Molecular Epidemiology of Staphylococcus aureus Nasal: Carriage and Wound Colonization in a Burn Centre

__Abstract__ Human skin is vital to the preservation of body fluid homeostasis, thermoregulation, protection against the harmful effects of UV-irradiation, and the prevention of tissue invasion by micro-organisms. Organisms of diverse species naturally colonise different layers of the skin. They interact via specific ligands with receptors in host tissues . Thermal injury creates a breach in the surface of the skin and alters the variety and exposition of specific host’ receptors. The wound resulting from such injury is a protein-rich environment consisting of avascular necrotic tissue that provides an even more favourable niche for microbial colonization and proliferation than healthy skin does . Although immediately following thermal injury, burn wounds are sterile, these wounds will soon become colonized with micro-organisms . Within hours or days, Gram-positive bacteria, including Staphylococcus aureus (S. aureus) will colonize the burn wound; Gram-negative species are isolated from wounds at a later stage post thermal injury

Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing

AbstractShiga toxin–producing Escherichia coli (STEC) is one of the major causes of human gastrointestinal disease and has been implicated in sporadic cases and outbreaks of diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome worldwide. In this study, we determined the molecular characteristics and phylogenetic relationship of STEC isolates, and their genetic diversity was compared to that of other E. coli populations. Whole genome sequencing was performed on 132 clinical STEC isolates obtained from the faeces of 129 Dutch patients with gastrointestinal complaints. STEC isolates of this study belonged to 44 different sequence types (STs), 42 serogenotypes and 14 stx subtype combinations. Antibiotic resistance genes were more frequently present in stx1-positive isolates compared to stx2 and stx1 + stx2–positive isolates. The iha, mchB, mchC, mchF, subA, ireA, senB, saa and sigA genes were significantly more frequently present in eae-negative than in eae-positive STEC isolates. Presence of virulence genes encoding type III secretion proteins and adhesins was associated with isolates obtained from patients with bloody diarrhoea. Core genome phylogenetic analysis showed that isolates clustered according to their ST or serogenotypes irrespective of stx subtypes. Isolates obtained from patients with bloody diarrhoea were from diverse phylogenetic backgrounds. Some STEC isolates shared common ancestors with non-STEC isolates. Whole genome sequencing is a powerful tool for clinical microbiology, allowing high-resolution molecular typing, population structure analysis and detailed molecular characterization of strains. STEC isolates of a substantial genetic diversity and of distinct phylogenetic groups were observed in this study

Detection of Campylobacter species and Arcobacter butzleri in stool samples by use of real-time multiplex PCR

The presence of Campylobacter (or Campylobacter-like) species in stools from patients suspected of infectious gastroenteritis (n = 493) was investigated using real-time PCR for detection of Arcobacter butzleri (hsp60 gene), Campylobacter coli (ceuE gene), Campylobacter jejuni (mapA), five acknowledged pathogenic Campylobacter spp. (C16S-Lund assay), and the Campylobacter genus (C16S-LvI assay). In total, 71.4% of the samples were positive for Campylobacter DNA (n = 352) by a Campylobacter genus-specific (C16S-LvI) assay. A total of 23 samples (4.7%) were positive in the C16S-Lund assay, used for detection of C. jejuni, C. coli, C. lari, C. upsaliensis, and C. hyointestinalis. Subsequent identification of these samples yielded detection frequencies (DF) of 4.1% (C. jejuni), 0.4% (C. coli), and 0.4% (C. upsaliensis). The DF of A. butzleri was 0.4%. Interestingly, sequencing of a subgroup (n = 46) of C16S-LvI PCR-positive samples resulted in a considerable number of Campylobacter concisus-positive samples (n = 20). PCR-positive findings with the C16S-Lund and C. jejuni/C. coli-specific assays were associated with more serious clinical symptoms (diarrhea and blood). Threshold cycle (CT) values of C. jejuni/C. coli PCR-positive samples were comparable to those of the C16S-Lund PCR (P =

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

Contains fulltext : 217640.pdf (publisher's version ) (Open Access

Additional file 4 of Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

Additional file 4. Genomes and phenotypic data used in GWAS. The phenotypic patient data used for the GWAS, including accession numbers of the genomes of the infected isolates are depicted in this table

Additional file 5 of Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

Additional file 5. Representative genomes. The accession numbers and publications of the representative genomes used in this study are depicted in this table