Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital

Perdigão, João; Modesto, Ana; Pereira, António; Neto, Oliveiro Caetano de Freitas; Matos, Vítor; Godinho, A.; Phelan, Jody; Charleston, James; Spadar, Anton; Sessions, Paola Flórez de; Hibberd, Martin L.; Campino, Susana; Costa, Ana Roberta Fusco da; Fernandes, Fernando Montezano; Ferreira, F.A.; Correia, Alan Blendo Bonfim; Gonçalves, Luísa; Clark, Taane G.; Duarte, Aida

doi:10.1099/mgen.0.000349

Cited by 18 publications

(32 citation statements)

References 51 publications

(76 reference statements)

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“…In contrast to previous studies [ 9 , 10 , 12 ], ST147-K64 K. pneumoniae is still the predominant clone in different healthcare settings in our area. Its identification in patients that are colonized or infected in multiple occasions throughout time, and its dispersion in other community-based healthcare-associated settings suggests possible reintroductions of this highly transmissible clone in the hospital.…”

Section: Discussioncontrasting

confidence: 99%

“…To our knowledge, this is the first study providing a comprehensive analysis of the molecular epidemiology of CPE in a single institution in our country in two different time-points of CPE spread, towards a comprehension of factors driving their extraordinary increase. The multiplicity of carbapenemase-producing clones and Enterobacterales species, together with data from previous studies in Portugal [ 7 , 9 , 10 , 12 ], highlights successful horizontal transfer of carbapenemases that might occur during gastrointestinal colonization, which represents an additional challenge for infection control.…”

Section: Discussionmentioning

confidence: 92%

“…The ST147 K. pneumoniae clone exhibiting K-type K64 has been one of the first responsible for KPC-3 spread in diverse healthcare settings in the north of Portugal [ 6 , 7 ]. It was responsible for the first large outbreak of CPE in a reference hospital from the north of Portugal in 2015 [ 8 ] and it has been described in other regions [ 9 , 10 ]. Analysis of recent CPE collections is still scarce and there is limited analysis on risk factors and the effect of infection control policies in a single institution.…”

Section: Introductionmentioning

confidence: 99%

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Multiplicity of Carbapenemase-Producers Three Years after a KPC-3-Producing K. pneumoniae ST147-K64 Hospital Outbreak

et al. 2020

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Carbapenem resistance rates increased exponentially between 2014 and 2017 in Portugal (~80%), especially in Klebsiella pneumoniae. We characterized the population of carbapanemase-producing Enterobacterales (CPE) infecting or colonizing hospitalized patients (2017–2018) in a central hospital from northern Portugal, where KPC-3-producing K. pneumoniae capsular type K64 has caused an initial outbreak. We gathered phenotypic (susceptibility data), molecular (population structure, carbapenemase, capsular type) and biochemical (FT-IR) data, together with patients’ clinical and epidemiological information. A high diversity of Enterobacterales species, clones (including E. coli ST131) and carbapenemases (mainly KPC-3 but also OXA-48 and VIM) was identified three years after the onset of carbapenemases spread in the hospital studied. ST147-K64 K. pneumoniae, the initial outbreak clone, is still predominant though other high-risk clones have emerged (e.g., ST307, ST392, ST22), some of them with pandrug resistance profiles. Rectal carriage, previous hospitalization or antibiotherapy were presumptively identified as risk factors for subsequent infection. In addition, our previously described Fourier Transform infrared (FT-IR) spectroscopy method typed 94% of K. pneumoniae isolates with high accuracy (98%), and allowed to identify previously circulating clones. This work highlights an increasing diversity of CPE infecting or colonizing patients in Portugal, despite the infection control measures applied, and the need to improve the accuracy and speed of bacterial strain typing, a goal that can be met by simple and cost-effective FT-IR based typing.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Multiplicity of Carbapenemase-Producers Three Years after a KPC-3-Producing K. pneumoniae ST147-K64 Hospital Outbreak

et al. 2020

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“…Inspection of the genetic environments of bla KPC-3 , bla CTX-M-15 , and bla OXA-48 revealed twenty-five out of the 28 KPC-3 producing isolates had the same genetic environment as part of the Tn4401d isoform, which is characterized by a 68 bp deletion between istB and the bla KPC gene when compared with the Tn4401b isoform [ 27 ]. This Tn4401b isoform was identified in the remaining three isolates Kp 5148 (ST34), Kp 5162 (ST451) and Kv 5163.…”

Section: Resultsmentioning

confidence: 99%

Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

et al. 2020

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The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

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“…Most ST types in our study are not frequently cited as ESBL-KP-causing outbreaks, except for ST15 [ 14 , 15 ], which appeared only as a satellite clone, and ST-37, a frequently found carbapenem- resistant strain [ 15 ]. Similarly, ESBL-KP clones responsible for other NICU outbreaks were not previously recognized as problematic nosocomial strains [ 6 , 7 ], which suggests that they were not part of the general hospital ecosystem.…”

Section: Discussionmentioning

confidence: 97%

Investigation of Outbreaks of Extended-Spectrum Beta-Lactamase-Producing Klebsiella Pneumoniae in Three Neonatal Intensive Care Units Using Whole Genome Sequencing

et al. 2020

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Infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are on a constant rise and are a noted cause of outbreaks in neonatal intensive care units (NICUs). We used whole genome sequencing (WGS) to investigate the epidemiology of consecutive and overlapping outbreaks caused by ESBL-KP in NICUs in three hospitals in close proximity. Clonality of 43 ESBL-KP isolates from 40 patients was determined by BOX-PCR. Short-read sequencing was performed on representative isolates from each clone. The dominant clones from each NICU were sequenced using long-read sequencing. Bioinformatics methods were used to define multilocus sequence type (MLST), analyze plasmid content, resistomes, and virulence factors. In each NICU, we found a unique dominant clone (ST985, ST37, and ST35), each belonging to a distinct sequence type (ST), as well as satellite clones. A satellite strain in NICU-2 (ST35) was the dominant strain in NICU-3, where it was isolated four weeks later, suggesting transmission. NICU-1- and NICU-2-dominant strains had blaCTX-M-15 carried on a similar transposable element (Tn3-ISEcp1) but at different locations: on a plasmid and on the chromosome, respectively. We concluded that the overlapping ESBL-KP outbreaks were a combination of clonal transmission within NICUs, possible transposable element transmission between NICUs, and repeated importation of ESBL-KP from the community.

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Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital

Cited by 18 publications

References 51 publications

Multiplicity of Carbapenemase-Producers Three Years after a KPC-3-Producing K. pneumoniae ST147-K64 Hospital Outbreak

Multiplicity of Carbapenemase-Producers Three Years after a KPC-3-Producing K. pneumoniae ST147-K64 Hospital Outbreak

Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

Investigation of Outbreaks of Extended-Spectrum Beta-Lactamase-Producing Klebsiella Pneumoniae in Three Neonatal Intensive Care Units Using Whole Genome Sequencing

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