مجال
التميز
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تميز دراسي و بحثي
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البحوث المنشورة
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البحث (1):
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عنوان البحث:
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Cronobacter
sakazakii ST4 Strains and Neonatal Meningitis, United States
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here
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تاريخ النشر:
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01/01/2013
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موجز عن البحث:
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To
overcome various limitations of phenotyping and 16S rDNA sequence analysis of
Cronobacter bacteria, we have established a comprehensive multilocus sequence
typing (MLST) scheme as an open access database resource (www.pubMLST.org/cronobacter)
(1). The scheme is based on 7 housekeeping genes (atpD, fusA, glnS, gltB,
gyrB, infB, ppsA; 3,036 nt concatenated length) and has been used to study
the diversity of the Cronobacter genus and new Cronobacter species (2-4).
Previously, we compared the sequence type profile to severity of infection by
compiling patient details, isolation site, and clinical signs and symptoms
for strains isolated from around the world during 1953-2008 (5). This study
revealed that most serious meningitis clinical cases caused by Cronobacter
spp. in neonates during the previous 30 years in 6 countries were caused by a
single sequence type (ST): C. sakazakii ST4. We were therefore interested in
applying the MLST method to the Cronobacter strains associated with the
highly publicized cases in the United States during December 2011 (6).
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البحث (2):
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عنوان البحث:
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Sialic acid utilization by
Cronobacter sakazakii
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تاريخ النشر:
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May 2013
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موجز عن البحث:
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BACKGROUND:
The Cronobacter
genus is composed of seven species, and can cause infections in all age
groups. Of particular concern is C. sakazakii, as this species is strongly
associated with severe and often fatal cases of necrotizing enterocolitis and
meningitis in neonates and infants. Whole genome sequencing has revealed that
the nanAKT gene cluster required for the utilisation of exogenous sialic acid
is unique to the C. sakazakii species (ESA_03609-13).Sialic acid is found in
breast milk, infant formula, intestinal mucin, and gangliosides in the brain,
hence its metabolism by C. sakazakii is of particular interest. Therefore its
metabolism could be an important virulence factor. To date, no laboratory
studies demonstrating the growth of C. sakazakii on sialic acid have been
published nor have there been reports of sialidase activity. The phylogenetic
analysis of the nan genes is of interest to determine whether the genes have
been acquired by horizontal gene transfer.
RESULTS:
Phylogenetic analysis
of 19 Cronobacter strains from 7 recognised species revealed the nanAKTR
genes formed a unique cluster, separate from other Enterobacteriaceae such as
E. coli K1 and Citrobacter koseri, which are also associated with neonatal
meningitis. The gene organisation was similar to Edwardsiella tarda in that
nanE gene (N-acetylmannosamine-6-phosphate-2epimerase) was not located within
the nanATK cluster. Laboratory studies confirmed that only C. sakazakii, and
not the other six Cronobacter species, was able to use sialic acid as a
carbon source for growth. Although the ganglioside GM1 was also used as
carbon source, no candidate sialidase genes were found in the genome, instead
the substrate degradation is probably due to β-galactosidase activity.
CONCLUSIONS:
Given the relatively recent evolution of both C.
sakazakii (15-23 million years ago) and sialic acid synthesis in vertebrates,
sialic acid utilization may be an example of co-evolution by one species of
the Cronobacter genus with the mammalian host. This has possibly resulted in
additional virulence factors contributing to severe life-threatening
infections in neonates due to the utilization of sialic acid from breast
milk, infant formula, milk (oligosaccharides), mucins lining the intestinal
wall, and even gangliosides in the brain after passing through the
blood-brain barrier
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البحث (3):
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عنوان البحث:
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Lack
of continuity between Cronobacter biotypes and species as determined using multilocus
sequence typing
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تاريخ النشر:
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08/06/2013
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موجز عن البحث:
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The accuracy of
the Cronobacter biotyping scheme was compared with the 7-loci multilocus
sequence typing scheme. Biotyping did not reliably assign species level
identification, as only half (17/31) of the biotype variants were unique to
any of the seven Cronobacter species and the remaining biotypes were shared
across the genus.
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البحث (4):
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عنوان البحث:
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Diversity
of the Cronobacter genus as revealed by multilocus sequence typing
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تاريخ النشر:
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09/2012
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موجز عن البحث:
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Cronobacter
(previously known as Enterobacter sakazakii) is a diverse bacterial genus
consisting of seven species: C. sakazakii, C. malonaticus, C. turicensis, C.
universalis, C. muytjensii, C. dublinensis, and C. condimenti. In this study,
we have used a multilocus sequence typing (MLST) approach employing the
alleles of 7 genes (atpD, fusA, glnS, gltB, gyrB, infB, and ppsA; total
length, 3,036 bp) to investigate the phylogenetic relationship of 325
Cronobacter species isolates. Strains were chosen on the basis of their
species, geographic and temporal distribution, source, and clinical outcome.
The earliest strain was isolated from milk powder in 1950, and the earliest
clinical strain was isolated in 1953. The existence of seven species was
supported by MLST. Intraspecific variation ranged from low diversity in C.
sakazakii to extensive diversity within some species, such as C. muytjensii
and C. dublinensis, including evidence of gene conversion between species.
The predominant species from clinical sources was found to be C. sakazakii.
C. sakazakii sequence type 4 (ST4) was the predominant sequence type of
cerebral spinal fluid isolates from cases of meningitis.
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البحث (5):
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عنوان البحث:
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Siccibacter
colletis sp. nov., a newSiccibacter species isolated fromplant material
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تاريخ النشر:
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02/2015
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موجز عن البحث:
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A
re-evaluation of the taxonomic position of two strains, 1383T and 2249
isolated from poppy seeds and tea leaves, which had been identified as Siccibacter
turicensis (formerly Cronobacter zurichensis) was carried out. The analysis
included phenotypic characterisation, 16S rRNA gene sequencing and
multi-locus sequence analysis (MLSA) of five housekeeping genes (atpD, fusA,
glnS, gyrB, infB; 2034 bp) and ribosomal MLSA (53 loci; 22511 bp). 16S rRNA
gene sequence and MLSA showed the strains formed an independent phylogenetic
lineage, with Siccibacter turicensis LMG 23730T as the closest neighbour.
Average-nucleotide identity analysis and phenotypic analysis confirmed that
these strains represent a novel species, for which the name Siccibacter
colletis sp. nov. is proposed. The type strain is 1383T (= NCTC 14934T = CECT
8567T=LMG 28204T).
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البحث (6):
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عنوان البحث:
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Draft
Genome Sequence of the Earliest Cronobacter sakazakii Sequence Type 4 Strain,
NCIMB 8272
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تاريخ النشر:
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09/2013
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موجز عن البحث:
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The
Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is
associated with severe cases of neonatal meningitis and persistence in
powdered infant formula. For genome sequencing of the earliest deposited
culture collection strain of Cronobacter sakazakii ST4, we used the strain
NCIMB 8272, originally isolated from milk powder in 1950
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البحث (7):
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عنوان البحث:
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Draft Genome
Sequences of Three Newly Identified Species in the Genus Cronobacter, C.
helveticus MG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T
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تاريخ النشر:
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09 – 10/2013
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موجز عن البحث:
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The Cronobacter genus until recently consisted
of seven species,C. sakazakii, C. malonaticus, C. turicensis, C. universalis,
C.muytjensii, C. dublinensis, and C. condimenti (1). In 2013, three new
Cronobacter species were proposed, C. zurichensis, C. pulveris, and C.
helveticus (2). Due to the association of Cronobacter with fatal neonatal
infections there is an international requirement for powdered infant formula
to be microbiologically tested for all members of the Cronobacter genus
(Codex Alimentarius Commission, code of hygienic practice for powdered
formulae for infants and young children, CXP_066e.pdf).
Therefore, the genome sequencing of these newly described species is
warranted for better understanding of the genus diversity and improved
detection methodology. This was undertaken using C. helveticus strain LMG23732T,
C. zurichensis strain LMG23730T, and C. Pulveris strain LMG24059 isolated
from powdered infant formula.
Bacterial DNA was extracted from 1-day cultures
using a GenElute bacterial genome kit (Sigma-Aldrich) and sequenced using an
Illumina HiSeq 2500 sequencing system. De novo assembly was performed using
Velvet (3). For further annotation we used the SEED-based automated
annotation system provided by the RAST server (4).
C. helveticus LMG23732T, C. pulveris LMG24059,
and C. Zurichensis LMG23730T generated 8,351,512, 5,000,582, and 6,613,368
high-quality paired-end reads of 150 bp in length, respectively.
The genome sizes were 4,530,369 bp, 4,900,556
bp, and 4,246,797 bp with G_C contents of 56%, 56.6%, and 57.8%,
respectively.
These were in 79, 125, and 103 contigs with
4,315,4,630, and 3,883 coding sequences (CDS), respectively, and
30-foldcoverage. TheCDSinclude traits previously described in Cronobacter(5).
These included genes associated with iron acquisition, stress response, heavy
metal resistance (arsenic, copper cobalt, zinc and cadmium),and phages. Genes
encoding proteins associated with several virulence-associated traits such as
adhesion and antibiotic resistance, including fluoroquinolones, fosfomycin,
_-lactamases, and multidrug efflux
pumps, were also determined.
Nucleotide
sequence accession numbers.The genome sequences of C. helveticus, C.
pulveris, and C. zurichensis have been deposited in GenBank under the
accession numbers AWFX00000000, AWFY00000000, and AWFZ00000000, respectively.
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البحث (8):
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عنوان البحث:
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Draft Genome
Sequence of a Meningitic Isolate of Cronobacter sakazakii Clonal Complex 4,
Strain 8399
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تاريخ النشر:
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2013
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موجز عن البحث:
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The Cronobacter sakazakii clonal lineage defined
as clonal complex 4 (CC4), composed of nine sequence types, is associated
with severe cases of neonatal meningitis. To date, only closely related C.
sakazakii sequence type 4 (ST4) strains have been sequenced. C. sakazakii
strain 8399, isolated from a case of neonatal meningitis, was sequenced as
the first non-ST4 C. sakazakii strain
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البحث (9):
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عنوان البحث:
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Comparative
analysis of genome sequences covering the seven Cronobacter species
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تاريخ النشر:
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16/11/2012
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موجز عن البحث:
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Species of Cronobacter are widespread in the
environment and are occasional food-borne athogens associated with serious
neonatal diseases, including bacteraemia, meningitis, and necrotising nterocolitis.
The genus is composed of seven species: C. akazakii, C. malonaticus, C.
turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti.
Clinical cases are associated with three species, C. malonaticus, C.
turicensis and, in particular, with C. sakazakii multilocus sequence type 4.
Thus, it is plausible that virulence determinants have evolved in certain
lineages.
We generated high quality sequence drafts for
eleven Cronobacter genomes representing the seven Cronobacter species,
including an ST4 strain of C. sakazakii. Comparative analysis of these
genomes together with the two publicly available genomes revealed Cronobacter
has over 6,000 genes in one or more strains and over 2,000 genes shared by
all Cronobacter. Considerable variation in the presence of traits such as
type six secretion systems, metal resistance (tellurite, copper and silver),
and adhesins were found. C. sakazakii is unique in the Cronobacter genus in
encoding genes enabling the utilization of exogenous sialic acid which may
have clinical significance. The C. sakazakii ST4 strain 701 contained
additional genes as compared to other C. sakazakii but none of them were
known specific virulence-related genes.
Genome comparison revealed that pair-wise DNA
sequence identity varies between 89 and 97% in the seven Cronobacter species,
and also suggested various degrees of divergence. Sets of universal core
genes and accessory genes unique to each strain were identified. These gene
sequences can be used for designing genus/species specific detection assays.
Genes encoding adhesins, T6SS, and metal resistance genes as well as
prophages are found in only subsets of genomes and have contributed
considerably to the variation of genomic content. Differences in gene content
likely contribute to differences in the clinical and environmental distribution
of species and sequence types.
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المؤتمرات العلمية:
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المؤتمر (1):
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عنوان المؤتمر:
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The 8th Saudi student conference
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تاريخ الإنعقاد:
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31 Jan – 01 Feb 2015
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مكان
الإنعقاد:
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London, UK
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طبيعة المشاركة:
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Poster presentation
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عنوان المشاركة:
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Application of
multilocus sequencing in the investigation of neonatal infections by
Cronobacter spp.
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ملخص المشاركة:
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Cronobacter spp.
(previously know as Enterobacter sakazakii) is opportunistic pathogen that
can cause serious infection in premature neonates. As a recently recognized
bacterial pathogen of considerable importance, regulatory control and
appropriate identification methods are required.
The FAO-WHO (2004)
requested that reliable detection and molecular typing methods are developed
for the control of this bacterium. In response we have established a
multilocus sequence typing scheme (MLST) and open access internationally
based database (http://www.pubMLST.org/cronobacter/).
This is supported by international contributors and currently includes the
profiles of 1005 strains and 108 whole genomes. The MLST scheme has advanced
our understanding of the Cronobacter genus, revealing predominant and stable
clones associated with neonatal meningitis.
In this study MLST
has been applied to clinical strains from Cronobacter outbreaks amongst
neonates. It revealed that (a) most of these isolates were in the C.
sakazakii ST4 clonal complex thus confirming the importance of this lineage
in sever Cronobacter infection, and (b) C. sakazakii is unique in the
Cronobacter genus in its utilization of exogenous sialic acid as a carbon
source. This later trait may have a role in the organism’s virulence as high
levels of sialic acid are accessible to bacteria in infant formula,
intestinal mucosa, and the brain.
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