scholarly journals 806. Uncluttering Case Clusters: Use of Rapid Sequencing to Exclude Transmission Events

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S497-S497
Author(s):  
Meredith Fahy ◽  
Dolores Suslak ◽  
Virginia M Pierce ◽  
Mohamad Sater ◽  
Miriam Huntley ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Conservation Of Resources ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Material Support ◽  
Corynebacterium Striatum ◽  
Neonatal Icu ◽  
Study Participants ◽  
Susceptibility Profiles ◽  
Epidemiological Characteristics

Abstract Background Newly identified multi-drug resistant organisms (MDRO) isolated from hospitalized patients with shared epidemiological characteristics can either represent transmission events or independent, unrelated acquisitions. Whole genome sequencing (WGS) can improve the efficiency of investigations triggered by MDRO cases with apparent epidemiological linkages by early exclusion of clonality. We report an implementation of WGS to investigate a cluster of methicillin-resistant Staphylococcus aureus (MRSA) and a cluster of carbapenem-resistant Enterobacterales (CRE) inpatient nosocomial infections. Methods Study participants included five Neonatal ICU (NICU) patients with nosocomial MRSA isolates recovered between June and August 2020, and two Respiratory Acute Care Unit (RACU) patients with nosocomial CRE infections in October 2020. Routine unit surveillance activities and characterization using standard epidemiologic criteria identified the isolates as nosocomial to their respective unit. The isolates then underwent WGS and single nucleotide polymorphism (SNP)-based relatedness analysis. Results The MRSA cluster included five neonates with either clinical or surveillance isolates. WGS identified one of the five isolates as methicillin susceptible S. aureus due to the absence of the mecA or mecC resistance gene, despite growth on chromogenic MRSA screening agar. WGS revealed each of the five isolates as belonging to a distinct multi locus sequence type (MLST) group with thousands of SNP differences between samples. The CRE cluster included two patients with Klebsiella pneumoniae isolated from clinical cultures within five days of each other with identical antimicrobial susceptibility profiles. WGS of the two isolates revealed that they belonged to different MLSTs and had tens of thousands of differing SNPs. WGS results suggest that a nosocomial transmission linking these infections was highly unlikely. For both investigations, WGS returned results within thirty-six hours of sample receipt. Figure 1. Corynebacterium striatum Respiratory Cultures January 2020-February 2021 Panel showing single nucleotide polymorphism (SNP) differences between isolates for respective clusters. Conclusion Apparent transmission events can be resource intensive to investigate and manage. The application of rapid WGS allowed for early discontinuation of cluster investigations and conservation of resources. Disclosures Virginia M. Pierce, MD, UpToDate, Inc. (Other Financial or Material Support, Author) Mohamad Sater, PhD, Day Zero Diagnostics (Employee, Shareholder) Miriam Huntley, PhD, Day Zero Diagnostics (Employee, Shareholder) Ian Herriott, BS, Day Zero Diagnostics (Employee, Shareholder) Tim Farrell, MS, Day Zero Diagnostics, Inc. (Employee, Shareholder) David C. Rosenberg, MD, Cepheid Diagnostics (Consultant)Day Zero Diagnostics (Consultant)SeLux Diagnostics (Consultant) Erica S. Shenoy, MD, PhD, Vertex Pharmaceuticals (Individual(s) Involved: Self): I gave a single lecture in 3/2020 for which I received financial compensation, Other Financial or Material Support

scholarly journals 1397. Modern Lineages of Mycobacterium tuberculosis Were Recently Introduced in Western India and Demonstrate Increased Transmissibility

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S783-S784
Author(s):  
Avika Dixit ◽  
Anju Kagal ◽  
Yasha Ektefaie ◽  
Luca Freschi ◽  
Rahul Lokhande ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mycobacterium Tuberculosis ◽  
Molecular Dating ◽  
Western India ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branch Lengths ◽  
Kolmogorov Smirnov ◽  
Study Participants ◽  
Ks Test

Abstract Background Mycobacterium tuberculosis (Mtb) transmissibility may vary between lineages (or variants) and this may contribute to the slow decline of tuberculosis incidence. The objective of our study was to compare transmissibility across four major lineages (L1-4) of Mtb in Pune, India. Methods We performed whole-genome sequencing (WGS) of Mtb isolated from sputum culture of adult patients with pulmonary TB. We performed genotypic susceptibility testing for both first- and second-line drugs using a previously validated random forest predictor. We identified single nucleotide polymorphisms and generated a multiple sequence alignment excluding drug resistance conferring mutations to avoid skewing the phylogeny due to convergent evolution in these regions. We used Bayesian molecular dating to generate phylogenies and compared tree characteristics using a two-sample Kolmogorov-Smirnov (KS) test. Results Of the 642 isolates from distinct study participants that underwent WGS, 612 met quality criteria. The median age of participants was 31 years (range 18-74), the majority were male (64.7%) and sputum smear-positive (83.3%), and 6.7% had co-infection with HIV (Table 1). There was no significant difference in baseline characteristics between lineages. The majority of isolates belonged to L3 (44.6%). The majority (61.1%) of multidrug-resistant (MDR, resistant to isoniazid and rifampin) isolates belonged to L2. In phylogenetic analysis, we found evidence of higher transmissibility of L2 as indicated by shorter branch lengths (i.e., less time had elapsed between transmission and sampling) and more genetic similarity (smaller pairwise single nucleotide polymorphism [SNP] distances) among L2 isolates as compared to other lineages (Figure 1). Branching times for L2 and L4 were smaller than L1 and L3 indicating recent introduction into the region (p < 0.001 [KS test]). Figure 1: Lineage-wise distribution of A) phylogenetic tree branch lengths (log) and B) pairwise single nucleotide polymorphism (SNP) distance, using 612 tuberculosis isolates from Pune, India. P values calculated using two-sample Kolmogorov-Smirnov test. Table 1: Demographic characteristics of study participants included in the study, by lineage. Conclusion Modern Mtb lineages (L2 and L4) were relatively recently introduced in western India, as compared to older lineages (L1 and L3), with the more drug-resistant L2 showing higher transmissibility. These findings highlight the need for early detection and treatment initiation to interrupt transmission with important implications for antimicrobial stewardship and heightened surveillance of TB resistance rates. Disclosures All Authors: No reported disclosures

scholarly journals The effect of alcohol abuse on the risk of acute non-biliary pancreatitis in carriers of the polymorphism rs7674870 gene SLC7A11 A>G

2020 ◽  
pp. 30-36
Author(s):  
Tatyana A. Samgina
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Alcohol Abuse ◽  
Clinical Symptoms ◽  
Gastrointestinal Diseases ◽  
Biliary Pancreatitis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Environment Analysis ◽  
Study Participants ◽  
Instrumental Methods

The aim was to determine the contribution of the rs7674870 single nucleotide polymorphism of the SLC7A11 A>G gene and alcohol abuse to the risk of acute pancreatitis. Materials and methods. The material for the study was DNA samples obtained from 469 unrelated patients with acute non-biliary pancreatitis and 572 unrelated individuals without gastrointestinal diseases. The average age of the patients was 48.9 ± 13.1, healthy individuals - 47.8 ± 12.1. The diagnosis and severity of ANP were based on clinical symptoms, laboratory and instrumental methods of investigation. The study participants were divided into two groups depending on the amount of alcohol consumed per week: (1) - less than 200 g per week and (2) - more than 200 g per week; according to frequency: (1) - 1 to 2 days a month or less and (2) - 1 or more days a week; and duration: (1) - up to 10 years and (2) - for 10 or more years. Genomic DNA was purified from the thawed blood samples by phenol chloroform extraction method. Genotyping was performed by real-time PCR by discriminating alleles using TaqMan probes on a CFX96 Bio-Rad Laboratories amplifier (USA) using commercial TaqMan SNP Genotyping Assays reagent kits from Applied Biosystems (USA). Associations of alleles and genotypes with a risk of ANP were evaluated by the odds ratio (OR). Statistical analysis was performed with Statistica 10 (StatSoft, USA), SNPstats. Results. We did not find any association of the rs7674870 single nucleotide polymorphism of the SLC7A11 A/G gene with the risk of ANP. However, the genotype-environment analysis revealed an association between the G/G SLC7A11 A/G rs7674870 genotype with a reduced risk of ANP in the absence of alcohol abuse in terms of frequency (OR=0.54, 95% CI=0.31-0.96, Р=0.02), duration (OR=0.66, 95% CI=0.44-0.99, Р=0.03), and amount of alcohol consumed per week (OR=0.63, 95% CI=0.41-0.97, Р=0.01). Conclusion. The results obtained may indicate that, in carriers of the G/G SLC7A11 A/G rs7674870 genotype, moderate consumption of alcohol compensates for pathological changes that can lead to the development of ANP.

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

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