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Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.

ABSTRACT: Providenciaspp. are ubiquitous Gram-negative bacteria of the familyEnterobacteriaceaethat are common opportunistic pathogens. In the present work, we have sequenced, annotated, and compared the draft genome ofProvidencia heimbachae, which was recovered from a diabetic foot ulcer. It is composed of 4.22 Mb and encodes 3,843 protein-coding genes and 79 RNA genes, including 11 rRNA genes.

SUBMITTER: Jneid J

PROVIDER: S-EPMC4832169 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.

Jneid Joanne J Benamar Samia S Pagnier Isabelle I Levy Pierre-Yves PY Lavigne Jean-Philippe JP La Scola Bernard B

Genome announcements 20160414 2

Providenciaspp. are ubiquitous Gram-negative bacteria of the familyEnterobacteriaceaethat are common opportunistic pathogens. In the present work, we have sequenced, annotated, and compared the draft genome ofProvidencia heimbachae, which was recovered from a diabetic foot ulcer. It is composed of 4.22 Mb and encodes 3,843 protein-coding genes and 79 RNA genes, including 11 rRNA genes. ...[more]

PMID: 27081141

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Project description:PurposeWe aimed to investigate the prevalence of diabetic retinopathy (DR) in patients with diabetic foot ulcer (DFU) and elucidate the association between DR and DFU severities and their shared risk factors.MethodsA retrospective review was conducted on DFU patients who underwent ophthalmic and vascular examinations within 6 months; 100 type 2 diabetic patients with DFU were included. The medical records of 2496 type 2 diabetic patients without DFU served as control data. DR prevalence and severity were assessed in DFU patients. DFU patients were compared with the control group regarding each clinical variable. Additionally, DFU patients were divided into two groups according to DR severity and compared.ResultsOut of 100 DFU patients, 90 patients (90%) had DR and 55 (55%) had proliferative DR (PDR). There was no significant association between DR and DFU severities (R = 0.034, p = 0.734). A multivariable analysis comparing type 2 diabetic patients with and without DFUs showed that the presence of DR [OR, 226.12; 95% confidence interval (CI), 58.07-880.49; p < 0.001] and proliferative DR [OR, 306.27; 95% CI, 64.35-1457.80; p < 0.001), higher HbA1c (%, OR, 1.97, 95% CI, 1.46-2.67; p < 0.001), higher serum creatinine (mg/dL, OR, 1.62, 95% CI, 1.06-2.50; p = 0.027), older age (years, OR, 1.12; 95% CI, 1.06-1.17; p < 0.001), higher pulse pressure (mmHg, OR, 1.03; 95% CI, 1.00-1.06; p = 0.025), lower cholesterol (mg/dL, OR, 0.94; 95% CI, 0.92-0.97; p < 0.001), lower BMI (kg/m2, OR, 0.87, 95% CI, 0.75-1.00; p = 0.044) and lower hematocrit (%, OR, 0.80, 95% CI, 0.74-0.87; p < 0.001) were associated with DFUs. In a subgroup analysis of DFU patients, the PDR group had a longer duration of diabetes mellitus, higher serum BUN, and higher serum creatinine than the non-PDR group. In the multivariable analysis, only higher serum creatinine was associated with PDR in DFU patients (OR, 1.37; 95% CI, 1.05-1.78; p = 0.021).ConclusionsDiabetic retinopathy is prevalent in patients with DFU and about half of DFU patients had PDR. No significant association was found in terms of the severity of these two diabetic complications. To prevent blindness, patients with DFU, and especially those with high serum creatinine, should undergo retinal examinations for timely PDR diagnosis and management.

Project description:Accurate identification of pathogens, rather than colonising bacteria, is a prerequisite for targeted antibiotic therapy to ensure optimal patient outcome in wounds, such as diabetic foot ulcers. Wound swabs are the easiest and most commonly used sampling technique but most published guidelines recommend instead removal of a tissue sample from the wound bed, which is a more complex process. The aim of this study was to assess the concordance between culture results from wound swabs and tissue samples in patients with suspected diabetic foot infection. Patients with a diabetic foot ulcer that is thought to be infected are being recruited from 25 sites across England in a cross-sectional study. The coprimary endpoints for the study are agreement between the two sampling techniques for three microbiological parameters: reported presence of likely isolates identified by the UK Health Protection Agency; resistance of isolates to usual antibiotic agents; and, the number of isolates reported per specimen. Secondary endpoints include appropriateness of the empiric antibiotic therapy prescribed and adverse events. Enrolling 400 patients will provide 80% power to detect a difference of 3% in the reported presence of an organism, assuming organism prevalence of 10%, discordance of 5% and a two-sided test at the 5% level of significance. Assumed overall prevalence is based on relatively uncommon organisms such as Pseudomonas. We will define acceptable agreement as κ>0.6. Concordance in diabetic foot ulcer infection (CODIFI) will produce robust data to evaluate the two most commonly used sampling techniques employed for patients with a diabetic foot infection. This will help determine whether or not it is important that clinicians take tissue samples rather than swabs in infected ulcers. This study has been approved by the Sheffield NRES Committee (Ref: 11/YH/0078) and all sites have obtained local approvals prior starting recruitment. NRES Ref: 11/YH/0078, UKCRN ID: 10440, ISRCTN: 52608451.

Dataset Information

Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.

Publications

Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.

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