Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

Abstract

Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin‐resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC ™9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain‐specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug‐resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug‐resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

“…The genes are annotated as PBP2b, PBP1b, PBP1a, and PBP2x, and have a low identity with PBP5 according to BLASTP. Despite the presence of these PBPs, however, E. durans KLDS6.0930 is sensitive to penicillin and ampicillin, a phenomenon also observed in E. hirae R17 (Peng et al, 2017). …”

“…Concerns about the use of enterococci as a double-edged sword have led to an increasing number of studies intended to evaluate the safety of certain enterococci strains (Kopit et al, 2014; Zhang et al, 2016; Peng et al, 2017). …”

The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review

“…This means a transdisciplinary approach across the humananimal-environment continuum in order to better understand the problem of AMR in enterococci (97). While enterococcal species other than E. faecium and E. faecalis were discussed in a few studies, in general, there were relatively few studies using a One-Health approach to compare animal, environmental (e.g., water and soil), and human samples (9,11,13,(39)(40)(41)(68)(69)(70)(71).…”

“…As AMR pathogens have emerged, the use of antimicrobials for prophylaxis and metaphylaxis in food producing animals has come under scrutiny for its potential to apply a selective pressure that contributes to the dissemination of AMR and MDR enterococci ( 7 , 11 ). Perhaps the most classic example is in poultry and swine where the previous use of a vancomycin-related glycopeptide, avoparcin, as a growth promoter was associated with carriage of vancomycin-resistant E. faecium (VREfm) in treated herds or flocks through cross-resistance ( 7 , 12 ).…”

Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles

“…The raw sequence reads were quality trimmed using Trimmomatic ( Bolger et al, 2014 ), sequences with a Phred score less than 25 were removed. To obtain an initial estimate of sequencing coverage of E. lacertideformus present in each library, the trimmed reads were mapped against the Enterococcus hirae strain R17 genome (NCBI GenBank accession CP015516 ) ( Peng et al, 2017 ) using the Burrow-Wheeler Aligner (BWA-MEM v0.7.12) with default settings ( Li and Durbin, 2009 ). This revealed that sample 10702.133 contained the highest coverage depth (mean 1006.52×) in comparison to samples 10706.1 and 10706.10, with mean coverages of 245.72× and 8.73×, respectively.…”