Analysis of transmission-related third-generation cephalosporin-resistant Enterobacterales by electronic data mining and core genome multi-locus sequence typing

Weber, A.; Neffe, L.; Diaz, L.A.P.; Thoma, N.; Aghdassi, S.J.S.; Denkel, L.A.; Maechler, F.; Behnke, M.; Häussler, S.; Gastmeier, P.; Kola, A.

doi:10.1016/j.jhin.2023.07.020

Cited by 2 publications

(2 citation statements)

References 27 publications

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“…Given the known capacity of 3GC-R K. pneumoniae to be transmitted in healthcare settings [2, 47], we used PopPUNK to identify nested populations of 3GC-R K. pneumoniae and subsequently performed PopPUNK cluster specific, core-genome-alignment inferred phylogenies masked for recombination to potentially identify transmission networks. We were able to identify 56 PopPUNK groups of which 14 included two or more isolates (i.e.…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

Selvaraj Anand,

Wu,

Bremer

et al. 2024

Microbial Genomics

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Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected ‘Texas-specific’ clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.

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Section: Resultsmentioning

confidence: 99%

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

Selvaraj Anand,

Wu,

Bremer

et al. 2024

Microbial Genomics

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“…Given the known capacity of 3GC-R Kp to be transmitted in healthcare settings [2, 46], we used PopPUNK to identify nested populations of 3GC-R Kp and subsequently performed PopPUNK cluster specific, core genome alignment inferred phylogenies masked for recombination to potentially identify transmission networks. We were able to identify 56 PopPUNK groups of which 14 included two or more isolates ( i.e.…”

Section: Resultsmentioning

confidence: 99%

Identification of A Novel CG307 Sub-clade in Third Generation Cephalosporin ResistantKlebsiella pneumoniaeCausing Invasive Infections in the United States

Anand,

Wu,

Bremer

et al. 2023

Preprint

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Despite the notable clinical impact, recent molecular epidemiology regarding third-generation cephalosporin-resistantKlebsiella pneumoniae(3GC-RKp) in the United States remains limited. We performed whole genome sequencing of 3GC-RKpbacteremia isolates collected from March 2016 to May 2022 at a tertiary care cancer center in Houston, TX using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics, and pan-genomic signatures of our 3GC-RKppopulation. Of the 194 3GC-RKpbacteremias that occurred during our study timeframe, we were able to analyze 153 (79%) bacteremia isolates, 126 initial and 27 recurrent isolates respectively. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant clonal group, CG307, accounted for 37 (29%) index isolates and displayed a significant correlation (Pearson correlation testP-value = 0.03) with the annual frequency of 3GC-RKpbacteremia. Within our CG307 cohort, 89% (33/37) of our isolates belong to the global rather than previously described Texas-specific clade. Strikingly, we identified a new CG307 sub-clade (i.e.,cluster 1 isolates) comprised of 18 isolates characterized by the chromosomally-encodedblaSHV-205and unique accessory genome content. This CG307 sub-clade was detected in various United States regions, with genome sequences from 24 additional strains becoming recently available in the NCBI SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-RKpbacteremia among cancer patients seen in Houston, TX and has recently been isolated throughout the United States.DATA SUMMARYWGS data sequenced during this study period was submitted to NCBI and can be accessed within BioProject PRJNA648389. WGS data from previous study of carbapenem non-susceptibleEnterobacteralescan be accessed from BioProject PRJNA836696. Assembly information and BioAccession numbers are provided in Table S1.IMPACT STATEMENTInfections due to 3rdgeneration cephalosporin resistantKlebsiella pneumoniae(3GC-RKp) are considered among the most urgent public health threats. However, molecular epidemiology studies on 3GC-RKpin the United States are limited. Our analysis indicates a preponderance of genetically diverse 3GC-RKpisolates harboring the key antimicrobial resistance determinantblaCTX-M-15at our institution. Importantly, however, we detected evidence of long duration transmission of highly genetically related CG307 and CG29 specific clusters at our institution. Interestingly, we rarely detected the pandemic CG258 lineage in our cohort and did not detect more than two genetically related CG258 isolates from this lineage. We found that 90% of our isolates from the most prevalent clonal group, CG307, belonged to a novel, nested-population of a “global” CG307 clade in contrast to the more commonly detected “Texas-specific” clade that has circulated in our region. We searched the NCBI SRA database using genomic markers of the novel CG307 clade and found evidence of this clade causing recent invasive infections in other locations across the United States. Our study highlights the shifting population dynamics ofK. pneumoniaecausing invasive infections and the necessity to continue AMR surveillance in order to identify emerging high-risk populations.

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Analysis of transmission-related third-generation cephalosporin-resistant Enterobacterales by electronic data mining and core genome multi-locus sequence typing

Cited by 2 publications

References 27 publications

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

Identification of A Novel CG307 Sub-clade in Third Generation Cephalosporin ResistantKlebsiella pneumoniaeCausing Invasive Infections in the United States

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