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ABSTRACT: The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point, or measures of dissimilarity between pairs of time-points. Although these approaches, which treat data as static snapshots of microbial communities, can identify shifts in overall community structure, they fail to capture the dynamic properties of individual members of the microbiota and their contributions to the underlying time-varying behavior of host ecosystems. To address the limitations of current methods, we present a computational framework that uses continuous-time dynamical models coupled with Bayesian dimensionality adaptation methods to identify time-dependent signatures of individual microbial taxa within a host as well as across multiple hosts. We apply our framework to a publicly available dataset of 16S rRNA gene sequences from stool samples collected over ten months from multiple human subjects, each of whom received repeated courses of oral antibiotics. Using new diversity measures enabled by our framework, we discover groups of both phylogenetically close and distant bacterial taxa that exhibit consensus responses to antibiotic exposure across multiple human subjects. These consensus responses reveal a timeline for equilibration of sub-communities of micro-organisms with distinct physiologies, yielding insights into the successive changes that occur in microbial populations in the human gut after antibiotic treatments. Additionally, our framework leverages microbial signatures shared among human subjects to automatically design optimal experiments to interrogate dynamic properties of the microbiota in new studies. Overall, our approach provides a powerful, general-purpose framework for understanding the dynamic behaviors of complex microbial ecosystems, which we believe will prove instrumental for future studies in this field.
PLoS Computational Biology 08/2012; 8(8):e1002624. · 5.22 Impact Factor
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ABSTRACT: The link between histologic acute chorioamnionitis and infection is well established in preterm deliveries, but less well-studied in term pregnancies, where infection is much less common.
We conducted a secondary analysis among 195 low-risk women with term pregnancies enrolled in a randomized trial. Histologic and microbiologic evaluation of placentas included anaerobic and aerobic cultures (including mycoplasma/ureaplasma species) as well as PCR. Infection was defined as ≥1,000 cfu of a single known pathogen or a ≥2 log difference in counts for a known pathogen versus other organisms in a mixed culture. Placental membranes were scored and categorized as: no chorioamnionitis, Grade 1 (subchorionitis and patchy acute chorioamnionitis), or Grade 2 (severe, confluent chorioamnionitis). Grade 1 or grade 2 histologic chorioamnionitis was present in 34% of placentas (67/195), but infection was present in only 4% (8/195). Histologic chorioamnionitis was strongly associated with intrapartum fever >38°C [69% (25/36) fever, 26% (42/159) afebrile, P<.0001]. Fever occurred in 18% (n = 36) of women. Most febrile women [92% (33/36)] had received epidural for pain relief, though the association with fever was present with and without epidural. The association remained significant in a logistic regression controlling for potential confounders (OR = 5.8, 95% CI = 2.2,15.0). Histologic chorioamnionitis was also associated with elevated serum levels of interleukin-8 (median = 1.3 pg/mL no histologic chorioamnionitis, 1.5 pg/mL Grade 1, 2.1 pg/mL Grade 2, P = 0.05) and interleukin-6 (median levels = 2.2 pg/mL no chorioamnionitis, 5.3 pg/mL Grade 1, 24.5 pg/mL Grade 2, P = 0.02) at admission for delivery as well as higher admission WBC counts (mean = 12,000 cells/mm(3) no chorioamnionitis, 13,400 cells/mm(3) Grade 1, 15,700 cells/mm(3) Grade 2, P = 0.0005).
Our results suggest histologic chorioamnionitis at term most often results from a noninfectious inflammatory process. It was strongly associated with fever, most of which was related to epidural used for pain relief. A more 'activated' maternal immune system at admission was also associated with histologic chorioamnionitis.
PLoS ONE 01/2012; 7(3):e31819. · 4.09 Impact Factor
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Laura E Riley,
Ann C Celi, Andrew B Onderdonk,
Drucilla J Roberts,
Lise C Johnson,
Lawrence C Tsen,
Lisa Leffert,
May C M Pian-Smith,
Linda J Heffner,
Susan T Haas,
Ellice S Lieberman
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ABSTRACT: To investigate the role of infection and noninfectious inflammation in epidural analgesia-related fever.
This was an observational analysis of placental cultures and serum admission and postpartum cytokine levels obtained from 200 women at low risk recruited during the prenatal period.
Women receiving labor epidural analgesia had fever develop more frequently (22.7% compared with 6% no epidural; P=.009) but were not more likely to have placental infection (4.7% epidural, 4.0% no epidural; P>.99). Infection was similar regardless of maternal fever (5.4% febrile, 4.3% afebrile; P=.7). Median admission interleukin (IL)-6 levels did not differ according to later epidural (3.2 pg/mL compared with 1.6 pg/mL no epidural; P=.2), but admission IL-6 levels greater than 11 pg/mL were associated with an increase in fever among epidural users (36.4% compared with 15.7% for 11 pg/mL or less; P=.008). At delivery, both febrile and afebrile women receiving epidural had higher IL-6 levels than women not receiving analgesia.
Epidural-related fever is rarely attributable to infection but is associated with an inflammatory state.
Obstetrics and Gynecology 03/2011; 117(3):588-95. · 4.73 Impact Factor
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ABSTRACT: The ability of Francisella tularensis to replicate in macrophages is critical for its pathogenesis, therefore intracellular growth assays are important tools for assessing virulence. We show that two lysis solutions commonly used in these assays, deionized water and deoxycholate in PBS, lead to highly inaccurate measurements of intracellular bacterial survival.
Journal of microbiological methods 03/2011; 85(3):230-2. · 2.43 Impact Factor
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mBio 01/2011; 2(2). · 5.31 Impact Factor
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ABSTRACT: The fetal response to intrauterine inflammatory stimuli appears to contribute to the onset of preterm labor as well as fetal injury, especially affecting newborns of extremely low gestational age. To investigate the role of placental colonization by specific groups of microorganisms in the development of inflammatory responses present at birth, we analyzed 25 protein biomarkers in dry blood spots obtained from 527 newborns delivered by Caesarean section in the 23rd to 27th gestation weeks. Bacteria were detected in placentas and characterized by culture techniques. Odds ratios for having protein concentrations in the top quartile for gestation age for individual and groups of microorganisms were calculated. Mixed bacterial vaginosis (BV) organisms were associated with a proinflammatory pattern similar to those of infectious facultative anaerobes. Prevotella and Gardnerella species, anaerobic streptococci, peptostreptococci, and genital mycoplasmas each appeared to be associated with a different pattern of elevated blood levels of inflammation-related proteins. Lactobacillus was associated with low odds of an inflammatory response. This study provides evidence that microorganisms colonizing the placenta provoke distinctive newborn inflammatory responses and that Lactobacillus may suppress these responses.
mBio 01/2011; 2(1):e00280-10. · 5.31 Impact Factor
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ABSTRACT: Gordonia species are aerobic actinomycetes recently recognized as causing human disease, often in the setting of intravascular catheter-related infections. We describe a case of Gordonia bronchialis bacteremia and pleural space infection in the absence of an indwelling intravascular catheter and review the breadth of reported infections with this emerging pathogen.
Journal of clinical microbiology 01/2011; 49(4):1662-6. · 4.16 Impact Factor
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ABSTRACT: Several broad-spectrum microbicides, including cellulose sulfate (CS), have passed conventional preclinical and phase I clinical safety evaluation and yet have failed to protect women from acquiring HIV-1 in phase II/III trials. Concerns have been raised that current preclinical algorithms are deficient in addressing the complexity of the microflora-regulated vaginal mucosal barrier. We applied a novel microflora-colonized model to evaluate CS and hydroxyethylcellulose (HEC), which is used as a "universal placebo" in microbicide trials. Cervicovaginal epithelial cultures were colonized with normal vaginal microflora isolates representing common Lactobacillus species used as probiotics (L. acidophilus and L. crispatus) or Prevotella bivia and Atopobium vaginae, most prevalent in the disturbed microflora of bacterial vaginosis (BV). At baseline, all strains maintained constant epithelium-associated CFUs without inducing cytotoxicity and apoptosis. CS selectively reduced epithelium-associated CFUs and (to a lesser extent) planktonic CFUs, most significantly affecting L. crispatus. Inducing only minor changes in sterile epithelial cultures, CS induced expression of innate immunity mediators (RANTES, interleukin-8 [IL-8], and secretory leukocyte protease inhibitor [SLPI]) in microflora-colonized epithelia, most significantly potentiating effects of bacteria causing BV. In the absence of CS, all bacterial strains except L. acidophilus activated NF-κB, although IL-8 and RANTES levels were increased by the presence of BV-causing bacteria only. CS enhanced NF-κB activation in a dose-dependent manner under all conditions, including L. acidophilus colonization. HEC remained inert. These results offer insights into possible mechanisms of CS clinical failure. The bacterially colonized cervicovaginal model reveals unique aspects of microflora-epithelium-drug interactions and innate immunity in the female genital tract and should become an integral part of preclinical safety evaluation of anti-HIV microbicides and other vaginal formulations. IMPORTANCE: This report provides experimental evidence supporting the concept that the vaginal microflora regulates the epithelial innate immunity in a species- and strain-specific manner and that topically applied microbicides may alter both the bacterial and epithelial components of this homeostatic interaction. Our data also highlight the importance of differentiating the effects of biomedical interventions on epithelium-associated versus conventional planktonic bacterial growth when assessing vaginal mucosal health and immunity.
mBio 01/2011; 2(6):e00168-11. · 5.31 Impact Factor
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Wendy S Garrett,
Carey A Gallini,
Tanya Yatsunenko,
Monia Michaud,
Andrea DuBois,
Mary L Delaney,
Shivesh Punit,
Maria Karlsson,
Lynn Bry,
Jonathan N Glickman,
Jeffrey I Gordon, Andrew B Onderdonk,
Laurie H Glimcher
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ABSTRACT: Disruption of homeostasis between the host immune system and the intestinal microbiota leads to inflammatory bowel disease (IBD). Whether IBD is instigated by individual species or disruptions of entire microbial communities remains controversial. We characterized the fecal microbial communities in the recently described T-bet(-/-) ×Rag2(-/-) ulcerative colitis (TRUC) model driven by T-bet deficiency in the innate immune system. 16S rRNA-based analysis of TRUC and Rag2(-/-) mice revealed distinctive communities that correlate with host genotype. The presence of Klebsiella pneumoniae and Proteus mirabilis correlates with colitis in TRUC animals, and these TRUC-derived strains can elicit colitis in Rag2(-/-) and WT adults but require a maternally transmitted endogenous microbial community for maximal intestinal inflammation. Cross-fostering experiments indicated a role for these organisms in maternal transmission of disease. Our findings illustrate how gut microbial communities work in concert with specific culturable colitogenic agents to cause IBD.
Cell host & microbe 09/2010; 8(3):292-300. · 13.02 Impact Factor
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ABSTRACT: Menstrual Toxic Shock Syndrome (mTSS) is thought to be associated with the vaginal colonization with specific strains of Staphylococcus aureus TSST-1 in women who lack sufficient antibody titers to this toxin. There are no published studies that examine the seroconversion in women with various colonization patterns of this organism. Thus, the aim of this study was to evaluate the persistence of Staphylococcus aureus colonization at three body sites (vagina, nares, and anus) and serum antibody to toxic shock syndrome toxin-producing Staphylococcus aureus among a small group of healthy, menstruating women evaluated previously in a larger study.
One year after the completion of that study, 311 subjects were recalled into 5 groups. Four samples were obtained from each participant at several visits over an additional 6-11 month period: 1) an anterior nares swab; 2) an anal swab; 3) a vagina swab; and 4) a blood sample. Gram stain, a catalase test, and a rapid S. aureus-specific latex agglutination test were performed to phenotypically identify S. aureus from sample swabs. A competitive ELISA was used to quantify TSST-1 production. Human TSST-1 IgG antibodies were determined from the blood samples using a sandwich ELISA method.
We found only 41% of toxigenic S. aureus and 35.5% of non-toxigenic nasal carriage could be classified as persistent. None of the toxigenic S. aureus vaginal or anal carriage could be classified as persistent. Despite the low persistence of S. aureus colonization, subjects colonized with a toxigenic strain were found to display distributions of antibody titers skewed toward higher titers than other subjects. Seven percent (5/75) of subjects became seropositive during recall, but none experienced toxic shock syndrome-like symptoms.
Nasal carriage of S. aureus appears to be persistent and the best predicator of subsequent colonization, whereas vaginal and anal carriage appear to be more transient. From these findings, it appears that antibody titers in women found to be colonized with toxigenic S. aureus remained skewed toward higher titers whether or not the colonies were found to be persistent or transient in nature. This suggests that colonization at some point in time is sufficient to elevate antibody titer levels and those levels appear to be persistent. Results also indicate that women can become seropositive without experiencing signs or symptoms of toxic shock syndrome.
BMC Infectious Diseases 01/2010; 10:249. · 3.12 Impact Factor
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Edward E S Nieuwenhuis,
Tetsuya Matsumoto,
Dicky Lindenbergh,
Rob Willemsen,
Arthur Kaser,
Ytje Simons-Oosterhuis,
Sylvia Brugman,
Keizo Yamaguchi,
Hiroki Ishikawa,
Yuji Aiba,
Yasuhiro Koga,
Janneke N Samsom,
Kenshiro Oshima,
Mami Kikuchi,
Johanna C Escher,
Masahira Hattori, Andrew B Onderdonk,
Richard S Blumberg
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ABSTRACT: The accumulation of certain species of bacteria in the intestine is involved in both tissue homeostasis and immune-mediated pathologies. The host mechanisms involved in controlling intestinal colonization with commensal bacteria are poorly understood. We observed that under specific pathogen-free or germ-free conditions, intragastric administration of Pseudomonas aeruginosa, E. coli, Staphylococcus aureus, or Lactobacillus gasseri resulted in increased colonization of the small intestine and bacterial translocation in mice lacking Cd1d, an MHC class I-like molecule, compared with WT mice. In contrast, activation of Cd1d-restricted T cells (NKT cells) with alpha-galactosylceramide caused diminished intestinal colonization with the same bacterial strains. We also found prominent differences in the composition of intestinal microbiota, including increased adherent bacteria, in Cd1d-/- mice in comparison to WT mice under specific pathogen-free conditions. Germ-free Cd1d-/- mice exhibited a defect in Paneth cell granule ultrastructure and ability to degranulate after bacterial colonization. In vitro, NKT cells were shown to induce the release of lysozyme from intestinal crypts. Together, these data support a role for Cd1d in regulating intestinal colonization through mechanisms that include the control of Paneth cell function.
The Journal of clinical investigation 05/2009; 119(5):1241-50. · 15.39 Impact Factor
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Andrew B Onderdonk
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ABSTRACT: It is hard for me to believe that I have served for almost ten years as Editor in Chief for the Journal of Clinical Microbiology. ...
Journal of clinical microbiology 04/2009; · 4.16 Impact Factor
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ABSTRACT: The present study compares the efficacy of various disinfectants against Bacillus anthracis spores. While Bleach Rite(®) and 10% bleach reduce spore numbers by 90% within 10 minutes, a long contact time is required for complete disinfection. By contrast, although SporGon(®) did not initially reduce the number of spores as quickly as Bleach Rite or 10% bleach, shorter contact times were required for complete eradication of viable spores.
Applied biosafety : journal of the American Biological Safety Association. 01/2009; 14(1):7-10.
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Erick Forno, Andrew B Onderdonk,
John McCracken,
Augusto A Litonjua,
Daniel Laskey,
Mary L Delaney,
Andrea M Dubois,
Diane R Gold,
Louise M Ryan,
Scott T Weiss,
Juan C Celedón
Clinical and Molecular Allergy 10/2008; · 1.39 Impact Factor
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ABSTRACT: The overtly healthy, nonpregnant uterus harbors bacteria, Mycoplasma and Ureaplasma. The extent of colonization remains elusive, as are relationships between isolated microorganisms, preterm labor and fetal inflammation.
Biopsy specimens of chorion parenchyma from 1083 placentas delivered before the beginning of the 28th week of gestation were cultured, and the placentas were examined histologically. The frequencies of individual microorganisms and groups of microorganisms were evaluated in strata of processes leading to preterm delivery, routes of delivery, gestational age, and placenta morphology.
Placentas delivered by cesarean section with preeclampsia had the lowest bacterial recovery rate (25%). Preterm labor had the highest rates, which decreased with increasing gestational age from 79% at 23 weeks to 43% at 27 weeks. The presence of microorganisms in placenta parenchyma was associated with the presence of neutrophils in the fetal stem vessels of the chorion or in the vessels of the umbilical cord.
The high rate of colonization appears to coincide with phenomena associated with preterm delivery and gestational age. The presence of microorganisms within placenta parenchyma is biologically important.
American journal of obstetrics and gynecology 08/2008; 199(1):52.e1-52.e10. · 3.28 Impact Factor
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ABSTRACT: To evaluate the adequacy of discharge room cleaning and the impact of a cleaning intervention on the presence of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) on environmental surfaces in intensive care unit (ICU) rooms.
Prospective environmental study.
Convenience sample of ICU rooms in an academic hospital. METHODS AND INTERVENTION: The intervention consisted of (1) a change from the use of pour bottles to bucket immersion for applying disinfectant to cleaning cloths, (2) an educational campaign, and (3) feedback regarding adequacy of discharge cleaning. Cleaning of 15 surfaces was evaluated by inspecting for removal of a preapplied mark, visible only with an ultraviolet lamp ("black light"). Six surfaces were cultured for MRSA or VRE contamination. Outcomes of mark removal and culture positivity were evaluated by chi(2) testing and generalized linear mixed models, clustering by room.
The black-light mark was removed from 44% of surfaces at baseline, compared with 71% during the intervention (P < .001). The intervention increased the likelihood of removal of black-light marks after discharge cleaning (odds ratio, 4.4; P < .001), controlling for ICU type (medical vs surgical) and type of surface. The intervention reduced the likelihood of an environmental culture positive for MRSA or VRE (proportion of cultures positive, 45% at baseline vs 27% during the intervention; adjusted odds ratio, 0.4; P = .02). Broad, flat surfaces were more likely to be cleaned than were doorknobs and sink or toilet handles.
Increasing the volume of disinfectant applied to environmental surfaces, providing education for Environmental Services staff, and instituting feedback with a black-light marker improved cleaning and reduced the frequency of MRSA and VRE contamination.
Infection Control and Hospital Epidemiology 07/2008; 29(7):593-9. · 3.67 Impact Factor
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Susan S Huang,
Daniel J Diekema,
David K Warren,
Gianna Zuccotti,
Patricia L Winokur,
Shailesh Tendolkar,
Linda Boyken,
Rupak Datta,
Rebecca M Jones,
Melissa A Ward,
Tanya Aubrey, Andrew B Onderdonk,
Christian Garcia,
Richard Platt
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ABSTRACT: Invasive disease following methicillin-resistant Staphylococcus aureus (MRSA) detection is common, regardless of whether initial detection involves colonization or infection. We assessed the genetic relatedness of isolates obtained > or =2 weeks apart representing either repeated infections or colonization-infection sets to determine if infections are likely to be caused by previously harbored strains. We found that MRSA infection following initial colonization or infection is caused by the same strain in most cases, suggesting that a single successful attempt at decolonization may prevent the majority of later infection.
Clinical Infectious Diseases 05/2008; 46(8):1241-7. · 9.15 Impact Factor
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ABSTRACT: Major injury is widely thought to predispose the injured host to opportunistic infections. This idea is supported by animal studies showing that major injury causes reduced resistance to polymicrobial sepsis induced by cecal ligation and puncture. Although cecal ligation and puncture represents a clinically relevant sepsis model, we wanted to test whether injury might also lead to greater susceptibility to peritoneal infection caused by a single common pathogen, Escherichia coli. Contrary to our expectation, we show herein that the LD(50) for sham-injured mice was 10(3) CFU of E. coli, whereas the LD(50) for burn-injured mice was 50 x 10(3) CFU at 7 days postinjury. This injury-associated enhanced resistance was apparent as early as 1 day after injury, and maximal resistance was observed at days 7 and 14. We found that burn-injured mice had higher numbers of circulating neutrophils and monocytes than did sham mice before infection and that injured mice were able to recruit greater numbers of neutrophils to the site of infection. Moreover, the peritoneal neutrophils in burn-injured mice were more highly activated than neutrophils from sham mice as determined by Mac-1 expression, superoxide generation, and bactericidal activity. Our findings suggest that the enhanced innate immune response that develops following injury, although it is commonly accepted as the mediator of the detrimental systemic inflammatory response syndrome, may also, in some cases, benefit the injured host by boosting innate immune antimicrobial defenses.
The Journal of Immunology 03/2008; 180(4):2450-8. · 5.79 Impact Factor
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ABSTRACT: The objective of the study was to quantify and identify aerobic and anaerobic bacteria as well as Mycoplasma and Ureaplasma in the chorionic parenchyma.
A sample of the chorionic parenchyma from neonates delivered between 23-27 completed weeks was cultured and tested by polymerase chain reaction (PCR) methods using universal bacterial primers for the presence of bacteria and mycoplasmas.
The culture positive rate was higher for vaginal deliveries (333/489; 68%) than for cesarean sections (363/876; 41%). Thirty percent of all culture-positive samples had only aerobic bacteria, 21% of the samples had only anaerobic bacteria, and 9% of the samples had only Mycoplasma/Ureaplasma. The mean concentration of Mycoplasma/Ureaplasma (4.00 +/- 1.11 log10 CFU/g) was significantly higher (P < .001) than the total count of either aerobes (3.24 +/- 1.12 log10 CFU/g) or anaerobes (2.89 +/- 0.99 log10 CFU/g). Staphylococcus sp. and Corynebacterium sp. as well as organisms associated with bacterial vaginosis were the most frequently recovered. A PCR product was not detected from either randomly selected or known culture-positive samples.
Approximately half of second-trimester placentas harbor organisms within the chorionic plate. The chorion parenchyma appears to harbor constituents that prevent the identification of bacterial deoxyribonucleic acid by PCR methods.
American journal of obstetrics and gynecology 01/2008; 198(1):110.e1-7. · 3.28 Impact Factor
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ABSTRACT: Wound infection is a common complication in diabetic patients. The progressive spread of infections and development of drug-resistant strains underline the need for further insights into bacterial behavior in the host in order to develop new therapeutic strategies. The aim of our study was to develop a large animal model suitable for monitoring the development and effect of bacterial infections in diabetic wounds.
Fourteen excisional wounds were created on the dorsum of diabetic and non-diabetic Yorkshire pigs and sealed with polyurethane chambers. Wounds were either inoculated with 2 x 108 Colony-Forming Units (CFU) of Staphylococcus aureus or injected with 0.9% sterile saline. Blood glucose was monitored daily, and wound fluid was collected for bacterial quantification and measurement of glucose concentration. Tissue biopsies for microbiological and histological analysis were performed at days 4, 8, and 12. Wounds were assessed for reepithelialization and wound contraction.
Diabetic wounds showed a sustained significant infection (>105 CFU/g tissue) compared to non-diabetic wounds (p < 0.05) over the whole time course of the experiment. S. aureus-inoculated diabetic wounds showed tissue infection with up to 8 x 107 CFU/g wound tissue. Non-diabetic wounds showed high bacterial counts at day 4 followed by a decrease and no apparent infection at day 12. Epidermal healing in S. aureus-inoculated diabetic wounds showed a significant delay compared with non-inoculated diabetic wounds (59% versus 84%; p < 0.05) and were highly significant compared with healing in non-diabetic wounds (97%; p < 0.001).
Diabetic wounds developed significantly more sustained infection than non-diabetic wounds. S. aureus inoculation leads to invasive infection and significant wound healing delay and promotes invasive co-infection with endogenous bacteria. This novel wound healing model provides the opportunity to closely assess infections during diabetic wound healing and to monitor the effect of therapeutical agents in vivo.
BMC Surgery 01/2008; 8:5. · 1.33 Impact Factor
