Caribbean multi-centre study of <i>Klebsiella pneumoniae</i>: whole genome sequencing, antimicrobial resistance and virulence factors

Heinz, Eva; Brindle, Richard; Morgan-McCalla, Andrina; Peters, Keisha; Thomson, Nicholas R.

doi:10.1101/541136

Cited by 5 publications

(6 citation statements)

References 30 publications

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“…SHV β-lactamases conferring intrinsic resistance to the penicillins were detected in 85.9% of the 9,705 nonredundant K. pneumoniae genomes (ESBL forms of SHV were detected in 10.0%). Acquired AMR was widespread (77.1% of genomes had at least one gene or mutation conferring acquired AMR detected) and 71.6% of genomes were predicted to be MDR (acquired resistance to ≥3 drug classes 50 ), a much higher rate than is reported in most geographical regions 3,[51][52][53] , reflecting the bias within public genome collections. The majority of genomes had a non-zero resistance score, reflecting the presence of ESBL and/or carbapenemase genes: 22.3%, 37.1% and 5.9% genomes had resistance scores of 1, 2 and 3 respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Kleborate has already been widely adopted by the Klebsiella research community-at least 74 studies have reported using the Kleborate software package, including larger-scale genome surveillance studies in South and Southeast Asia, the Caribbean and the United States 31,51,52 (full list in Supplementary Data 10). Kleborate is freely available as a standalone command-line tool for local high-throughput analyses or incorporation into existing bioinformatics workflows (https://github.com/katholt/Kleborate), and can be easily accessed through the online tool Pathogenwatch (https://pathogen.watch/).…”

Section: Discussionmentioning

confidence: 99%

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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

et al. 2021

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Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

et al. 2021

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“…Kleborate has already been widely adopted by the Klebsiella research community – at least 74 studies have reported using the Kleborate software package, including larger-scale genome surveillance studies in South and Southeast Asia, the Caribbean and the United States 31,49,50 (full list in Table S11 ). Kleborate is freely available as a standalone command-line tool for local high-throughput analyses or incorporation into existing bioinformatics workflows (https://github.com/katholt/Kleborate), and can be easily accessed through the online tool PathogenWatch (https://pathogen.watch/).…”

Section: Discussionmentioning

confidence: 99%

Genomic surveillance framework and global population structure forKlebsiella pneumoniae

Mmc

et al. 2020

Preprint

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K. pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.

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“…4 Heinz et al have found resistance genes circulating in the Caribbean region. 5 In a study from Jamaica by Nicholson et al, it was found that 18.2% of K. pneumoniae produced ESBLs, while there were no ESBL producing E. Coli. 6 This resistance in K. pneumoniae was also found by Christian et al in Jamaica.…”

Section: Introductionmentioning

confidence: 97%

Surveillance of Phenotypic Extended Spectrum Beta-Lactamase Resistance in Blood Isolates at a Hospital in East Trinidad

Nagassar¹

2021

Caribb Med J

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Background The Centres for Disease Control and Prevention (CDC) and World Health Organization (WHO) list extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae as serious threats and priority pathogens. This study identified phenotypic resistance patterns to these pathogens in east Trinidad, West Indies. We also aimed to set up and test a pilot surveillance system aligned to WHO’s Global Antimicrobial Surveillance System (WHO-GLASS). Methods Two key bacterial isolates, Escherichia coli and Klebsiella pneumoniae were used and one specimen, blood, was used to test a pilot surveillance system. Data for resistance patterns, for Sangre Grande Hospital (SGH), for ESBL producing E. coli and K. pneumoniae were downloaded from the Microscan Autoscan© for the period 2013 – 2016. ESBL presence in bacteria resistant to Cefotaxime (CTX), Ceftazidime (CAZ) and Ceftriaxone (CRO) were recorded. Data were stored in a Microsoft Excel© spreadsheet and inputted into IBM© SPSSv22. Data were displayed as resistance percentages for the year. No patient data were collected. Simple descriptive statistics were used. Results The number of organisms recovered from the database for the period 2013 to 2016 were:134E. coli and 59K. pneumoniae. Phenotypic resistance rates for ESBLs for 2013 to 2016 were: Ecoli: 2013: Resistance ranged from 22.2-29.6% with maximum resistance seen for CTX. 2014: Resistance ranged from 12.9- 22.2%, with maximum resistance seen for CRO. 2015: Resistance ranged from 21.4- =26.2%, with maximum resistance seen for CTX. 2016: Resistance ranged from 29.4- 32.4%, with maximum resistance seen for CRO and CTX. K pneumoniae: 2013: Resistance was 40% for all 3rd generation Cephalosporins. 2014: Resistance was 16.7% for all 3rd generation Cephalosporins. 2015: Resistance was 16.7% for all 3rd generation Cephalosporins. 2016: Resistance ranged from 52.6 – 63.2%, with maximum resistance seen for CAZ. Conclusion Phenotypic resistance rates in K. pneumoniae and E. coli were generally high. There was an overall increase in resistance from 2013 to 2016 for both K. pneumoniae and E. coli with greater resistance being seen in K. pneumoniae.

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Caribbean multi-centre study of Klebsiella pneumoniae: whole genome sequencing, antimicrobial resistance and virulence factors

Cited by 5 publications

References 30 publications

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Genomic surveillance framework and global population structure forKlebsiella pneumoniae

Surveillance of Phenotypic Extended Spectrum Beta-Lactamase Resistance in Blood Isolates at a Hospital in East Trinidad

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