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. 2019 Mar 25:8:55.
doi: 10.1186/s13756-019-0508-4. eCollection 2019.

Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia

Muhammad Farman #  1   2 , Muhammad Yasir #  1   3 , Rashad R Al-Hindi  2 , Suha A Farraj  1 , Asif A Jiman-Fatani  4   5 , Maha Alawi  4   6 , Esam I Azhar  1   3
Affiliations

Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia

Muhammad Farman et al. Antimicrob Resist Infect Control. .

Abstract

Background: Enterococcus faecalis is a ubiquitous member of the gut microbiota and has emerged as a life- threatening multidrug-resistant (MDR) nosocomial pathogen. The aim of this study was to survey the prevalence of multidrug-resistant and epidemiologically important strains of E. faecalis in the western region of Saudi Arabia using phenotypic and whole genome sequencing approaches.

Methods: In total, 155 patients positive for E. faecalis infection were included in this study. The isolates were identified by MALDI-TOF, and screen for antimicrobial resistance using VITEK-2 system. Genome sequencing was performed with paired-end strategy using MiSeq platform.

Results: Seventeen sequence types (STs) were identified through multilocus sequence typing (MLST) analysis of the E. faecalis genomes, including two novels STs (ST862 and ST863). The most common STs in the Saudi patients were ST179 and ST16 from clonal complex 16 (CC16). Around 96% (n = 149) isolates were MDR. The antibiotics quinupristin/dalfopristin, clindamycin, and erythromycin demonstrated almost no coverage, and high-level streptomycin, gentamycin, and ciprofloxacin demonstrated suboptimal coverage. Low resistance was observed against vancomycin, linezolid, and ampicillin. Moreover, 34 antimicrobial resistance genes and variants, and three families of insertion sequences were found in the E. faecalis genomes, which likely contributed to the observed antimicrobial resistance. Twenty-two virulence factors, which were mainly associated with biofilm formation, endocarditis, cell adherence, and colonization, were detected in the isolates.

Conclusions: Diverse STs of E. faecalis, including strains associated with common nosocomial infections are circulating in the healthcare facility of Saudi Arabia and carried multi-drug resistance, which has important implications for infection control.

Keywords: Antimicrobial resistance genes; Enterococcus faecalis; Multidrug-resistance; Multilocus sequence typing; Saudi Arabia.

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Conflict of interest statement

This study was approved by the ethical research committee of the Faculty of Medicine at King Abdulaziz University (HA-02-J-008), under the reference number (235–15) and performed according to the approved guidelines. Formal consent was therefore not required.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Antimicrobial resistance and susceptibility profile of the tested antibiotics against E. faecalis isolates. The x-axis values are expressed in percentage
Fig. 2
Fig. 2
Phylogenetic linkage among E. faecalis isolates based on SNPs in core genomes. Colored branches indicate the three dominant lineages and the outer colored ring indicates the nationality
Fig. 3
Fig. 3
Global distribution of E. faecalis STs identified in Saudi Arabia. New STs are presented in red color, whereas other STs were found in different countries
Fig. 4
Fig. 4
UPGMA dendrogram from the pattern of pairwise differences in alleles that revealed the genetic relationships of STs among the E. faecalis isolates, along with the country (Ctry), infection (Inf), specimen source, and antibiotic resistance (AR) information. HA, hospital-acquired; CA, community-acquired; UC, urine-catheter; UM, urine-midstream; Bl, blood; WS, wound swab; TAS, tracheal aspirate; TS, tissue swab; PF, peritoneal fluid
Fig. 5
Fig. 5
Antimicrobial resistance genes patterns identified from genome sequencing of 44 E. faecalis isolates. Total 34 resistance genes and variants were found in the analyzed genomes
See this image and copyright information in PMC

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