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Long DR, Bryson-Cahn C, Waalkes A, Holmes EA, Penewit K, Tavolaro C, Bellabarba C, Zhang F, Chan JD, Fang FC, Lynch JB, Salipante SJ. Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery. Sci Transl Med 2024; 16:eadk8222. [PMID: 38598612 DOI: 10.1126/scitranslmed.adk8222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Celeste Tavolaro
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlo Bellabarba
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fangyi Zhang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jeannie D Chan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pharmacy, Harborview Medical Center, University of Washington School of Pharmacy, Seattle, WA 98104, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA
| | - John B Lynch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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Uberoi A, McCready-Vangi A, Grice EA. The wound microbiota: microbial mechanisms of impaired wound healing and infection. Nat Rev Microbiol 2024:10.1038/s41579-024-01035-z. [PMID: 38575708 DOI: 10.1038/s41579-024-01035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.
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Affiliation(s)
- Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Gupta S, Poret AJ, Hashemi D, Eseonu A, Yu SH, D'Gama J, Neel VA, Lieberman TD. Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin. Microbiol Spectr 2023; 11:e0330022. [PMID: 36541798 PMCID: PMC9927587 DOI: 10.1128/spectrum.03300-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Infections are relatively rare following cutaneous surgical procedures, despite the potential for wound exposure to pathogens both during surgery and throughout the healing process. Although gut commensals are believed to reduce the risk of intestinal infections, an analogous role for skin commensals has not been described. In fact, the microbiome of normally healing surgical skin wounds has not yet been profiled using culture-independent techniques. We characterized the wound microbiome in 53 patients who underwent skin cancer surgery and healed without signs or symptoms of infection. A week after surgery, several bacterial species displayed significant differences in relative abundance when compared to control, nonoperated skin from the same patient. The relative abundance of the most common bacterium found on intact skin, Cutibacterium acnes, was reduced in wounds 5-fold. Staphylococcus aureus, a frequent cause of postoperative skin infections, was enriched 6.4-fold in clinically noninfected wounds, suggesting active suppression of pathogenicity. Finally, members of the Corynebacterium genus were the dominant organism in postoperative wounds, making up 37% of the average wound microbiome. The enrichment of these bacteria in normally healing wounds suggests that they might be capable of providing colonization resistance. Future studies focused on the biological and clinical significance of the wound microbiome may shed light on normal wound healing and potential therapeutic opportunities to mitigate infection risk. IMPORTANCE Commensal bacteria on skin may limit the ability of pathogenic bacteria to cause clinically significant infections. The bacteria on healing acute wounds, which might provide such a protective effect, have not been described using culture-independent approaches in the absence of antibiotics. We compare the microbiome of wounds a week after skin cancer removal surgery with intact skin from the same patient. We find that the potentially pathogenic species S. aureus is common on these healing wounds despite the absence of symptoms or signs of infection. We report that bacteria often considered as potential skin probiotics, including Staphylococcus epidermidis, do not reach high relative abundance in wound microbiomes. In contrast, specific members of the Corynebacterium genus, rarely associated with infections, were significantly enriched in healing wounds compared to intact skin. Future work is needed to see if Corynebacterium species or derivatives thereof could be employed to lower the risk of wound infection.
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Affiliation(s)
- Sameer Gupta
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | - Alexandra J. Poret
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David Hashemi
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | | | - Sherry H. Yu
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | | | - Victor A. Neel
- Department of Dermatology, MGH, Boston, Massachusetts, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Ragon Institute of MIT, MGH, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Abbas M, Gaïa N, Buchs NC, Delaune V, Girard M, Andrey DO, Meyer J, Schrenzel J, Ris F, Harbarth S, Lazarevic V. Changes in the gut bacterial communities in colon cancer surgery patients: an observational study. Gut Pathog 2022; 14:2. [PMID: 34983654 PMCID: PMC8729125 DOI: 10.1186/s13099-021-00477-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 02/02/2023] Open
Abstract
Background Colon surgery has been shown to modulate the intestinal microbiota. Our objective was to characterize these changes using state-of-the-art next generation sequencing techniques. Methods We performed a single-centre prospective observational cohort study to evaluate the changes in the gut microbiota, i.e., taxon distribution, before and after elective oncologic colon surgery in adult patients with different antimicrobial prophylaxis regimens (standard prophylaxis with cefuroxime/metronidazole versus carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] carriers). We obtained rectal samples on the day of surgery, intraoperative luminal samples, and rectal or stoma samples 3 days after surgery. We performed metataxonomic analysis based on sequencing of the bacterial 16S rRNA gene marker. Similarities and differences between bacterial communities were assessed using Bray–Curtis similarity, visualised using principal coordinates analysis and statistically tested by PERMANOVA. Comparison of taxa relative abundance was performed using ANCOM. Results We included 27 patients between March 27, 2019 and September 17, 2019. The median age was 63.6 years (IQR 56.4–76.3) and 44% were females. Most (81%) patients received standard perioperative prophylaxis as they were not ESBL carriers. There was no significant association between ESBL carriage and differences in gut microbiome. We observed large and significant increases in the genus Enterococcus between the preoperative/intraoperative samples and the postoperative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Conclusion This hypothesis-generating study showed rapid changes in the rectal microbiota following colon cancer surgery. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00477-7.
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Affiliation(s)
- Mohamed Abbas
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Nicolas C Buchs
- Division of Digestive Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Vaihere Delaune
- Division of Digestive Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Diego O Andrey
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Jeremy Meyer
- Division of Digestive Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Bacteriology, Geneva University Hospitals, Geneva, Switzerland
| | - Frédéric Ris
- Division of Digestive Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.,Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
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The Association of Gut Microbiota and Complications in Gastrointestinal-Cancer Therapies. Biomedicines 2021; 9:biomedicines9101305. [PMID: 34680424 PMCID: PMC8533200 DOI: 10.3390/biomedicines9101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
The therapy of gastrointestinal carcinomas includes surgery, chemo- or immunotherapy, and radiation with diverse complications such as surgical-site infection and enteritis. In recent years, the microbiome’s influence on different diseases and complications has been studied in more detail using methods such as next-generation sequencing. Due to the relatively simple collectivisation, the gut microbiome is the best-studied so far. While certain bacteria are sometimes associated with one particular complication, it is often just the loss of alpha diversity linked together. Among others, a strong influence of Fusobacterium nucleatum on the effectiveness of chemotherapies is demonstrated. External factors such as diet or specific medications can also predispose to dysbiosis and lead to complications. In addition, there are attempts to treat developed dysbiosis, such as faecal microbiota transplant or probiotics. In the future, the underlying microbiome should be investigated in more detail for a better understanding of the precipitating factors of a complication with specific therapeutic options.
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