  
Makoto Kuroda ◽  
Yuki Fujii ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Sewage Treatment ◽  
Indian States ◽  
Content Type ◽  
Sewage Treatment Plants ◽  
E Coli ◽  
Resistance Determinants ◽  
Carbapenem Resistant ◽  
Extended Spectrum

ABSTRACTTo determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistantEscherichia coliisolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446E. coliisolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%)E. coliisolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. TheblaNDMgene was detected in 14/21 carbapenem-resistantE. coliisolates:blaNDM-1in 2 isolates,blaNDM-5in 7 isolates, andblaNDM-7in 5 isolates. TheblaCTX-Mgene was detected in 112 isolates (66.3%):blaCTX-M-15in 108 isolates andblaCTX-M-55in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of theblaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.

scholarly journals Effect of Variants of Penicillin-Binding Protein 2 on Cephalosporin and Carbapenem Susceptibilities in Neisseria gonorrhoeae

2015 ◽  
Vol 59 (8) ◽  
pp. 5003-5006 ◽  
Author(s):  
Amrita Bharat ◽  
Walter Demczuk ◽  
Irene Martin ◽  
Michael R. Mulvey
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Binding Protein ◽  
Penicillin Binding Protein ◽  
Wild Type ◽  
Molecular Surveillance ◽  
Content Type ◽  
Extended Spectrum ◽  
The Relationship

ABSTRACTTo characterize the relationship between penicillin-binding protein 2 (PBP2/penA) and susceptibility to extended-spectrum cephalosporins (ESCs) and carbapenem antibiotics, we compared 17 PBP2 variants inNeisseria gonorrhoeae. Nonmosaic and mosaic variants of PBP2 caused decreased susceptibility to ESCs and, to a lesser extent, to carbapenems. An A501P substitution in mosaic XXXIV_A501P conferred decreased susceptibility to ESCs but restored carbapenem susceptibility to wild-type levels. These results could aid the molecular surveillance of antimicrobial resistance to these agents.

scholarly journals A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhixiang Yu ◽  
Haiyan He ◽  
Yanan Chen ◽  
Qiuhe Ji ◽  
Min Sun
Keyword(s):  
Cox Regression ◽  
Expression Profiles ◽  
Critical Role ◽  
Gene Signature ◽  
Cancer Genome ◽  
Training Data ◽  
Hub Genes ◽  
Validation Data ◽  
Data Set ◽  
Cox Regression Analysis

AbstractOvarian cancer (OV) is a common type of carcinoma in females. Many studies have reported that ferroptosis is associated with the prognosis of OV patients. However, the mechanism by which this occurs is not well understood. We utilized Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) to identify ferroptosis-related genes in OV. In the present study, we applied Cox regression analysis to select hub genes and used the least absolute shrinkage and selection operator to construct a prognosis prediction model with mRNA expression profiles and clinical data from TCGA. A series of analyses for this signature was performed in TCGA. We then verified the identified signature using International Cancer Genome Consortium (ICGC) data. After a series of analyses, we identified six hub genes (DNAJB6, RB1, VIMP/ SELENOS, STEAP3, BACH1, and ALOX12) that were then used to construct a model using a training data set. The model was then tested using a validation data set and was found to have high sensitivity and specificity. The identified ferroptosis-related hub genes might play a critical role in the mechanism of OV development. The gene signature we identified may be useful for future clinical applications.

scholarly journals Molecular Analyses of TEM Genes and Their Corresponding Penicillinase-Producing Neisseria gonorrhoeae Isolates in Bangkok, Thailand

2011 ◽  
Vol 56 (2) ◽  
pp. 916-920 ◽  
Author(s):  
Shu-ichi Nakayama ◽  
Chanwit Tribuddharat ◽  
Sasiprapa Prombhul ◽  
Ken Shimuta ◽  
Somporn Srifuengfung ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Public Health Problem ◽  
Major Public Health Problem ◽  
Sexual Network ◽  
Genetic Event ◽  
Content Type ◽  
Extended Spectrum ◽  
Resistance To Penicillin ◽  
High Level ◽  
International Awareness

ABSTRACTNeisseria gonorrhoeaeis a major public health problem globally, especially because the bacterium has developed resistance to most antimicrobials introduced for first-line treatment of gonorrhea. In the present study, 96N. gonorrhoeaeisolates with high-level resistance to penicillin from 121 clinical isolates in Thailand were examined to investigate changes related to their plasmid-mediated penicillin resistance and their molecular epidemiological relationships. A β-lactamase (TEM) gene variant,blaTEM-135, that may be a precursor in the transitional stage of a traditionalblaTEM-1gene into an extended-spectrum β-lactamase (ESBL), possibly causing high resistance to all extended-spectrum cephalosporins inN. gonorrhoeae, was identified. Clonal analysis using multilocus sequence typing (MLST) andN. gonorrhoeaemultiantigen sequence typing (NG-MAST) revealed the existence of a sexual network among patients from Japan and Thailand. Molecular analysis of theblaTEM-135gene showed that the emergence of this allele might not be a rare genetic event and that the allele has evolved in different plasmid backgrounds, which results possibly indicate that it is selected due to antimicrobial pressure. The presence of theblaTEM-135allele in the penicillinase-producingN. gonorrhoeaepopulation may call for monitoring for the possible emergence of ESBL-producingN. gonorrhoeaein the future. This study identified ablaTEMvariant (blaTEM-135) that is a possible intermediate precursor for an ESBL, which warrants international awareness.

scholarly journals Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Lang Yang ◽  
Bing Lü ◽  
Quanyi Wang ◽  
Kaiying Wang ◽  
Yanfeng Lin ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Bacillary Dysentery ◽  
Shigella Flexneri ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Local Expansion ◽  
Resistance Determinants ◽  
Genetic Features ◽  
Beijing China

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.

scholarly journals Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae: a Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Adam L. Bailey ◽  
Robert F. Potter ◽  
Meghan A. Wallace ◽  
Caitlin Johnson ◽  
Gautam Dantas ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Susceptibility Testing ◽  
Clinical Laboratory ◽  
Phenotypic Characterization ◽  
First Line ◽  
Content Type ◽  
Gradient Diffusion

ABSTRACT The objectives of this study were to perform genomic and phenotypic characterization of antimicrobial resistance in Neisseria gonorrhoeae isolates recovered from urine samples from patients in St. Louis, MO, USA. Sixty-four clinical isolates were banked over a 2-year period and subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion (penicillin, tetracycline, cefuroxime, and ciprofloxacin) and gradient diffusion (tetracycline, doxycycline, azithromycin, ceftriaxone, cefixime, ciprofloxacin, gemifloxacin, and delafloxacin). The medical records for the patients were evaluated to determine the demographics, location, and prescribed treatment regimen. Isolate draft genomes were assembled from Illumina shotgun sequencing data, and resistance determinants were identified by ResFinder and PointFinder. Of the 64 isolates, 97% were nonsusceptible to penicillin, with resistant isolates all containing the blaTEM-1b gene; 78 and 81% of isolates were nonsusceptible to tetracycline and doxycycline, respectively, with resistant isolates all containing the tet(M) gene. One isolate was classified as non-wild-type to azithromycin, and all isolates were susceptible to ceftriaxone; 89% of patients received this combination of drugs as first-line therapy. Six percent of isolates were resistant to ciprofloxacin, with most resistant isolates containing multiple gyrA and parC mutations. Correlation between disk and gradient diffusion AST devices was high for tetracycline and ciprofloxacin (R2 > 99% for both). The rates of N. gonorrhoeae antibiotic resistance in St. Louis are comparable to current rates reported nationally, except ciprofloxacin resistance was less common in our cohort. Strong associations between specific genetic markers and phenotypic susceptibility testing hold promise for the utility of genotype-based diagnostic assays to guide directed antibiotic therapy. IMPORTANCE Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is most commonly diagnosed using a DNA-based detection method that does not require growth and isolation of N. gonorrhoeae in the laboratory. This is problematic because the rates of antibiotic resistance in N. gonorrhoeae are increasing, but without isolating the organism in the clinical laboratory, antibiotic susceptibility testing cannot be performed on strains recovered from clinical specimens. We observed an increase in the frequency of urine cultures growing N. gonorrhoeae after we implemented a total laboratory automation system for culture in our clinical laboratory. Here, we report on the rates of resistance to multiple historically used, first-line, and potential future-use antibiotics for 64 N. gonorrhoeae isolates. We found that the rates of antibiotic resistance in our isolates were comparable to national rates. Additionally, resistance to specific antibiotics correlated closely with the presence of genetic resistance genes, suggesting that DNA-based tests could also be designed to guide antibiotic therapy for treating gonorrhea.

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