Microbiology of diabetic foot infections: from Louis Pasteur to 'crime scene investigation'.
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ABSTRACT:
SUBMITTER: Spichler A
PROVIDER: S-EPMC4286146 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
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Microbiology of diabetic foot infections: from Louis Pasteur to 'crime scene investigation'.
Spichler Anne A Hurwitz Bonnie L BL Armstrong David G DG Lipsky Benjamin A BA
BMC medicine 20150107
Were he alive today, would Louis Pasteur still champion culture methods he pioneered over 150 years ago for identifying bacterial pathogens? Or, might he suggest that new molecular techniques may prove a better way forward for quickly detecting the true microbial diversity of wounds? As modern clinicians faced with treating complex patients with diabetic foot infections (DFI), should we still request venerated and familiar culture and sensitivity methods, or is it time to ask for newer molecular ...[more]
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Project description:BackgroundDiabetic foot ulcers are a common complication of poorly controlled diabetes and often become infected, termed diabetic foot infection. There have been numerous studies of the microbiology of diabetic foot infection but no meta-analysis has provided a global overview of these data. This meta-analysis aimed to investigate the prevalence of bacteria isolated from diabetic foot infections using studies of any design which reported diabetic foot infection culture results.MethodsThe Medline, EMBASE, Web of Science and BIOSIS electronic databases were searched for studies published up to 2019 which contained microbiological culture results from at least 10 diabetic foot infection patients. Two authors independently assessed study eligibility and extracted the data. The main outcome was the prevalence of each bacterial genera or species.ResultsA total of 112 studies were included, representing 16,159 patients from which 22,198 microbial isolates were obtained. The organism most commonly identified was Staphylococcus aureus, of which 18.0% (95% CI 13.8-22.6%; I2 = 93.8% [93.0-94.5%]) was MRSA. Other highly prevalent organisms were Pseudomonas spp., E. coli and Enterococcus spp. A correlation was identified between Gross National Income and the prevalence of Gram positive or negative organisms in diabetic foot infections.ConclusionThe microbiology of diabetic foot infections is diverse, but S. aureus predominates. The correlation between the prevalence of Gram positive and negative organisms and Gross National Income could reflect differences in healthcare provision and sanitation. This meta-analysis has synthesised multiple datasets to provide a global overview of the microbiology of diabetic foot infections that will help direct the development of novel therapeutics.
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Project description:This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes. They then BLAST (Basic Local Alignment Search Tool) the in silico PCR results to confirm that the PCR primers are designed to amplify genomic fragments of the cardiac actin gene in both dogs and humans. Finally, they use DNA quantification techniques, PCR, and agarose gel electrophoresis to identify the culprit and they confirm results by analyzing Sanger sequencing. Student learning gains were demonstrated by successful execution of the lab and by analysis and interpretation of data in the completion of laboratory reports. The student learning gains were also demonstrated by increased performance on a post-laboratory assessment compared to the pre-assessment. A post-activity assessment also revealed that students perceived gains in the skills and conceptual knowledge associated with the student learning outcomes. Finally, assessment of this introductory molecular biology and bio-informatics activity reveals that it allows first-year students to develop higher-order data analysis and interpretation skills.
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Project description:BACKGROUND:This study represents the first Scottish retrospective analysis of the microbiology of diabetic foot infections (DFIs). The aims were to compare the microbiological profile of DFIs treated at a Scottish tertiary hospital to that in the literature, gather data regarding antimicrobial resistance and investigate potential trends between the microbiological results and nature or site of the clinical sample taken and age or gender of the patients. METHODS:A retrospective analysis of wound microbiology results was performed, data were obtained from one multidisciplinary outpatient foot clinic during the 12?months of the year 2017. Seventy-three patients and 200 microbiological investigations were included. In cases of soft tissue infection, the deepest part of a cleansed and debrided wound was sampled. In cases of osteomyelitis a bone biopsy was obtained. Factors influencing the pattern of microbial growth or prevalence of Staphylococcus aureus were investigated. RESULTS:Of the 200 microbiological investigations, 62% were culture positive, of which 37.9% were polymicrobial and 62.1% monomicrobial. Among the monomicrobial results (n =?77), most were Gram positive isolates (96.1%) and the most frequently isolated bacteria was S. aureus (84.4%). No methicillin-resistant S. aureus was reported. The prevalence of S. aureus in DFIs was associated with increasing age (p =?0.021), but no evidence of association with gender, anatomical sample site or sample material was found. CONCLUSION:The microbiological profile of DFIs in Scotland resembles that reported elsewhere in the UK. In this context, Gram positive organisms, primarily S. aureus, are most frequently isolated from DFIs. The S. aureus isolates identified were largely susceptible to antibiotic therapy. An association between increasing patient age and the prevalence of S. aureus in DFIs was observed.
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Project description:The purpose of this prospective observational study was to evaluate the richness and diversity of bacteria in samples from diabetic foot infections using a culturomics approach. Bacterial culture findings from wound samples were analyzed together with clinical characteristics and treatment outcomes. We included 43 patients admitted to a French referral center with a moderate to severe diabetic foot infection. The 30,000 colonies identified yielded 53 different bacterial species. The global α-Shannon diversity was 3.34 and the bacterial richness per patient was 4 ± 2. Of all the identified bacterial species, 19 (35.8%) had never been previously cultured or identified by molecular methods from diabetic foot ulcers. Most of the samples were polymicrobial (N = 38; 88.3%). Of all the isolated species, the most prevalent were Staphylococcus aureus (N = 28; 52.8%), Enterococcus faecalis (N = 24; 45.2%), Enterobacter cloacae (N = 12; 22.6%), Staphylococcus lugdunensis (N = 10; 18.7%), Staphylococcus epidermidis (N = 6; 11.3%), Proteus mirabilis (N = 6; 11.3%), and Finegoldia magna (N = 5; 9.4%). The only factor associated with wound improvement after a 1-month follow-up was the presence of E. faecalis (p = 0.012) when compared with patients without wound improvement. This study confirms the complementary role of culturomics in the exploration of complex microbiota. Further studies on a larger scale are needed to fully understand the clinical importance of the microbiota of diabetic foot infections.
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Project description:BackgroundThe success of forensic DNA analysis is limited by the size, quality and purity of biological evidence found at crime scenes. Sample impurities can inhibit PCR, resulting in partial or negative DNA profiles. Various DNA purification methods are applied to remove impurities, for example, employing centrifugal filter devices. However, irrespective of method, DNA purification leads to DNA loss. Here we evaluate the filter devices Amicon Ultra 30 K and Microsep 30 K with respect to recovery rate and general performance for various types of PCR-inhibitory crime scene samples.MethodsRecovery rates for DNA purification using Amicon Ultra 30 K and Microsep 30 K were gathered using quantitative PCR. Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the general performance and inhibitor-removal properties of the two filter devices. Additionally, the outcome of long-term routine casework DNA analysis applying each of the devices was evaluated.ResultsApplying Microsep 30 K, 14 to 32% of the input DNA was recovered, whereas Amicon Ultra 30 K retained 62 to 70% of the DNA. The improved purity following filter purification counteracted some of this DNA loss, leading to slightly increased electropherogram peak heights for blood on denim (Amicon Ultra 30 K and Microsep 30 K) and saliva on envelope (Amicon Ultra 30 K). Comparing Amicon Ultra 30 K and Microsep 30 K for purification of DNA extracts from mock crime scene samples, the former generated significantly higher peak heights for rape case samples (P-values <0.01) and for hairs (P-values <0.036). In long-term routine use of the two filter devices, DNA extracts purified with Amicon Ultra 30 K were considerably less PCR-inhibitory in Quantifiler Human qPCR analysis compared to Microsep 30 K.ConclusionsAmicon Ultra 30 K performed better than Microsep 30 K due to higher DNA recovery and more efficient removal of PCR-inhibitory substances. The different performances of the filter devices are likely caused by the quality of the filters and plastic wares, for example, their DNA binding properties. DNA purification using centrifugal filter devices can be necessary for successful DNA profiling of impure crime scene samples and for consistency between different PCR-based analysis systems, such as quantification and STR analysis. In order to maximize the possibility to obtain complete STR DNA profiles and to create an efficient workflow, the level of DNA purification applied should be correlated to the inhibitor-tolerance of the STR analysis system used.
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Project description:Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.
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Project description:ObjectiveThe purpose of this study was to evaluate the disparities in the outcomes of White, African American (AA) and non-AA minority (Hispanics and Native Americans (NA)), patients admitted in the hospitals with diabetic foot infections (DFIs).Research design and methodsThe HCUP-Nationwide Inpatient Sample (2002 to 2015) was queried to identify patients who were admitted to the hospital for management of DFI using ICD-9 codes. Outcomes evaluated included minor and major amputations, open or endovascular revascularization, and hospital length of stay (LOS). Incidence for amputation and open or endovascular revascularization were evaluated over the study period. Multivariable regression analyses were performed to assess the association between race/ethnicity and outcomes.ResultsThere were 150,701 admissions for DFI, including 98,361 Whites, 24,583 AAs, 24,472 Hispanics, and 1,654 Native Americans (NAs) in the study cohort. Overall, 45,278 (30%) underwent a minor amputation, 9,039 (6%) underwent a major amputation, 3,151 underwent an open bypass, and 8,689 had an endovascular procedure. There was a decreasing incidence in major amputations and an increasing incidence of minor amputations over the study period (P < .05). The risks for major amputation were significantly higher (all p<0.05) for AA (OR 1.4, 95%CI 1.4,1.5), Hispanic (OR 1.3, 95%CI 1.3,1.4), and NA (OR 1.5, 95%CI 1.2,1.8) patients with DFIs compared to White patients. Hispanics (OR 1.3, 95%CI 1.2,1.5) and AAs (OR 1.2, 95%CI 1.1,1.4) were more likely to receive endovascular intervention or open bypass than Whites (all p<0.05). NA patients with DFI were less likely to receive a revascularization procedure (OR 0.6, 95%CI 0.3, 0.9, p = 0.03) than Whites. The mean hospital length of stay (LOS) was significantly longer for AAs (9.2 days) and Hispanics (8.6 days) with DFIs compared to Whites (8.1 days, p<0.001).ConclusionDespite a consistent incidence reduction of amputation over the past decade, racial and ethnic minorities including African American, Hispanic, and Native American patients admitted to hospitals with DFIs have a consistently significantly higher risk of major amputation and longer hospital length of stay than their White counterparts. Native Americans were less likely to receive revascularization procedures compared to other minorities despite exhibiting an elevated risk of an amputation. Further study is required to address and limit racial and ethnic disparities and to further promote equity in the treatment and outcomes of these at-risk patients.
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