Whole Genome Analysis of Three Multi-Drug Resistant Listeria innocua and Genomic Insights Into Their Relatedness With Resistant Listeria monocytogenes.

Menghan Li,Shaofei Yan,Séamus Fanning,Fengqin Li,Jin Xu

doi:10.3389/fmicb.2021.694361

Abstract

Listeria innocua are Gram-positive rod-shaped bacteria, which are not generally infectious as opposed to Listeria monocytogenes. However, the comparatively high genomic similarity between both along with on occasion, their coexistence in similar ecological niches may present the opportunity for resistance or virulence gene transfer. In this study, three multi-drug resistant L. innocua originally cultured from food were put forward for long-read genome sequencing. Chromosome and plasmid genomes were assembled and annotated. Analysis demonstrated that the resistant phenotypes correlated well with genotypes. Three plasmids pLI42, pLI203, and pLI47-1 were identified which harbor resistance islands. Sequence alignments suggested that plasmids pLI42 and pLI203 were highly similar to a previously sequenced L. monocytogenes plasmid pLR1. Similarly, another three types of resistance gene islands were observed on chromosome, including tet(M) gene islands (transposon Tn916 orthologs), dfrG gene islands and optrA-erm(A) gene islands. All three L. innocua isolates possessed listeria pathogenicity island-4 (LIPI-4) which is linked to cases of mengitis. Further genome environment and phylogenic analysis of regions flanking LIPI-4 of L. innocua and L. monocytogenes showed that these may have common origins and with the potential to transmit from the former. Our findings raise the possible need to include both L. monocytogenes and L. innocua in food surveillance programs so as to further understand of the origins of antimicrobial resistance and virulence markers of public health importance in L. monocytogenes.

Highlights

Listeria species are Gram-positive and facultative anaerobic bacteria that exist in soil, water and the animal gut
AMR genotypes corresponded well with the phenotypes described by Antibiotics Susceptibility Testing (AST) analysis, where the three multidrug resistant (MDR) isolates harbored resistance genes, respectively, for aminoglycoside, macrolidelincosamide-streptogramin B (MLSb), phenicol, tetracycline, and sulfamethoxazole resistance
Annotation of resistance genes showed that plasmid pLI42, pLI47-1, and pLI203 carried multiple antibiotic resistance genes including ant(6)-Ia, aph(3 )-IIIa, catA8, dfrG, erm(B), lnu(A), lnu(B), lsa(E), msr(D), mef (A), spw and tet(S), associating resistances of amikacin, aminoglycoside, chloramphenicol, kanamycin, lincosamide, macrolide, tetracycline, trimethoprim, streptogramin, and streptomycin

Summary

Introduction

Listeria species are Gram-positive and facultative anaerobic bacteria that exist in soil, water and the animal gut Members of this genus are found to contaminate certain types of foods and the associated food processing environment thereby representing a risk for public health (Finlay, 2001). To better describe the genomic evolution and potential for horizontal gene transfer (HGT) between L. monocytogenes and L. innocua, the findings of comparative genomics analyses were reported in previous studies (Buchrieser et al, 2003; Hain et al, 2006). These data highlighted the close genetic relationship existing between L. monocytogenes and L. innocua. Data indicated that L. innocua may have evolved through gene elimination and acquisition from the same pathogenic ancestor of L. monocytogenes (Chen et al, 2009)

Methods

Results

Discussion

Conclusion