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Epidemiology and Surveillance

Genomic Study of blaIMI-Positive Enterobacter cloacae Complex in Singapore over a Five-Year Study Period

Sophie Octavia, Tse Hsien Koh, Oon Tek Ng, Kalisvar Marimuthu, Indumathi Venkatachalam, Raymond T. P. Lin, Jeanette W. P. Teo
Sophie Octavia
aNational Public Health Laboratory, National Center for Infectious Diseases, Singapore
cNational Centre for Infectious Diseases, Singapore
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Tse Hsien Koh
bSingapore General Hospital, Department of Microbiology, Singapore
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Oon Tek Ng
cNational Centre for Infectious Diseases, Singapore
dTan Tock Seng Hospital, Department of Infectious Diseases, Singapore
eNanyang Technological University, Lee Kong Chian School of Medicine, Singapore
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Kalisvar Marimuthu
cNational Centre for Infectious Diseases, Singapore
eNanyang Technological University, Lee Kong Chian School of Medicine, Singapore
fNational University of Singapore, Yong Loo Lin School of Medicine, Singapore
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Indumathi Venkatachalam
gSingapore General Hospital, Department of Infectious Diseases, Singapore
iSingapore General Hospital, Department of Infection Prevention & Epidemiology, Singapore
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Raymond T. P. Lin
aNational Public Health Laboratory, National Center for Infectious Diseases, Singapore
cNational Centre for Infectious Diseases, Singapore
hNational University Hospital, Department of Laboratory Medicine, Singapore
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Jeanette W. P. Teo
hNational University Hospital, Department of Laboratory Medicine, Singapore
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  • ORCID record for Jeanette W. P. Teo
DOI: 10.1128/AAC.00510-20
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ABSTRACT

The blaIMI gene is rarely detected outside the Enterobacter genus. Genomic characterization of 87 blaIMI-positive Enterobacter cloacae complex members revealed that the largest phylogenomic clade was made up of E. cloacae subsp. cloacae (71.3%), followed by the newly described species E. bugandensis (13.8%), E. sichuanensis (10.3%), and E. roggenkampii (4.6%). IMI-1 was the predominant carbapenemase variant (86/87, 98.9%). All the blaIMI genes were associated with chromosomally integrated Xer-dependent integrative mobile elements (IMEXs), with two new variants detected.

INTRODUCTION

The imipenemases (IMI) are a relatively uncommon group of Ambler class A carbapenemases (1). Although typically associated with the Enterobacter cloacae complex (ECC), IMI-type genes have on rare occasion been found outside the Enterobacter spp. For example, plasmid-mediated IMI-2 has been found in Escherichia coli (2) and in Klebsiella variicola (3). blaIMI can be both chromosomally and plasmid encoded. IMI-1, IMI-4 (4), IMI-7 (4), and IMI-9 (5) variants are chromosomally located, whereas IMI-2 (6), IMI-3 (7), IMI-5, and IMI-6 (8) are plasmid encoded.

Xer recombinase-dependent integrative mobile elements (IMEXs) are presumably responsible for the mobility of blaIMI-type in the Enterobacter (8). It is hypothesized that the EcloIMEX elements exit the chromosome through recombination mediated by the XerD/C recombinases (9). This form of site-specific and Xer recombination-dependent mechanism of mobility appears to limit the diffusion of this group of carbapenemases, in comparison to other types of more “freely” mobile genetic elements such as transposons and genetic islands. However, some blaIMI types may be acquired by IncFII plasmids and associated with insertion sequences (2, 3).

A local study had previously investigated the genomic features of 16 blaIMI-positive Enterobacter isolates obtained from a single hospital (4). Here, we undertook the effort to describe the population structure, antimicrobial resistance genes, and genetic context of blaIMI-positive isolates from a larger collection (n = 87) which had been collected via a national surveillance program for non-carbapenem- susceptible Enterobacteriales. The genomic data from the initial 16 isolates were also incorporated into this study. A total of 87 nonduplicate blaIMI-positive isolates were collected over 2011 to 2015. These isolates came from a retrospective collection of phenotypically carbapenem-resistant Enterobacteriaceae deposited at the reference National Public Health Laboratory, Singapore (see the Material and Methods in the supplemental materials). PCR screening was used to determine the carbapenemase genotype. Of the 87 blaIMI-positive isolates, 5 were clinical isolates and 82 were from screening rectal swabs (see the Material and Methods in the supplemental materials). The blaIMI-positive isolates made up 3.1% (87/2815) of all carbapenemase genotypes screened at the reference laboratory for the duration of the study period. Illumina MiSeq sequencing (Illumina Inc., San Diego, CA, USA) was used to generate 300-bp paired-end reads which were then assembled. An average sequencing depth of 60× was achieved for the genomes. Raw reads for all isolates have been deposited in NCBI under the BioProject ID PRJNA632459. Detailed microbiological methods and genomics analysis are presented in the supplemental materials.

ECC is polyphyletic, with current literature indicating that Enterobacter spp. genomic structure is diverse (10). For example, in a comparative genomics study investigating 97 clinical carbapenemase-producing Enterobacter spp. (none encoding blaIMI), 18 phylogenomic groups were deduced (11). A similarly varied population structure was reflected in Boyd’s study (8), where 9 blaIMI-bearing genomes generated four different phylogenomic groups. In contrast, our population structure for Enterobacter bearing blaIMI appears to be rather restricted, with 87 genomes classified into only 4 clades (Fig. 1). Our largest clade was made up of E. cloacae subsp. cloacae (62/87, 71.3%), followed by E. bugandensis (12/87, 13.8%), E. sichuanensis (9/87, 10.3%), and E. roggenkampii (4/87, 4.6%) (Fig. 1). The average nucleotide identity (ANI) values for within-clade isolates was >98%, and <91% ANI compared to other nonclade genomes, hence lending support for the phylogenetic clustering.

FIG 1
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FIG 1

Core SNP phylogenetic tree of 87 blaIMI-type Enterobacter spp. The metadata includes specimen source, sequence types (ST), and the presence of resistance genes. Genomes with black branch labels belong to E. cloacae, orange branch labels to E. roggenkampii, green branch labels represent E. sichuanensis, and red branch labels belong to E. bugandensis. The presence of resistance determinants is represented by blue squares. The bootstrap values are indicated on the nodes. NCBI genome accession numbers are provided in brackets after the species name. The tree was illustrated using iTOL v4 (https://itol.embl.de/). Scale bars represent nucleotide substitutions per site. The symbol * indicates the sequence type was assigned based on the next closest sequence type.

The ECC bacteria are diverse and associated with a wide range of serious nosocomial infections, such as pneumonia, urinary tract infections, and septicemia, and the emergence of carbapenem resistance in the ECC severely limits the treatment options. E. bugandensis is a recently described species associated with neonatal sepsis (12). It is considered to be an emerging pathogen with a multidrug resistant (MDR) phenotype (13). Contemporary genomic investigations have reclassified E. roggenkampii as a distinct novel species rather than a subspecies of E. hormaechei (14). E. sichuanensis is a newly described species first recovered from a urine specimen in Sichuan, China (15). Carbapenemase carriage has been reported in E. bugandensis (blaNDM-5 and blaIMI-1) (16, 17) and E. roggenkampii (blaNDM-1) (18), as well as in E. sichuanensis (blaKPC) (11). Interestingly, our E. sichuanensis isolates clustered with a locally collected environmental air sample, E. sichuanensis SGAir0282 (Fig. 1), which was a noncarbapenemase producer. Single-nucleotide polymorphism (SNP) analysis of IMI-bearing E. sichuanensis revealed nucleotide differences of more than 40,000 compared to E. sichuanensis SGAir0282, suggesting that the study isolates were not clonally related to the environmental sample.

IMI-1 was the predominant carbapenemase variant (86/87, 98.9%) with only one other isolate carrying IMI-4. No other carbapenemases or plasmid-mediated mcr colistin resistance were found. Also detected was blaCMH-3-like, a recently described AmpC type β-lactamase of the E. cloacae complex that is closely related to blaMIR and blaACT (19). The presence of chromosomally mediated AmpC β-lactamase was detected in all the genomes. Acquired aminoglycoside (aadA2, aph(3′)-Ia, strA, and strB) and quinolone (qnrS) resistance determinants were also sporadically detected (Fig. 1). The quinolone-resistance determining regions (QRDR) of gyrA, gyrB, and parC did not reveal the presence of substitutions commonly associated with quinolone resistance, such as Ser83 in GyrA, Ser463 in GyrB, and Ser80 in ParC (20) (Table S2 in the supplemental material).

Epidemic high-risk carbapenem-resistant Enterobacter lineages belonging to clonal complexes (CC) CC74 (including sequence type [ST] 78), CC114 (including ST66), and CC171 (10, 11) were not observed in our study. Overall, the sequence types for E. cloacae subsp. cloacae were diverse, with 24 different STs (Fig. 1). The majority (22/25, 88%) of the non-E. cloacae subsp. cloacae, i.e., E. bugandensis, E. sichuanensis, and E. roggenkampii had previously unassigned STs (Fig. 1) (Table S2), which was not unexpected as these were newly described species. We noted a cluster of 11 clonal E. bugandensis sequence types possessing the same MLST, with <18 single nucleotide polymorphisms (SNPs). By comparison, ∼52,000 SNPs were observed between this cluster and the E. bugandensis reference genomes (Fig. 1). The 11 isolates originated from different patients, which hinted at the possibility of hospital spread. However, based on deeper epidemiological investigation, we were not able to attribute association at ward, procedure, or department level.

The initial description of an Enterobacter Xer-dependent integrative mobile element, EludIMEX-1, was from E. ludwigii (9), which harbored NMC (a close variant of IMI). The EludIMEX-1 was later redesignated EcloIMEX-1 as more IMEX elements from E. cloacae complex were characterized (8) (Fig. 2). Currently there are eight different EcoIMEX elements with relatively heterogenous organization between them (4) (Fig. 2). Diverse EcloIMEX variants types were detected in our study, namely, EcloIMEX-2, -3, -7, and -8, as well as two new variants which we designated EcloIMEX-9 and -10 (Fig. 2). The distribution of EcloIMEX variants showed that EcloIMEX-8 was the most predominant type (32/87, 36.8%) (Fig. 1). There appeared to be no association between the Enterobacter species and the type of EcloIMEX variant (Fig. 1).

FIG 2
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FIG 2

Comparison of blanmcA (EcloIMEX-1) and blaIMI-harboring genetic elements from reference types (EcloIMEX-2 to -8) and sequenced isolates (n = 87). Short vertical pink bars represent XerC/XerD recombination sites. The red arrows represent blaIMI and its repressor. White arrows represent genes that encode metabolic functions. Hypothetical proteins are indicated by light grey arrows. Easyfig (https://mjsull.github.io/Easyfig/) was used to produce the linear BLAST comparisons for the blaIMI genetic structures.

In all the isolates, the EcloIMEX was chromosomally integrated at the same position, i.e., the intergenic region between the sugar efflux transporter B, setB, and an elongation factor P-like protein, yeiP (Fig. 2). This feature was also observed in previous work (4, 8). The sequences flanking blaIMI-1, spanning setB to the recombinase gene, are typically homologous/conserved regions of ∼18 kb exhibiting 90% to 99% sequence identity (8) (Fig. 2). Genes in this region include a protease, ABC transporter, methyl viologen resistance protein SmvA (major facilitator superfamily efflux pump), and a glycosyltransferase. The same gene conservation was also observed in the new variants EcloIMEX-9 and -10 (Fig. 2). The exceptions are EcloIMEX-7 (4) and EcloIMEX-8 (21), which have lost the recombinase gene.

The structure of EcloIMEX-8 (GenBank accession no. MG547711) is very close to that of EcloIMEX-7 (GenBank accession no. KY680208.1), with 99% nucleotide sequence homology. E. cloacae complex isolates bearing blaIMI in EcloIMEX-8 elements were responsible for a clonal outbreak in the French overseas department of Mayotte (21). It was interesting to note that EcloIMEX-7 was the first instance of an EcloIMEX isolated from a nonclinical E. cloacae complex obtained from farmed shrimp (22). Unfortunately, the occurrence of carbapenemase-producing microorganisms in food-producing animals is not unusual (23).

In this study, we did not detect epidemic high-risk carbapenem-resistant Enterobacter lineages. Instead, diverse STs of IMI-producing ECC were observed in our collection of isolates. Additionally, non-E. cloacae subsp. cloacae have been isolated from screening rectal swabs with a possible hospital cluster due to E. bugandensis, suggesting the widespread dissemination of IMI across ECC. IMI-1 remained the most predominant variant. The blaIMI genetic regions were not plasmid borne but were carried on different Enterobacter Xer-dependent integrative mobile elements, including the two newly designated variants. Our findings provide further insights into the diversity of IMI-producing ECC in nosocomial settings.

ACKNOWLEDGMENTS

Grant support was provided by the NMRC Clinician-Scientist Individual Research Grant (NMRC/CIRG/1463/2016), Singapore Ministry of Education Academic Research Fund Tier 2 grant: New Delhi Metallo-Beta-Lactamase: A global multicenter, whole-genome study (MOE2015-T2-2-096), NMRC Collaborative Grant: Collaborative Solutions Targeting Antimicrobial Resistance Threats in Health Systems (CoSTAR-HS) (NMRC CGAug16C005), and NMRC Clinician Scientist Award (NMRC/CSA-INV/0002/2016). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

We have no conflicts of interest to declare.

FOOTNOTES

    • Received 17 March 2020.
    • Returned for modification 21 April 2020.
    • Accepted 23 May 2020.
    • Accepted manuscript posted online 1 June 2020.
  • Supplemental material is available online only.

  • Copyright © 2020 American Society for Microbiology.

All Rights Reserved.

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Genomic Study of blaIMI-Positive Enterobacter cloacae Complex in Singapore over a Five-Year Study Period
Sophie Octavia, Tse Hsien Koh, Oon Tek Ng, Kalisvar Marimuthu, Indumathi Venkatachalam, Raymond T. P. Lin, Jeanette W. P. Teo
Antimicrobial Agents and Chemotherapy Jul 2020, 64 (8) e00510-20; DOI: 10.1128/AAC.00510-20

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Genomic Study of blaIMI-Positive Enterobacter cloacae Complex in Singapore over a Five-Year Study Period
Sophie Octavia, Tse Hsien Koh, Oon Tek Ng, Kalisvar Marimuthu, Indumathi Venkatachalam, Raymond T. P. Lin, Jeanette W. P. Teo
Antimicrobial Agents and Chemotherapy Jul 2020, 64 (8) e00510-20; DOI: 10.1128/AAC.00510-20
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KEYWORDS

Enterobacter
Enterobacteriaceae
antimicrobial resistance
carbapenemase
imipenemase
phylogenomics
whole genome

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