bla OXA-48 -like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

• Published in: Microbial genomics Vol. 7; no. 5
• Main Authors: Hendrickx, Antoni P A, Landman, Fabian, de Haan, Angela, Witteveen, Sandra, van Santen-Verheuvel, Marga G, Schouls, Leo M, The Dutch Cpe Surveillance Study Group
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 07-05-2021
• Subjects: Anti-Bacterial Agents; beta-Lactamases - genetics; beta-Lactamases - metabolism; Carbapenem-Resistant Enterobacteriaceae - genetics; Carbapenems; Drug Resistance, Multiple, Bacterial - genetics; Enterobacteriaceae Infections - microbiology; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Infections - microbiology; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Klebsiella Infections - microbiology; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - metabolism; Multilocus Sequence Typing; Netherlands; Plasmids - genetics; Netherlands; blaOXA-181; blaOXA-244; genomes; blaOXA-48; blaOXA-232
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.000512

Carbapenem-hydrolysing enzymes belonging to the OXA-48-like group are encoded by
-like alleles and are abundant among
in the Netherlands. Therefore, the objective here was to investigate the characteristics, gene content and diversity of the
-like carrying plasmids and chromosomes of
and
collected in the Dutch national surveillance from 2014 to 2019 in comparison with genome sequences from 29 countries. A combination of short-read genome sequencing with long-read sequencing enabled the reconstruction of 47 and 132 complete
-like plasmids for
and
, respectively. Seven distinct plasmid groups designated as pOXA-48-1 to pOXA-48-5, pOXA-181 and pOXA-232 were identified in the Netherlands which were similar to internationally reported plasmids obtained from countries from North and South America, Europe, Asia and Oceania. The seven plasmid groups varied in size, G+C content, presence of antibiotic resistance genes, replicon family and gene content. The pOXA-48-1 to pOXA-48-5 plasmids were variable, and the pOXA-181 and pOXA-232 plasmids were conserved. The pOXA-48-1, pOXA-48-2, pOXA-48-3 and pOXA-48-5 groups contained a putative conjugation system, but this was absent in the pOXA-48-4, pOXA-181 and pOXA-232 plasmid groups. pOXA-48 plasmids contained the PemI antitoxin, while the pOXA-181 and pOXA-232 plasmids did not. Furthermore, the pOXA-181 plasmids carried a
type IV secretion system, while the pOXA-48 plasmids and pOXA-232 lacked this system. A group of non-related pOXA-48 plasmids from the Netherlands contained different resistance genes, non-IncL-type replicons or no replicons. Whole genome multilocus sequence typing revealed that the
-like plasmids were found in a wide variety of genetic backgrounds in contrast to chromosomally encoded
-like alleles. Chromosomally localized
and
alleles were located on genetic elements of variable sizes and comprised regions of pOXA-48 plasmids. The
-like genetic element was flanked by a direct repeat upstream of IS1R, and was found at multiple locations in the chromosomes of
. Lastly,
isolates carrying
or
were mostly resistant for meropenem, whereas
,
and chromosomal
or
isolates were mostly sensitive. In conclusion, the overall
-like plasmid population in the Netherlands is conserved and similar to that reported for other countries, confirming global dissemination of
-like plasmids. Variations in size, presence of antibiotic resistance genes and gene content impacted pOXA-48, pOXA-181 and pOXA-232 plasmid architecture.