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Open Access 01-12-2018 | Research

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

Authors: Gopal R. Gopinath, Hannah R. Chase, Jayanthi Gangiredla, Athmanya Eshwar, Hyein Jang, Isha Patel, Flavia Negrete, Samantha Finkelstein, Eunbi Park, TaeJung Chung, YeonJoo Yoo, JungHa Woo, YouYoung Lee, Jihyeon Park, Hyerim Choi, Seungeun Jeong, Soyoung Jun, Mijeong Kim, Chaeyoon Lee, HyeJin Jeong, Séamus Fanning, Roger Stephan, Carol Iversen, Felix Reich, Günter Klein, Angelika Lehner, Ben D. Tall

Published in: Gut Pathogens | Issue 1/2018

Abstract

Background

Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains.

Results

In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene.

Conclusions

Until this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains.

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Title: Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples
Authors: Gopal R. Gopinath
Hannah R. Chase
Jayanthi Gangiredla
Athmanya Eshwar
Hyein Jang
Isha Patel
Flavia Negrete
Samantha Finkelstein
Eunbi Park
TaeJung Chung
YeonJoo Yoo
JungHa Woo
YouYoung Lee
Jihyeon Park
Hyerim Choi
Seungeun Jeong
Soyoung Jun
Mijeong Kim
Chaeyoon Lee
HyeJin Jeong
Séamus Fanning
Roger Stephan
Carol Iversen
Felix Reich
Günter Klein
Angelika Lehner
Ben D. Tall
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: Gut Pathogens / Issue 1/2018
Electronic ISSN: 1757-4749
DOI: https://doi.org/10.1186/s13099-018-0238-9

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Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

Abstract

Background

Results

Conclusions

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Abstract

Background

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Conclusions

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