Heteroresistance to Amikacin in Carbapenem-Resistant Klebsiella pneumoniae Strains

Heteroresistance can lead to treatment failure and is difficult to detect by the methods currently employed by clinical laboratories. The aim of this study was to investigate the prevalence of the amikacin-heteroresistant Klebsiella pneumoniae strains and explore potential amikacin heteroresistance mechanism through whole-genome sequencing (WGS) and quantitative reverse-transcription PCR (qRT-PCR). In this study, 13 isolates (8.39%) were considered as amikacin-heteroresistant K. pneumoniae strains among a total of 155 K. pneumoniae strains. The majority of the heterogeneous phenotypes (11/13, 84.61%) was unstable and the minimal inhibitory concentrations (MICs) fully or partially reverted back to the level of susceptibility of the parental isolate. The frequency of heteroresistant subpopulation ranged from 2.94×10−7 to 5.59×10−6. Whole-genome sequencing and single-nucleotide variants (SNVs) analysis showed that there were different nucleotide and resultant amino acid alterations among an amikacin-heteroresistant strain S38 and the resistant subpopulation S38L in several genes. Quantitative reverse-transcription PCR analysis revealed that the increased expression of aminoglycoside resistance genes detected in amikacin-heteroresistant K. pneumoniae strains might be associated with amikacin heteroresistance. The findings raise concerns for the emergence of amikacin-heteroresistant K. pneumoniae strains and the use of amikacin as therapy for the treatment of multidrug-resistant K. pneumoniae strains.

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Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern

Microbiology Spectrum ◽

10.1128/spectrum.00816-21 ◽

2021 ◽

Author(s):

Carmen Losada ◽

Carla Rico-Luna ◽

Álvaro Otero-Sobrino ◽

Andrea Molero-Salinas ◽

Sergio Buenestado-Serrano ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Reverse Transcription ◽

Whole Genome ◽

Rt Pcr ◽

Reverse Transcription Pcr

Reverse transcription-PCRs (RT-PCRs) targeting SARS-CoV-2 variant of concern (VOC) mutations have been developed to simplify their tracking. We evaluated an assay targeting E484K/N501Y to identify B.1.351/P1. Whole-genome sequencing (WGS) confirmed only 72 (59.02%) of 122 consecutive RT-PCR P.1/B.1.351 candidates. Prescreening RT-PCRs must target a wider set of mutations, updated from WGS data from emerging variants.

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Whole-genome sequencing supports the delineation of the multidrug-resistant CG14 and CG15 Klebsiella pneumoniae clones

10.26226/morressier.56d5ba2cd462b80296c9697a ◽

2016 ◽

Author(s):

Angela Novais

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome

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Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2018.06.016 ◽

2018 ◽

Vol 284 ◽

pp. 31-39 ◽

Cited By ~ 9

Author(s):

Laurenda Carter ◽

Hannah R. Chase ◽

Charles M. Gieseker ◽

Nicholas R. Hasbrouck ◽

Cynthia B. Stine ◽

...

Keyword(s):

Sequence Analysis ◽

Bacillus Cereus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Pcr Analysis ◽

Toxin Gene ◽

Whole Genome ◽

Dried Foods

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Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae

Scientific Reports ◽

10.1038/srep20840 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 55

Author(s):

Kai Zhou ◽

Mariette Lokate ◽

Ruud H. Deurenberg ◽

Marga Tepper ◽

Jan P. Arends ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Extended Spectrum

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Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae

Journal of Infection ◽

10.1016/j.jinf.2018.11.003 ◽

2019 ◽

Vol 78 (3) ◽

pp. 187-199 ◽

Cited By ~ 4

Author(s):

Melanie D. Spencer ◽

Kathryn Winglee ◽

Catherine Passaretti ◽

Ashlee M. Earl ◽

Abigail L. Manson ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Carbapenem Resistant

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Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

Clinical Microbiology and Infection ◽

10.1016/j.cmi.2015.07.001 ◽

2015 ◽

Vol 21 (11) ◽

pp. 1001-1007 ◽

Cited By ~ 27

Author(s):

Y. Jiang ◽

Z. Wei ◽

Y. Wang ◽

X. Hua ◽

Y. Feng ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Hospital Outbreak

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

10.1101/316976 ◽

2018 ◽

Cited By ~ 4

Author(s):

Maxime Garcia ◽

Szilveszter Juhos ◽

Malin Larsson ◽

Pall I. Olason ◽

Marcel Martin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Open Source ◽

Genome Sequencing ◽

Development Project ◽

Whole Genome ◽

Sequencing Analysis ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Insertion And Deletion ◽

Sample Heterogeneity

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

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