Clinical and Microbiological Characteristics of Community-Onset Carbapenem-Resistant Enterobacteriaceae Isolates

Abstract

Objective: The aim of this study was to investigate the clinical and microbiological features of community-onset CRE (CO-CRE) obtained from outpatients at a tertiary hospital in China.

Patients and methods: We isolated 64 CRE strains from outpatients and divided them into three groups: 36 hospital-acquired CRE (HA-CRE), 28 CO-CRE including 15 community-acquired CRE (CA-CRE) and 13 healthcare-associated CRE (HCA-CRE). Clinical information was collected. The antibiotic susceptibilities of the 28 CO-CRE strains were tested. Whole-genome sequencing (WGS) was conducted, and then drug resistance gene analysis was performed. CgMLST and SNP comparisons were used to analyze the genomic relationship with E. coli and K. pneumoniae strains, respectively.

Results: In this study, the 28 CO-CRE isolates included K. pneumoniae (53.6%), E. coli (28.6%), E. cloacae (7.1%), C. freundii (7.1%) and E. asburiae (3.6%). The CO-CRE isolates were mainly isolated from urine samples (75%). The ceftazidime/avibactam resistance rate of community-onset E. coli was significantly higher than that of community-onset K. pneumoniae, while the aztreonam, ciprofloxacin, levofloxacin, and chloramphenicol resistance rates were significantly lower (P<0.05). Thirteen of the 15 K. pneumoniae strains belonged to ST11 containing bla_KPC-2. Correspondingly, 8 E. coli strains belonged to 7 STs, and they all were NDM producers. K. pneumoniae belonged to two major clusters, while E. coli was sporadic. The number of SNPs separating ST11 K. pneumoniae isolates ranged from 7 to 2154.

Conclusion: Community-onset CRE is not rare, and the dissemination of E. coli was sporadic while K. pneumoniae was clonal spread with similar STs as HA-CRE. Active surveillance of CRE in the community setting is in demand.

Keywords: E. coli; K. pneumoniae; MLST; cgMLST; community-acquired CRE; healthcare-associated CRE.

Figure 1

The study design flow chart.

Figure 2

(A) Antibiotic-resistance rate comparisons of 9 community-acquired K. pneumoniae (CA-KP) and 6 healthcare-associated K. pneumoniae (HCA-KP) isolates to 20 common agents, with no significant difference (P>0.05). The red dotted line provides a reference with a rate of 50%. (B) Antibiotic-resistance rate comparisons of 5 community-acquired E. coli (CA-EC) and 6 healthcare-associated E. coli (HCA-EC) isolates to 20 common agents, with no significant difference (P>0.05). The red dotted line provides a reference with a rate of 50%. (C) Nonsusceptible rate comparisons of 15 community-onset K. pneumoniae (CO-KP) and 8 community-onset E. coli (CO-EC) isolates to 20 common agents. The significant P-value is marked above the bar chart (P<0.05). The red dotted line provides a reference with a rate of 50%.

Figure 3

(A) Minimum spanning tree of core genome sequences of K. pneumoniae collected from 2015~2018 (n = 25, 15CO-KP and 10HA-KP). The cluster distance threshold is 15 alleles. Each circle (node) represents one or multiple identical sequences. The number between the nodes illustrates the number of target genes with different alleles. The text in each circle indicates the case identifier. The sequence types were labeled above the circles. (B) Minimum spanning tree of core genome sequences of E. coli collected from 2015~2018 (n =11, 8 CO-EC and 3 HA-EC). The cluster distance threshold is 10 alleles. Each circle (node) represents one or multiple identical sequences. The number between the nodes illustrates the number of target genes with different alleles. The text in each circle indicates the case identifier.

Figure 4

The number of single-nucleotide polymorphisms (SNPs) between each ST11 K. pneumoniae strain heatmap. The deeper the color is, the larger the SNP quantity scale. # indicates core genome SNP differences ≤10.