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Genomic Characterization of Tissue Invasive Klebsiella pneumoniae Complex in a Hospital System with a Focus on Species Distribution and Hypervirulence

https://doi.org/10.1101/2020.11.04.369173

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogenetic Groups Among Klebsiella pneumoniae Isolates from Brazil: Relationship with Antimicrobial Resistance and Origin

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Antibacterial Activity of Halophilic Bacteria Against Drug-Resistant Microbes Associated with Diabetic Foot Infections

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Clinical and microbiological characteristics of community-acquired thoracic empyema or complicated parapneumonic effusion caused by Klebsiella pneumoniae in Taiwan

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Monomicrobial Klebsiella pneumoniae necrotizing fasciitis: an emerging life-threatening entity

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Detection of multiple hypervirulent Klebsiella pneumoniae strains in a New York City hospital through screening of virulence genes

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Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43

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Clinical and molecular characteristics of multi-clone carbapenem-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae isolates in a tertiary hospital in Beijing, China

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Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya

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Draft genome of a hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae with novel sequence type ST2320 isolated from a chronic liver disease patient

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Phenotypic and molecular characterization of Klebsiella spp. isolates causing community-acquired infections

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Urinary Tract Infection Antibiotic Resistance in the United States

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Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.

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Erratum to “Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.” [Res Microbiol 170 (3) (2019) 165–170]

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Klebsiella pneumoniae liver abscess: a new invasive syndrome

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Pathogen Distribution and Antimicrobial Resistance Among Pediatric Healthcare-Associated Infections Reported to the National Healthcare Safety Network, 2011–2014

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Fast gapped-read alignment with Bowtie 2

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Within-host evolution of bacterial pathogens

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Molecular epidemiology of Klebsiella variicola obtained from different sources

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Klebsiella variicola, A Novel Species with Clinical and Plant-Associated Isolates

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Association between rmpA and magA Genes and Clinical Syndromes Caused by Klebsiella pneumoniae in Taiwan

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Primary Liver Abscess Due toKlebsiella pneumoniaein Taiwan

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Serum‐Induced Iron‐Acquisition Systems and TonB Contribute to Virulence inKlebsiella pneumoniaeCausing Primary Pyogenic Liver Abscess

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Predictors of Septic Metastatic Infection and Mortality among Patients withKlebsiella pneumoniaeLiver Abscess

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The Epidemiology of Ventilator-Associated Pneumonia in a Network of Community Hospitals: A Prospective Multicenter Study

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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Genomic Characterization of a Multidrug-Resistant and Hypermucoviscous/Hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae ST4417 Isolated from a Sewage Treatment Plant

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The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

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Prokka: rapid prokaryotic genome annotation

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

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Outbreak of Hypervirulent Multidrug-resistantKlebsiella variicolaCausing High Mortality in Neonates in Bangladesh

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Complex molecular epidemiology of extended-spectrum -lactamases in Klebsiella pneumoniae: a long-term perspective from a single institution in Madrid

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Occurrence of colistin-resistant hypervirulent Klebsiella variicola

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Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

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Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages

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Interactive Tree Of Life (iTOL) v4: recent updates and new developments

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Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior…

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Prevalence of hypervirulent Klebsiella pneumoniae-associated genes rmpA and magA in two tertiary hospitals in Houston, TX, USA

inferredcites →https://doi.org/10.1099/jmm.0.001143openalex-snapshot

Klebsiella variicola causing nosocomial transmission among neonates – an emerging pathogen?

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Identification of Klebsiella capsule synthesis loci from whole genome data

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Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

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The role of Klebsiella pneumoniae rmpA in capsular polysaccharide synthesis and virulence revisited

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VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

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D³ Data-Driven Documents

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Two Hypervirulent Klebsiella pneumoniae Isolates Producing a bla KPC-2 Carbapenemase from a Canadian Patient

inferredcites →https://doi.org/10.1128/aac.01019-15openalex-snapshot

Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance

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High Prevalence of Hypervirulent Klebsiella pneumoniae Infection in China: Geographic Distribution, Clinical Characteristics, and Antimicrobial Resistance

inferredcites →https://doi.org/10.1128/aac.02246-18openalex-snapshot

Emergence of OXA-232 Carbapenemase-Producing Klebsiella pneumoniae That Carries a pLVPK-Like Virulence Plasmid among Elderly Patients in China

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Next-Generation-Sequencing-Based Hospital Outbreak Investigation Yields Insight into Klebsiella aerogenes Population Structure and Determinants of Carbapenem Resistance and Pathogenicity

inferredcites →https://doi.org/10.1128/cmr.00001-19openalex-snapshot

Hypervirulent Klebsiella pneumoniae

inferredcites →https://doi.org/10.1128/genomea.01057-17openalex-snapshot

Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

inferredcites →https://doi.org/10.1128/iai.54.3.603-608.1986openalex-snapshot

Correlation of the virulence of Klebsiella pneumoniae K1 and K2 with the presence of a plasmid encoding aerobactin

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Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis

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Multiplex PCR Analysis for Rapid Detection of Klebsiella pneumoniae Carbapenem-Resistant (Sequence Type 258 [ST258] and ST11) and Hypervirulent (ST23, ST65, ST86, and ST375) Strains

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Identification of Biomarkers for Differentiation of Hypervirulent Klebsiella pneumoniae from Classical K. pneumoniae

inferredcites →https://doi.org/10.1128/jcm.00825-18openalex-snapshot

Closing the Brief Case: Klebsiella variicola —Identifying the Misidentified

inferredcites →https://doi.org/10.1128/jcm.00826-18openalex-snapshot

The Brief Case: Klebsiella variicola —Identifying the Misidentified

inferredcites →https://doi.org/10.1128/jcm.01206-19openalex-snapshot

Clinical and Molecular Characteristics of Klebsiella pneumoniae Isolates Causing Bloodstream Infections in Japan: Occurrence of Hypervirulent Infections in Health Care

inferredcites →https://doi.org/10.1155/2013/828741openalex-snapshot

Population‐Based Surveillance for Hypermucoviscosity Klebsiella pneumoniae Causing Community‐Acquired Bacteremia in Calgary, Alberta

inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot

The RAST Server: Rapid Annotations using Subsystems Technology

inferredcites →https://doi.org/10.1186/s12866-017-1148-6openalex-snapshot

Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection

inferredcites →https://doi.org/10.1186/s12879-019-4498-xopenalex-snapshot

Clinical characteristics in blood stream infections caused by Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae: a comparative study, Japan, 2014–2017

inferredcites →https://doi.org/10.1186/s12941-017-0191-3openalex-snapshot

Systematic review and meta-analysis of mortality of patients infected with carbapenem-resistant Klebsiella pneumoniae

inferredcites →https://doi.org/10.1186/s13059-014-0524-xopenalex-snapshot

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

inferredcites →https://doi.org/10.1186/s13073-018-0587-5openalex-snapshot

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

inferredcites →https://doi.org/10.1186/s13073-019-0706-yopenalex-snapshot

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0113539openalex-snapshot

Klebsiella variicola Is a Frequent Cause of Bloodstream Infection in the Stockholm Area, and Associated with Higher Mortality Compared to K. pneumoniae

inferredcites →https://doi.org/10.2147/idr.s191892openalex-snapshot

High prevalence of KPC-2-producing hypervirulent Klebsiella pneumoniae causing meningitis in Eastern China

inferredcites →https://doi.org/10.2147/ijgm.s166940openalex-snapshot

Clinical and microbiological characteristics and occurrence of Klebsiella pneumoniae infection in Japan

inferredcites →https://doi.org/10.3201/eid0802.010025openalex-snapshot

Community-Acquired Klebsiella pneumoniae Bacteremia: Global Differences in Clinical Patterns

inferredcites →https://doi.org/10.3201/eid2203.151466openalex-snapshot

Liver Abscess Caused by Infection with Community-AcquiredKlebsiella quasipneumoniaesubsp.quasipneumoniae

inferredcites →https://doi.org/10.3389/fcimb.2017.00182openalex-snapshot

Outbreak by Hypermucoviscous Klebsiella pneumoniae ST11 Isolates with Carbapenem Resistance in a Tertiary Hospital in China

inferredcites →https://doi.org/10.3389/fmicb.2018.03000openalex-snapshot

Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry

inferredcites →https://doi.org/10.3389/fpubh.2019.00229openalex-snapshot

An Outbreak of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae in an Intensive Care Unit of a Major Teaching Hospital in Wenzhou, China

inferredcites →https://doi.org/10.4161/viru.22718openalex-snapshot

Hypervirulent (hypermucoviscous) Klebsiella pneumoniae

inferredcites →https://doi.org/10.7717/peerj-cs.20openalex-snapshot

CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3390/toxins13050346openalex-snapshot

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