scholarly journals Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections

2018 ◽  
Vol 56 (5) ◽  
Author(s):  
Bin Chang ◽  
Masatomo Morita ◽  
Ken-ichi Lee ◽  
Makoto Ohnishi
Keyword(s):  
Streptococcus Pneumoniae ◽  
Clonal Complex ◽  
Underlying Disease ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Severe Underlying Disease ◽  
Hospital Acquired Pneumonia ◽  
Hospital Acquired

ABSTRACT Streptococcus pneumoniae colonizes the nasopharyngeal mucus in healthy individuals and can cause otitis media, pneumonia, and invasive pneumococcal diseases. In this study, we analyzed S. pneumoniae strains that caused 19 pneumonia episodes in long-term inpatients with severe underlying disease in a hospital during a period of 14 months (from January 2014 to February 2015). Serotyping and whole-genome sequencing analyses revealed that 18 of the 19 pneumonia cases were caused by S. pneumoniae strains belonging to 3 genetically distinct groups: clonal complex 9999 (CC9999), sequence type 282 (ST282), and ST166. The CC9999 and ST282 strains appeared to have emerged separately by a capsule switch from the pandemic PMEN 1 strain (Spain 23F -ST81). After all the long-term inpatients were inoculated with the 23-valent pneumococcal polysaccharide vaccine, no other nosocomial pneumonia infections occurred until March 2016.

scholarly journals First Whole-Genome Sequence of a Highly Resistant Klebsiella pneumoniae Sequence Type 14 Strain Isolated from Sudan

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
Sofia B. Mohamed ◽  
Sumaya Kambal ◽  
Abdalla Munir ◽  
Nusiba Abdalla ◽  
Mohamed Hassan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Sequence ◽  
Significant Proportion ◽  
Opportunistic Pathogen ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired

Klebsiella pneumoniae is an opportunistic pathogen that accounts for a significant proportion of hospital-acquired infections and is a leading cause of nosocomial outbreaks. Here, we describe the genomic sequence of a highly resistant K. pneumoniae sequence type 14 (ST14) strain isolated from Sudan.

scholarly journals Nosocomial Outbreak of Drug-Resistant Streptococcus pneumoniae Serotype 9V in an Adult Respiratory Medicine Ward

2016 ◽  
Vol 55 (3) ◽  
pp. 776-782 ◽  
Author(s):  
Elita Jauneikaite ◽  
Zareena Khan-Orakzai ◽  
Georgia Kapatai ◽  
Susannah Bloch ◽  
Julie Singleton ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Lower Respiratory Tract ◽  
Sequence Type ◽  
Resistance Pattern ◽  
Whole Genome ◽  
Drug Resistant ◽  
Nosocomial Outbreak ◽  
Content Type ◽  
Rapid Transmission ◽  
Case Presentations

ABSTRACT Streptococcus pneumoniae infections arising in hospitalized patients are often assumed to be sporadic and linked to community acquisition. Here, whole-genome sequencing was used to demonstrate nosocomial acquisition of antimicrobial-resistant sequence type 156 (ST156) serotype 9V S. pneumoniae in 3 respiratory patients that resulted in two bacteremias and one lower respiratory tract infection. Two of the cases arose in patients who had recently been discharged from the hospital and were readmitted from the community. Nosocomial spread was suspected solely because of the highly unusual resistance pattern and case presentations within 24 h of one another. The outbreak highlights the potential for rapid transmission and the short incubation period in the respiratory ward setting.

scholarly journals Complete Genome Sequence of the Arcobacter skirrowii Type Strain LMG 6621

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee
Keyword(s):  
Genome Sequence ◽  
Fecal Sample ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
The United Kingdom ◽  
Veterinary Importance

Arcobacter skirrowii is a species of veterinary importance, originally recovered from the feces, aborted fetuses, and preputial fluids of livestock. We present here the whole-genome sequence of the A. skirrowii type strain LMG 6621 (= 449/80T = CCUG 10374T), isolated in the United Kingdom from a lamb diarrheal fecal sample.

scholarly journals Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain UPM 260, Isolated from a Broiler Chicken in Perak, Malaysia

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Najwa Syahirah Roslan ◽  
Shagufta Jabeen ◽  
Nurulfiza Mat Isa ◽  
Abdul Rahman Omar ◽  
Mohd Hair Bejo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Salmonella Enterica ◽  
Broiler Chicken ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Typhimurium Strain ◽  
Serovar Typhimurium

ABSTRACT Salmonella enterica subsp. enterica serovar Typhimurium is one of several well-categorized Salmonella serotypes recognized globally. Here, we report the whole-genome sequence of S. Typhimurium strain UPM 260, isolated from a broiler chicken.

scholarly journals Whole-Genome Sequence of Lactobacillus salivarius DJ-sa-01, Isolated from Chicken Small Intestine

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Dongjun Kim ◽  
Mun-Ju Cho ◽  
Seungchan Cho ◽  
Yongjun Lee ◽  
Sung June Byun ◽  
...  
Keyword(s):  
Small Intestine ◽  
Genome Sequence ◽  
Probiotic Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lactobacillus Salivarius ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Circular Chromosome

We have identified the whole-genome sequence of Lactobacillus salivarius DJ-sa-01, a potential probiotic strain for poultry, isolated from a chicken small intestine. We used the PacBio and Illumina platforms to obtain the sequence of the entire single circular chromosome.

scholarly journals Complete Genome Sequence of Streptococcus oralis SF100, Isolated from Blood Cultures from a Patient with Infective Endocarditis

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
Ji Hee Lee ◽  
Hyun Jung Ji ◽  
Ho Seong Seo ◽  
Paul M. Sullam
Keyword(s):  
Infective Endocarditis ◽  
Animal Models ◽  
Oral Cavity ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Blood Cultures ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Streptococcus Oralis

Streptococcus oralis is a commensal viridans group streptococcus of the human oral cavity and a frequent cause of endovascular infection. Here, we report the complete whole-genome sequence of S. oralis strain SF100, which was originally isolated from the blood of a patient with infective endocarditis. This strain contains the lysogenic bacteriophage SM1, which enhances the virulence of SF100 in animal models of endocardial infection.

scholarly journals Draft Genome Sequence of Acholeplasma laidlawii Isolated from the Conjunctiva of a Heifer with Infectious Bovine Keratoconjunctivitis

2021 ◽  
Vol 10 (4) ◽  
Author(s):  
Gloria Gioia ◽  
Maria F. Addis ◽  
Laura B. Goodman ◽  
Patrick K. Mitchell ◽  
Belinda Thompson ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Infectious Bovine Keratoconjunctivitis ◽  
Acholeplasma Laidlawii

ABSTRACT Acholeplasma laidlawii can be isolated from cattle environments and different body sites of bovines. It is still under evaluation if A. laidlawii acts as a primary pathogen. Here, we present the whole-genome sequence of A. laidlawii isolated from the conjunctiva of a heifer with infectious bovine keratoconjunctivitis.

scholarly journals Finished Whole-Genome Sequence of Clostridium argentinense Producing Botulinum Neurotoxin Type G

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Jessica L. Halpin ◽  
Karen Hill ◽  
Shannon L. Johnson ◽  
David Carlton Bruce ◽  
T. Brian Shirey ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Botulinum Neurotoxin ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Reference Quality

ABSTRACT Here, we present a closed genome sequence for Clostridium argentinense strain 89G, the first strain identified to produce botulinum neurotoxin type G (BoNT/G). Although discovered in 1970, to date, there have been no reference quality sequences publicly available for this species.

scholarly journals Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

2015 ◽  
Vol 81 (17) ◽  
pp. 6024-6037 ◽  
Author(s):  
Matthew J. Stasiewicz ◽  
Haley F. Oliver ◽  
Martin Wiedmann ◽  
Henk C. den Bakker
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Content Type ◽  
Food Borne ◽  
Clonal Spread

ABSTRACTWhile the food-borne pathogenListeria monocytogenescan persist in food associated environments, there are no whole-genome sequence (WGS) based methods to differentiate persistent from sporadic strains. Whole-genome sequencing of 188 isolates from a longitudinal study ofL. monocytogenesin retail delis was used to (i) apply single-nucleotide polymorphism (SNP)-based phylogenetics for subtyping ofL. monocytogenes, (ii) use SNP counts to differentiate persistent from repeatedly reintroduced strains, and (iii) identify genetic determinants ofL. monocytogenespersistence. WGS analysis revealed three prophage regions that explained differences between three pairs of phylogenetically similar populations with pulsed-field gel electrophoresis types that differed by ≤3 bands. WGS-SNP-based phylogenetics found that putatively persistentL. monocytogenesrepresent SNP patterns (i) unique to a single retail deli, supporting persistence within the deli (11 clades), (ii) unique to a single state, supporting clonal spread within a state (7 clades), or (iii) spanning multiple states (5 clades). Isolates that formed one of 11 deli-specific clades differed by a median of 10 SNPs or fewer. Isolates from 12 putative persistence events had significantly fewer SNPs (median, 2 to 22 SNPs) than between isolates of the same subtype from other delis (median up to 77 SNPs), supporting persistence of the strain. In 13 events, nearly indistinguishable isolates (0 to 1 SNP) were found across multiple delis. No individual genes were enriched among persistent isolates compared to sporadic isolates. Our data show that WGS analysis improves food-borne pathogen subtyping and identification of persistent bacterial pathogens in food associated environments.

scholarly journals Sequence Type 273 Carbapenem-Resistant Klebsiella pneumoniae Carrying bla NDM-1 and bla IMP-4

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Lu Liu ◽  
Yu Feng ◽  
Haiyan Long ◽  
Alan McNally ◽  
Zhiyong Zong
Keyword(s):  
Klebsiella Pneumoniae ◽  
Southeast Asia ◽  
Human Blood ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Transmissible Plasmid ◽  
Long Read

ABSTRACT A carbapenem-resistant Klebsiella pneumoniae isolate was recovered from human blood. Its whole-genome sequence was obtained using Illumina and long-read MinION sequencing. The strain belongs to sequence type 273 (ST273), which was found recently and caused an outbreak in Southeast Asia. It has two carbapenemase genes, bla NDM-1 (carried by an ST7 IncN self-transmissible plasmid) and bla IMP-4 (located on a self-transmissible IncHI5 plasmid). Non-KPC-producing ST237 may represent a lineage of carbapenem-resistant K. pneumoniae , which warrants further monitoring.

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