Population genomics of Klebsiella pneumoniae

Wyres, Kelly L.; Lam, Margaret M C; Holt, Kathryn E.

doi:10.1038/s41579-019-0315-1

Cited by 680 publications

(903 citation statements)

References 146 publications

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“…Other genomic islands previously identified in the reference strain Kp52.145 [6], as well as genes coding for type-III fimbriae ( mrk cluster) and the phospholipase D ( pld1 ), were also present. Contrary to other hypervirulent Kp sublineages such as CG23, no heavy-metal resistance (lead, copper, silver and tellurium) gene clusters were detected [4, 13].…”

Section: Resultsmentioning

confidence: 99%

“…Population biology studies have shown that HvKp infections are caused by a limited number of lineages, such as clonal group (CG) 23, CG65 and CG380 [3]. These lineages often harbour a combination of chromosomal pathogenicity factors (K1 or K2 capsular types) and accessory virulence factors, in particular regulators of the mucoid phenotype (RmpA/RmpA2) and siderophores (aerobactin [ iro ] and salmochelin [ iut ]) carried by plasmids [4].…”

Section: Introductionmentioning

confidence: 99%

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Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

et al. 2020

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Klebsiella pneumoniae (Kp) reference strain Kp52.145 is widely used in experimental Klebsiella pathophysiology. Since 1935, only one other strain of the same sublineage (sequence type ST66, capsular serotype K2) was isolated (AJ210, Australia). Here, we describe a community-acquired invasive infection caused by a ST66-K2 Kp strain in France. Four hypermucoviscous Kp isolates responsible for acute otitis media, meningitis, bacteraemia and bacteriuria, respectively, were obtained from a patient with a history of chronic alcoholism and diabetes mellitus, and infected with HIV. The isolates were characterized by phenotypic and genomic methods. The four genetically identical ST66-K2 isolates presented a full antimicrobial susceptibility profile, including to ampicillin, corresponding to a single strain (SB5881), which was more closely related to AJ210 (135 SNPs) than to Kp52.145 (388 SNPs). Colibactin and yersiniabactin gene clusters were present on the integrative and conjugative element ICEKp10 in the chromosome. The two plasmids from Kp52.145 were detected in SB5881. In addition to carrying genes for virulence factors RmpA, aerobactin and salmochelin, plasmid II has acquired in SB5881, the conjugation machinery gene cluster from plasmid I. We report the first case of community-acquired infection caused by a hypervirulent ST66-K2 Kp strain in Europe. This demonstrates the long-term persistence of the high-virulence and laboratory model ST66-K2 sublineage. The combination of a conjugative apparatus and major virulence genes on a single plasmid may contribute to the co-occurrence of hypervirulence and multidrug resistance in single Kp strains.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

et al. 2020

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“…To carry out a phylogenetic analysis, we added to our two K. pneumoniae genomes, the sequences of 32 published ST152 genomes [ 6 , 30 , 31 , 32 ]. Draft genomes were annotated using Prokka (version 1.11) [ 33 ] and the pangenome analysis was done using Roary (version 3.6.0) [ 34 ] and BLASTp with an 80% identity cut-off.…”

Section: Methodsmentioning

confidence: 99%

The New Klebsiella pneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria—Genetic Characteristics by WGS

Wysocka

Zamudio

Oggioni

et al. 2020

Genes

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Klebsiella pneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). Using whole genome sequencing (WGS) data, we showed that the strains belong to the ST152 lineage with the KL149 capsular serotype, but without rmpA/magA genes, which is typical for HM+ hypervirulent Kp. These new strains carried virulence-associated genes that predispose for urinary tract infections (UTIs). Likewise, both strains carried the ecp gene encoding pilus common for extended-spectrum β-lactamase (ESBL) Escherichia coli. Although the two ST152 isolates were closely related and differed by only nine single nucleotide polymorphisms (SNPs) in their chromosomes, they had different plasmid compositions and chromosomal elements, with isolate KP28872 carrying an ESBL plasmid and an integrative conjugative element. These two isolates are an example of the high plasticity of the K. pneumoniae accessory genome. The identification of patients with ABU matched with the correct epidemiological profiling of isolates could facilitate interventions to prevent or rapidly treat K. pneumoniae infections.

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“…Antibiotic resistant bacteria pose a major challenge in clinics. Urinary tract infection (UTI) with extensively drug-resistant Klebsiella pneumonia (ERKp) is a challenging infectious complication in immunocompromised patients, such as transplant recipients, and patients with cancer and diabetes [1][2][3]. The efficacy of antibiotics in treating UTIs is decreasing.…”

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confidence: 99%

Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiella pneumoniae

Bao

Zeng

et al. 2020

Emerging Microbes & Infections

120

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Population genomics of Klebsiella pneumoniae

Cited by 680 publications

References 146 publications

Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

The New Klebsiella pneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria—Genetic Characteristics by WGS

Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiella pneumoniae

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