Detecting aerobic bacterial diversity in patients with diabetic foot wounds using ERIC-PCR: a preliminary communication

Molecular Typing of Multidrug-Resistant Acinetobacter baumannii Isolates from Clinical Specimens by ERIC-PCR and MLVA

Acinetobacter baumannii, a Gram-negative and oxidase-negative bacterium, is a major cause of nosocomial infections, leading to high mortality rates in hospitalized patients. The use of 2 prominent molecular typing methods (i.e., enterobacterial repetitive intergenic consensus-polymerase chain reaction [ERIC-PCR] and multiple-locus variable-number tandem repeat [VNTR] analysis [MLVA]) for genotyping A. baumannii isolates has proven to be an effective approach in assessing the clonal relation of these isolates and managing their outbreaks. A total of 100 A. baumannii isolates were collected from immunocompromised patients hospitalized in the intensive care unit (ICU) of a hospital in Zanjan City, Iran. Their antibiotic resistance ability (especially aminoglycoside resistance) was studied by disc diffusion tests. The genetic typing of A. baumannii was studied using ERIC-PCR and MLVA methods. All isolates were resistant to 3 or more antibiotics and regarded as multidrug-resistant (MDR). Additionally, 32% of the isolates were resistant to all antibiotics tested, and 91% were extensively drug-resistant (XDR). The increased rate of aminoglycoside-resistant A. baumannii in ICU patients, with an increased incidence of aminoglycoside-modifying enzymes of aac (6')-Ib, ant (3″)-I, and aph (2″)-Id. ERIC-PCR has likewise shown an increased level of diversity in A. baumannii isolates. According to the ERIC-PCR patterns, isolates were classified as 4 clusters, while according to the MLVA patterns, isolates were classified as 9 distinct clusters. ERIC-PCR and MLVA assays serve as useful genotyping methods to assess the genetic variety or clonal relatedness of A. baumannii isolates.

Evaluation of Polymerase Chain Reaction in the Identification and Quantification of Clinically Relevant Bacterial Species in Lower Extremity Wound Infections

Identification of bacteria by polymerase chain reaction (PCR) is known to be more sensitive than culture, which brings to question the clinical applicability of the results. In this study, we evaluate the ability of PCR to detect clinically relevant bacterial species in lower extremity wound infections requiring operative debridement, as well as the quantitative change in biodiversity and bacterial load reflected by PCR during the course of treatment. Thirty-four infected lower extremity were examined by analysis of 16S ribosomal RNA subunit and by culture. McNemar's test was used to measure the concordance of clinically relevant bacterial species identified by PCR compared to culture during each debridement. Change in wound biodiversity from initial presentation to final closure was evaluated by Wilcoxon signed-rank test. Kaplan-Meier survival curve was used to characterize change in measured bacterial load over the course of operative debridement. A total of 15 and 12 clinically relevant bacterial species were identified by PCR and culture, respectively. The most common bacterial species identified were Coagulase-negative Staphylococcus, Staphylococcus aureus, and Enterococcus spp. PCR was less likely to detect Enterococcus spp. on initial debridement and Coagulase-negative Staphylococcus on closure in this study population. A significant decrease in mean number of clinically relevant species detected from initial debridement to closure was reflected by culture (p = .0188) but not by PCR (p = .1848). Both PCR (p = .0128) and culture (p = .0001) depicted significant reduction in mean bacterial load from initial debridement to closure. PCR is able to identify common clinically relevant bacterial species in lower extremity surgical wound infections. PCR displays increased sensitivity compared to culture with relation to detection of biodiversity, rather than bacterial load. Molecular diagnostics and conventional culture may serve a joint purpose to assist with rendering clinical judgment in complex wound infections.

Culturomics Approach to Identify Diabetic Foot Infection Bacteria

The main goal of the study was to evaluate the usefulness of the culturomics approach in the reflection of diabetic foot infections (DFIs) microbial compositions in Poland. Superficial swab samples of 16 diabetic foot infection patients (Provincial Polyclinical Hospital in Toruń, Poland) were subjected to culturing using 10 different types of media followed by the identification via the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Biotyper platform. Identified 204 bacterial isolates representing 18 different species—mostly Enterococcus faecalis (63%) and Staphylococcus aureus (44%). Most of the infections (81%) demonstrated a polymicrobial character. Great differences in the species coverage, the number of isolated Gram-positive and Gram-negative bacteria, and the efficiency of the microbial composition reflection between the investigated media were revealed. The use of commonly recommended blood agar allowed to reveal only 53% of the entire microbial composition of the diabetic foot infection samples, which considerably improved when the chromagar orientation and vancomycin-resistant enterococi agar were applied. In general, efficiency increased in the following order: selective < universal < enriched < differential media. Performed analysis also revealed the impact of the culture media composition on the molecular profiles of some bacterial species, such as Corynebacterium striatum, Proteus mirabilis or Morganella morganii that contributed to the differences in the identification quality. Our results indicated that the culturomics approach can significantly improve the accuracy of the reflection of the diabetic foot infections microbial compositions as long as an appropriate media set is selected. The chromagar orientation and vancomycin-resistant enterococi agar media which were used for the first time to study diabetic foot infection microbial profiles demonstrate the highest utility in the culturomics approach and should be included in further studies directed to find a faster and more reliable diabetic foot infection diagnostic tool.

Analysis of the microbiota in the diabetic foot ulcers: Is research standardization required?

Background: Complications of infected wounds in patients with diabetic foot ulcer (DFU) are one of the greatest challenges in modern medicine. Analysis of the microbiological profile of infected ulcers may significantly improve treatment results. The aim of the study was to determine the profile of pathogens isolated in patients with DFU and to compare the results of other centers. Materials and Methods: A retrospective study was carried out on 137 patients with DFU hospitalized at the Department of Diabetology and Internal Diseases, Medical University of Warsaw in 2011-2014. The analysis included the results of 200 microbiological cultures tested for fungi, aerobic and anaerobic bacteria. Statistical analysis was used to test differences in HbA1c values in relation to the strain of the most commonly cultured bacteria and the relationship between glycemic control and most frequently isolated pathogens. Results: Seventy-nine bacterial species were isolated in 183 positive cultures. Gram-negative bacteria predominated with the highest percentage of representatives of Enterobacterales. The most often isolated bacteria were Serratia marcescens, Pseudomonas aeruginosa, Proteus mirabilis and methicillin-susceptible Staphylococcus aureus. The Kruskal-Wallis test revealed that HbA1c concentrations were different in groups infected with different strains of bacteria (p = 0.0087). Isolation of Escherichia coli and Morganella morganii was more often associated with poor control of diabetes. Conclusions: The study revealed statistically significant differences in the frequency of microorganisms isolated from the wounds of patients with DFU. The discrepancies in the results of other studies published in this field indicate the need for standardization of the research design.

Identification and characterization of two bacteriophages with lytic activity against multidrug-resistant Escherichia coli

Escherichia coli is an opportunistic bacterial pathogen that causes a wide range of nosocomial infections. The emergence of multidrug resistance in E. coli poses a severe threat to global health. Phage therapies are an alternative method to control multidrug-resistant pathogens, which have been attracting increasing attention. Owing to their ability to lyse bacteria specifically and efficiently, bacteriophages are considered novel antimicrobial agents. In this study, we used multidrug-resistant E. coli as an indicator and isolated, characterized, and compared two new phages of the Siphoviridae family referred to as vB_EcoS_XF and vB_EcoS_XY2. These phages were able to infect several pathogenic multidrug-resistant E. coli strains. A short latent period and large burst size ensured their rapidly reproduction in host cells. Their tolerance of high temperatures and high pH levels meant that remained stable when used to control pathogenic E. coli strains. No obvious cytotoxicity was observed when either HEK293 T or A549 cells were incubated with these two phages. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. Genomic analysis revealed that no toxic proteins or antibiotic proteins were encoded. Genome comparison and phylogenetic analysis indicated that the phages identified show high similarity with E. coli phages of the genus Kagunavirus. The desirable characteristics of the novel phages identified make them good potential therapeutic candidates, and components of phage cocktails to treat multidrug-resistant E. coli in the future.

UV-B Radiation Stress Causes Alterations in Whole Cell Protein Profile and Expression of Certain Genes in the Rice Phyllospheric Bacterium Enterobacter cloacae

Among the different types of UV radiation, UV-B radiation (280-315 nm) has gained much attention mainly due to its increasing incidence on the Earth’s surface leading to imbalances in natural ecosystems. This study deals with the effects of UV-B radiation on the proteome and gene expression in a rice phyllospheric bacterium, Enterobacter cloacae. Of the five bacteria isolated from rice leaves, E. cloacae showed the highest level of resistance to UV-B and total killing occurred after 8 h of continuous exposure to UV-B. Reactive oxygen species were induced by UV-B exposure and increased with increasing duration of exposure. Protein profiling by SDS-PAGE and 2-dimensional gel electrophoresis (2-DE) revealed major changes in the number as well as expression of proteins. Analysis of 2-DE gel spots indicated up/down-regulation of several proteins under the stress of UV-B radiation. Thirteen differentially expressed proteins including two hypothetical proteins were identified by MALDI-TOF MS and assigned to eight functional categories. Both the hypothetical proteins (gi 779821175 and gi 503938301) were over-expressed after UV-B irradiation; gi 503938301 was characterized as a member of FMN reductase superfamily whereas gi 779821175 seems to be a structural protein as it did not show any functional domain. That the expression of certain proteins under UV-B stress is indeed up-regulated was confirmed by qRT-PCR. Transcript analysis of selected gene including genes of hypothetical proteins (cp011650 and cp002886) showed over-expression under UV-B stress as compared to untreated control cultures. Although this study deals with a limited number of proteins, identification of differentially expressed proteins reported herein may prove useful in future studies especially for assessing their significance in the protection mechanism of bacteria against UV-B radiation stress.

Aerobic bacterial profile and antibiotic resistance in patients with diabetic foot infections

INTRODUCTION

This study aimed to determine the frequencies of bacterial isolates cultured from diabetic foot infections and assess their resistance and susceptibility to commonly used antibiotics.

METHODS

This prospective study included 41 patients with diabetic foot lesions. Bacteria were isolated from foot lesions, and their antibiotic susceptibility pattern was determined using the Kirby-Bauer disk diffusion method and/or broth method [minimum inhibitory concentration (MIC)].

RESULTS

The most common location of ulceration was the toe (54%), followed by the plantar surface (27%) and dorsal portion (19%). A total of 89 bacterial isolates were obtained from 30 patients. The infections were predominantly due to Gram-positive bacteria and polymicrobial bacteremia. The most commonly isolated Gram-positive bacteria were Staphylococcus aureus, followed by Staphylococcus saprophyticus, Staphylococcus epidermidis, Streptococcus agalactiae, and Streptococcus pneumoniae. The most commonly isolated Gram-negative bacteria were Proteus spp. and Enterobacterspp., followed by Escherichia coli, Pseudomonasspp., and Citrobacterspp. Nine cases of methicillin-resistant Staphylococcus aureus (MRSA) had cefoxitin resistance, and among these MRSA isolates, 3 were resistant to vancomycin with the MIC technique. The antibiotic imipenem was the most effective against both Gram-positive and Gram-negative bacteria, and gentamicin was effective against Gram-negative bacteria.

CONCLUSIONS

The present study confirmed the high prevalence of multidrug-resistant pathogens in diabetic foot ulcers. It is necessary to evaluate the different microorganisms infecting the wound and to know the antibiotic susceptibility patterns of the isolates from the infected wound. This knowledge is crucial for planning treatment with the appropriate antibiotics, reducing resistance patterns, and minimizing healthcare costs.

Isolation and Genetic Analysis of Multidrug Resistant Bacteria from Diabetic Foot Ulcers

Severe diabetic foot ulcers (DFUs) patients visiting Sir Sunderlal Hospital, Banaras Hindu University, Varanasi, were selected for this study. Bacteria were isolated from swab and deep tissue of 42 patients, for examining their prevalence and antibiotic sensitivity. DFUs of majority of the patients were found infected with Enterococcus spp. (47.61%), Escherichia coli (35.71%), Staphylococcus spp. (33.33%), Alcaligenes spp. (30.95%), Pseudomonas spp. (30.95%), and Stenotrophomonas spp. (30.95%). Antibiotic susceptibility assay of 142 bacteria with 16 antibiotics belonging to eight classes showed the presence of 38 (26.76%) isolates with multidrug resistance (MDR) phenotypes. MDR character appeared to be governed by integrons as class 1 integrons were detected in 26 (68.42%) isolates. Altogether six different arrays of genes (aadA1, aadB, aadAV, dhfrV, dhfrXII, and dhfrXVII) were found within class 1 integron. Gene cassette dhfrAXVII-aadAV (1.6 kb) was present in 12 (3 Gram positive and 9 Gram negative) isolates and was conserved across all the isolates as evident from RFLP analysis. In addition to the presence of class 1 integron, six β-lactamase resistance encoding genes namely bla TEM, bla SHV, bla OXA, bla CTX-M-gp1, bla CTX-M-gp2, and bla CTX-M-gp9 and two methicillin resistance genes namely mecA and femA and vancomycin resistance encoding genes (vanA and vanB) were identified in different isolates. Majority of the MDR isolates were positive for bla TEM (89.47%), bla OXA (52.63%), and bla CTX-M-gp1 (34.21%). To our knowledge, this is the first report of molecular characterization of antibiotic resistance in bacteria isolated from DFUs from North India. In conclusion, findings of this study suggest that class-1 integrons and β-lactamase genes contributed to the MDR in above bacteria.

Pitfalls in diagnosing diabetic foot infections

Although the diagnosis of a diabetic foot infection is made based on clinical symptoms and signs, we also use blood laboratory, microbiological and radiological studies to make treatment decisions. All of these diagnostic studies have pitfalls that can lead to a delay in diagnosis. Such delays will likely lead to further tissue damage and to a higher chance of amputation. One of these pitfalls is that some clinicians rely on microbiological, rather than clinical data, to diagnose infection. Though subjective by nature, clinical signs predict outcome of foot infections accurately. Another pitfall is that microbiological data can be misleading. All wounds harbour microorganisms; therefore, a positive wound culture does not mean that a wound is infected. Furthermore, the outcome of cultures of wound swabs does not correlate well with culture results of tissue biopsies. Therapy guidance by wound swab will likely lead to overtreatment of non-pathogenic organisms. Genotyping might have a role in identifying previously unrecognized (combinations of) pathogens in diabetic foot infection, bacteria in sessile phenotype and non-culturable pathogens, e.g. in cases where antibiotics have already been administered. One more pitfall is that the diagnosis of osteomyelitis remains difficult. Although the result of percutaneous bone biopsy is the reference standard for osteomyelitis, some other diagnostic modalities can aid in the diagnosis. A combination of several of these diagnostic tests is probably a good strategy to achieve a higher diagnostic accuracy. Relying on a single test will likely lead to misidentification of patients with osteomyelitis with associated overtreatment and undertreatment.

Choice of wound care in diabetic foot ulcer: A practical approach

Diabetic foot ulcers are the consequence of multiple factors including peripheral neuropathy, decreased blood supply, high plantar pressures, etc., and pose a significant risk for morbidity, limb loss and mortality. The critical aspects of the wound healing mechanism and host physiological status in patients with diabetes necessitate the selection of an appropriate treatment strategy based on the complexity and type of wound. In addition to systemic antibiotics and surgical intervention, wound care is considered to be an important component of diabetic foot ulcer management. This article will focus on the use of different wound care materials in diabetic foot. From a clinical perspective, it is important to decide on the wound care material depending on the type and grade of the ulcer. This article will also provide clinicians with a simple approach to the choice of wound care materials in diabetic foot ulcer.

2012 Infectious Diseases Society of America clinical practice guideline for the diagnosis and treatment of diabetic foot infections

Foot infections are a common and serious problem in persons with diabetes. Diabetic foot infections (DFIs) typically begin in a wound, most often a neuropathic ulceration. While all wounds are colonized with microorganisms, the presence of infection is defined by ≥2 classic findings of inflammation or purulence. Infections are then classified into mild (superficial and limited in size and depth), moderate (deeper or more extensive), or severe (accompanied by systemic signs or metabolic perturbations). This classification system, along with a vascular assessment, helps determine which patients should be hospitalized, which may require special imaging procedures or surgical interventions, and which will require amputation. Most DFIs are polymicrobial, with aerobic gram-positive cocci (GPC), and especially staphylococci, the most common causative organisms. Aerobic gram-negative bacilli are frequently copathogens in infections that are chronic or follow antibiotic treatment, and obligate anaerobes may be copathogens in ischemic or necrotic wounds. Wounds without evidence of soft tissue or bone infection do not require antibiotic therapy. For infected wounds, obtain a post-debridement specimen (preferably of tissue) for aerobic and anaerobic culture. Empiric antibiotic therapy can be narrowly targeted at GPC in many acutely infected patients, but those at risk for infection with antibiotic-resistant organisms or with chronic, previously treated, or severe infections usually require broader spectrum regimens. Imaging is helpful in most DFIs; plain radiographs may be sufficient, but magnetic resonance imaging is far more sensitive and specific. Osteomyelitis occurs in many diabetic patients with a foot wound and can be difficult to diagnose (optimally defined by bone culture and histology) and treat (often requiring surgical debridement or resection, and/or prolonged antibiotic therapy). Most DFIs require some surgical intervention, ranging from minor (debridement) to major (resection, amputation). Wounds must also be properly dressed and off-loaded of pressure, and patients need regular follow-up. An ischemic foot may require revascularization, and some nonresponding patients may benefit from selected adjunctive measures. Employing multidisciplinary foot teams improves outcomes. Clinicians and healthcare organizations should attempt to monitor, and thereby improve, their outcomes and processes in caring for DFIs.

Molecular and culture-based assessment of the microbial diversity of diabetic chronic foot wounds and contralateral skin sites

Wound debridement samples and contralateral (healthy) skin swabs acquired from 26 patients attending a specialist foot clinic were analyzed by differential isolation and eubacterium-specific PCR-denaturing gradient gel electrophoresis (DGGE) in conjunction with DNA sequencing. Thirteen of 26 wounds harbored pathogens according to culture analyses, with Staphylococcus aureus being the most common (13/13). Candida (1/13), pseudomonas (1/13), and streptococcus (7/13) were less prevalent. Contralateral skin was associated with comparatively low densities of bacteria, and overt pathogens were not detected. According to DGGE analyses, all wounds contained significantly greater eubacterial diversity than contralateral skin (P < 0.05), although no significant difference in total eubacterial diversity was detected between wounds from which known pathogens had been isolated and those that were putatively uninfected. DGGE amplicons with homology to Staphylococcus sp. (8/13) and S. aureus (2/13) were detected in putatively infected wound samples, while Staphylococcus sp. amplicons were detected in 11/13 noninfected wounds; S. aureus was not detected in these samples. While a majority of skin-derived DGGE consortial fingerprints could be differentiated from wound profiles through principal component analysis (PCA), a large minority could not. Furthermore, wounds from which pathogens had been isolated could not be distinguished from putatively uninfected wounds on this basis. In conclusion, while chronic wounds generally harbored greater eubacterial diversity than healthy skin, the isolation of known pathogens was not associated with qualitatively distinct consortial profiles or otherwise altered diversity. The data generated support the utility of both culture and DGGE for the microbial characterization of chronic wounds.

Sepsis in diabetes: A bad duo

Increasing incidence of morbidity and mortality of diabetic subjects due to infection necessitates the understanding of its patho-biology and further remedial measures for its prevention and treatment. The increased incidence of infection is because of systemic illness that has compromising effects on multiple organs including the nervous, vascular, musculoskeletal, and immunologic systems of the diabetic patients. Many factors contribute to this condition including hyperglycemia, insulin deficiency, ischemia and impaired immunity. Sepsis, as a separate entity, lead to destruction of cytokine network that can be fatal. Compromised defense mechanisms due to sepsis and cytokine dysregulation in diabetic patients make the situation worse. Early identification of local infection by applying advanced molecular tools, appropriate selection of antibiotics, intensive wound management, control of glycemic status and supportive treatment can reduce the rate of morbidity and mortality due to sepsis in patients with diabetes.