The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample

Abstract

Plasmid transfer is one important mechanism how antimicrobial resistance can spread between different species, contributing to the rise of multidrug resistant bacteria (MDRB) worldwide. Here were present whole genome sequencing (WGS) data of two MDRB isolates, an Escherichia coli and a Klebsiella quasipneumoniae, which were isolated from a single patient. Detailed analysis of long-read sequencing data identified an identical F2:A-:B- lncFII plasmid containing blaCTX-M-27 in both isolates, suggesting horizontal plasmid exchange between the two species. As the plasmid of the E. coli strain carried multiple copies of the resistance cassette, the genomic data correlated with the increased antimicrobial resistance (AMR) detected for this isolate. Our case report demonstrates how long-read sequencing data of MDRB can be used to investigate the role of plasmid mediate resistance in the healthcare setting and explain resistance phenotypes.

Plasmid-encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates

“…Our data indicate that tandem duplication of the same transposon is also a quite common transposition event as observed in three out of four cases, i.e., in pairs I, III, and IV. In accordance with this observation, a few cases of IS 26 -mediated ESBL gene duplications were described before ( Garza-Ramos et al., 2009 ; Tamamura-Andoh et al., 2021 ; van Almsick et al., 2022 ), and also the association of IS 26 and bla CTX-M genes was already described in Enterobacteriaceae in a systematic study ( Shropshire et al., 2022 ). Interestingly, neither documented IS 26 transposon with ESBL genes nor a high sequence similarity could be found in the databases of TnCentral ( Ross et al., 2021 ) or Transposon Registry ( Tansirichaiya et al., 2019 ) yet.…”

“…In addition, we hypothesize that the increased resistance level to ceftazidime correlates with the number of ESBL gene copies encoded on the plasmid. Only very few reported cases of ESBL gene duplications found this correlation between genotypic and phenotypic resistance so far ( Tamamura-Andoh et al., 2021 ; van Almsick et al., 2022 ). However, in accordance, this observation has been described before for other AMR genes ( Coppi et al., 2020 ; Han et al., 2021 ).…”

TEM,CTX-M,SHV Genes in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a County Clinical Emergency Hospital Romania-Predominance of CTX-M-15

“…The penicillin and cephalosporin resistance patterns observed in our strains can be explained by the excessive use of ceftriaxone and cefotaxime in the empirical therapy in hospitals, and hospitalization itself has been identified as a risk factor for infection with ESBL-producing Enterobacteriaceae as plasmids carrying genes that encode ESBLs can be easily transmitted horizontally between different bacteria in the hospital environment [45][46][47].…”

Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon

“…Only ESBL-E were subjected to whole-genome sequencing (WGS) as described recently ( 21 ). Subsequently, we performed multilocus sequence typing (MLST) and core genome MLST (cgMLST) if a species-specific scheme was available at https://www.cgmlst.org ( 22 ).…”