scholarly journals Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States

2016 ◽  
Vol 22 (12) ◽  
pp. 1002.e1-1002.e8 ◽  
Author(s):  
B.J. Metcalf ◽  
S. Chochua ◽  
R.E. Gertz ◽  
Z. Li ◽  
H. Walker ◽  
...  
Keyword(s):  
United States ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
The United States ◽  
Whole Genome ◽  
Resistance Determinants

scholarly journals 1470. Epidemiology of Invasive Pneumococcal Disease (IPD) Following 18 years of Pneumococcal Conjugate Vaccine (PCV) Use in the United States

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S736-S737
Author(s):  
Tamara Pilishvili ◽  
Ryan Gierke ◽  
Monica M Farley ◽  
William Schaffner ◽  
Ann Thomas ◽  
...  
Keyword(s):  
United States ◽  
Older Adults ◽  
Genome Sequencing ◽  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
The United States ◽  
Census Bureau ◽  
Incidence Rates ◽  
Whole Genome ◽  
Vaccine Type

Abstract Background PCVs have been recommended for U.S. children since 2000. A 7-valent vaccine (PCV7) was introduced in 2000. This was replaced by a 13-valent vaccine (PCV13) in 2010. PCV13 was also recommended for adults aged ≥ 65 years in August 2014. We evaluated PCV impact on IPD. Methods IPD cases (isolation of pneumococcus from sterile sites) were identified through CDC’s Active Bacterial Core surveillance during 1998-2018. Isolates were serotyped by Quellung or whole genome sequencing and classified as PCV13-type and non-vaccine-type (NVT). Incidence rates (cases/100,000) were calculated using U.S. Census Bureau population denominators. Results From 1998 through 2018, overall IPD rates among children aged < 5 years decreased by 93% (from 95 to 7 cases/100,000). PCV13-type IPD decreased by 98% (from 88 to 2 cases/100,000). Among adults aged ≥ 65 years, overall IPD rates decreased by 60% (from 61 to 25 cases/100,000). PCV13-type IPD rates declined 86% (from 46 to 7 cases/100,000). Declines were most dramatic in the years following PCV7 introduction, with additional declines after PCV13 introduction in children (Figures 1 and 2). Serotypes 3, 19A, and 19F caused most of the remaining PCV13-type IPD. NVT IPD rates did not change significantly among children. Among adults aged 50-64 years, NVT IPD increased by 83% (from 6 to 12 cases/100,000) (p< 0.01). Among adults aged ≥ 65 years, NVT IPD increased by 22% (from 15 to 18 cases/100,000) (p< 0.01). The most common NVTs in 2018 were 22F (10% of all IPD), 9N (7%) and 15A (5%). Among children, the proportion of cases with meningitis increased from 5% to 14% (p< 0.01), and the proportion with pneumonia/empyema increased from 17% to 31% (p< 0.01). Among adults, the proportion of cases with meningitis did not change (3%), while the proportion with pneumonia/empyema increased from 72% to 76% (p=0.01). Figure 1: Incidence of invasive pneumococcal disease among children aged < 5 years, 1998-2018 Figure 2: Incidence of invasive pneumococcal disease among adults aged ≥ 65 years, 1998-2018 Conclusion Overall IPD incidence among children and adults decreased following PCV introduction for children, driven primarily by reductions in PCV-type IPD. NVT IPD increased in older adults, but these increases did not eliminate reductions from PCV13-type IPD. Disclosures Lee Harrison, MD, GSK (Consultant)Merck (Consultant)Pfizer (Consultant)Sanofi Pasteur (Consultant)

scholarly journals Genomic Analysis of a Pan-Resistant Isolate ofKlebsiella pneumoniae, United States 2016

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Tom J. B. de Man ◽  
Joseph D. Lutgring ◽  
David R. Lonsway ◽  
Karen F. Anderson ◽  
Julia A. Kiehlbauch ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome ◽  
Beta Lactams ◽  
Content Type

ABSTRACTAntimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. Here, we report the genomic characterization of an unusualKlebsiella pneumoniae, nonsusceptible to all 26 antibiotics tested, that was isolated from a U.S. patient. The isolate harbored four known beta-lactamase genes, including plasmid-mediatedblaNDM-1andblaCMY-6, as well as chromosomalblaCTX-M-15andblaSHV-28, which accounted for resistance to all beta-lactams tested. In addition, sequence analysis identified mechanisms that could explain all other reported nonsusceptibility results, including nonsusceptibility to colistin, tigecycline, and chloramphenicol. Two plasmids, IncA/C2 and IncFIB, were closely related to mobile elements described previously and isolated from Gram-negative bacteria from China, Nepal, India, the United States, and Kenya, suggesting possible origins of the isolate and plasmids. This is one of the firstK. pneumoniaeisolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as nonsusceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline.IMPORTANCEAntimicrobial resistance is a major public health threat worldwide. Bacteria that are nonsusceptible or resistant to all antimicrobials available are of major concern to patients and the public because of lack of treatment options and potential for spread. AKlebsiella pneumoniaestrain that was nonsusceptible to all tested antibiotics was isolated from a U.S. patient. Mechanisms that could explain all observed phenotypic antimicrobial resistance phenotypes, including resistance to colistin and beta-lactams, were identified through whole-genome sequencing. The large variety of resistance determinants identified demonstrates the usefulness of whole-genome sequencing for detecting these genes in an outbreak response. Sequencing of isolates with rare and unusual phenotypes can provide information on how these extremely resistant isolates develop, including whether resistance is acquired on mobile elements or accumulated through chromosomal mutations. Moreover, this provides further insight into not only detecting these highly resistant organisms but also preventing their spread.

scholarly journals Analysis of Virulence and Antimicrobial Resistance Gene Carriage in Staphylococcus aureus Infections in Equids Using Whole-Genome Sequencing

mSphere ◽  
2021 ◽  
Author(s):  
Sara V. Little ◽  
Andrew E. Hillhouse ◽  
Sara D. Lawhon ◽  
Laura K. Bryan
Keyword(s):  
United States ◽  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome ◽  
Large Collection ◽  
Content Type ◽  
Antimicrobial Resistance Gene

This is one of the first studies to perform whole-genome sequencing (WGS) of a large collection of Staphylococcus aureus isolates, both methicillin resistant and susceptible, collected from horses. A large proportion of the isolates carry leucocidin PQ (LukPQ), making this one of the first reports of such carriage in the United States.

scholarly journals Whole Genome Sequencing Resource of the European Larch Canker Pathogen Lachnellula willkommii for Molecular Diagnostic Marker Development

2020 ◽  
Vol 110 (7) ◽  
pp. 1255-1259
Author(s):  
Emily Giroux ◽  
Guillaume J. Bilodeau
Keyword(s):  
United States ◽  
North America ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
The United States ◽  
Molecular Diagnostic ◽  
Whole Genome ◽  
European Larch ◽  
The North

The filamentous ascomycete fungus Lachnellula willkommii is the causal agent of European larch canker (ELC), one of the most destructive diseases of larch in Europe and a regulated plant pathogen of quarantine significance in Canada and the United States. L. willkommii was first detected in Massachusetts, North America in 1927 on a larch plantation cultivated with nursery stock imported from Great Britain. Despite the decades of practices aimed at eliminating the pathogen, it has reappeared in coastal areas of Canada and the United States. There is concern ELC could spread throughout the range of eastern larch, a transcontinental species typical of the Boreal forest that spans the North American landscape. There is geographic range overlap between several nonpathogenic indigenous Lachnellula species and the reported distribution of L. willkommii in North America. Morphological and biological methods to distinguish L. willkommii are often inadequate as the fungus does not always produce the phenotypic structures that distinguish it from these other saprophytic Lachnellula species. Whole genome sequencing technologies were used to obtain the draft genome sequences of L. willkommii and six other Lachnellula species. Molecular markers identified from the genomic data may be used to discriminate L. willkommii from its nonpathogenic relatives.

scholarly journals Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States

2019 ◽  
Vol 16 (7) ◽  
pp. 441-450 ◽  
Author(s):  
Eric Brown ◽  
Uday Dessai ◽  
Sherri McGarry ◽  
Peter Gerner-Smidt
Keyword(s):  
Public Health ◽  
United States ◽  
Food Safety ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

2016 ◽  
Vol 60 (9) ◽  
pp. 5515-5520 ◽  
Author(s):  
Patrick F. McDermott ◽  
Gregory H. Tyson ◽  
Claudine Kabera ◽  
Yuansha Chen ◽  
Cong Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
The United States ◽  
Whole Genome ◽  
Content Type ◽  
Structural Resistance ◽  
Retail Meat

ABSTRACTLaboratory-basedin vitroantimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidalSalmonellaand correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred fortySalmonellaof 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n =59) in the 104 human isolates than in the 536 retail meat isolates (n =36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum β-lactamases (ESBLs) (blaCTX-M1andblaSHV2a) in retail meat isolates ofSalmonellain the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidalSalmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

scholarly journals SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data

2019 ◽  
Vol 85 (23) ◽  
Author(s):  
Shaokang Zhang ◽  
Hendrik C. den Bakker ◽  
Shaoting Li ◽  
Jessica Chen ◽  
Blake A. Dinsmore ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Draft Genome ◽  
The United States ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Link Type

ABSTRACT SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole-genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here, we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include (i) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes, (ii) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies, and (iii) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common U.S. serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification. IMPORTANCE Serotyping is the basis of public health surveillance of Salmonella. It remains a first-line subtyping method even as surveillance continues to be transformed by whole-genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole-genome-sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large-scale surveillance of Salmonella by whole-genome sequencing.

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