Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland

Abstract

We sequenced all nonduplicate 934 VIM/IMP carbapenemase-producing Enterobacterales (CPE) reported in Poland during 2006-2019 and found ≈40% of the isolates (n = 375) were Enterobacter spp. During the study period, incidence of those bacteria gradually grew in nearly the entire country. The major factor affecting the increase was clonal spread of several E. hormaechei lineages responsible for multiregional and interregional outbreaks (≈64% of all isolates), representing mainly the pandemic sequence type (ST) 90 or the internationally rare ST89 and ST121 clones. Three main VIM-encoding integron types efficiently disseminated across the clone variants (subclones) with various molecular platforms. Those variants were predominantly Pseudomonas aeruginosa-derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. Another prevalent type, found in 34 STs, were In916-like elements, spreading in Europe recently with a lineage of IncA-like plasmids.

Keywords: E. hormaechei; Enterobacter; Enterobacterales; Poland; ST89; ST90; VIM; antimicrobial resistance; bacteria.

Figure 1

Population structure of Enterobacter spp. isolates identified in a genome-based epidemiologic analysis of VIM/IMP carbapenemase-producing Enterobacter spp., Poland, 2006–2019. The minimum-spanning tree was constructed on the basis of 7-loci multilocus sequence type data. Each circle represents 1 ST, and each fragment of a pie chart corresponds to 1 isolate. The size of a circle is proportional to the number of isolates of that ST. Connecting lines infer phylogenetic relatedness in terms of several allelic differences (thick solid line indicates a single-locus variant, thin solid line indicates a double-locus variant). ST, sequence type.

Figure 2

Geographic distribution and clonal analysis of Enterobacter hormaechei clonal complex 90 (ST90 and ST1762) in Poland, 2006–2019. A) Geographic distribution of the isolates; main administrative regions are labeled. Circles represent medical centers where the isolates were recorded. Sizes of the circles are proportional to numbers of cases of infection. B) SNP-based minimum-spanning tree of the isolates. Lengths of branches are related to numbers of SNPs between linked isolates. Numbers of SNPs are indicated above the branches or next to the dots. SNP, single nucleotide polymorphism; ST, sequence type.