Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae.

Mohammad Hamidian,Max Laurence Cummins,Steven Philip Djordjevic

doi:10.3390/microorganisms8020161

Mohammad Hamidian, Max Laurence Cummins + Show 1 more

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https://doi.org/10.3390/microorganisms8020161

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Journal: Microorganisms	Publication Date: Jan 23, 2020
Citations: 26	License type: CC BY 4.0

Affiliation: University of Technology Sydney

Abstract

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.

Highlights

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that carries diverse antibiotic resistance genes, often conferring multidrug resistance [1]
SGI1 was shown to be associated with globally dispersed Salmonella enterica serovar Typhimurium DT104 that rose to prominence in the 1980s
Bitsliced Genomic Signature Indexes (BIGSI) [9] allows for ultra-fast searching of bacterial and viral genomic data for nucleotide sequences of interest, providing access to the 457,000 whole genome sequence (WGS) datasets uploaded to Sequence Read Archive (SRA) prior to December, 2017

Summary

Introduction

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that carries diverse antibiotic resistance genes, often conferring multidrug resistance [1]. Variants of SGI1, including some that carry genes encoding resistance to critically important antimicrobials, have been identified within diverse serovars of Salmonella enterica and other Gammaproteobacteria including Proteus, Acinetobacter, Morganella, Providencia, Enterobacter, and Escherichia [2,3,4,5,6], all of which are known human and/or animal pathogens. Numerous Gram-negative genera carry the trmE gene, the integration site for SGI1 [8], suggesting that SGI1 may be dispersed more broadly in Gammaproteobacteria than is reported in the literature. We aimed to explore the SRA to garner a greater understanding of inter-genera distribution of this clinically important integrative genomic element

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