scholarly journals Time-dependent displacement of commensal skin microbes by pathogens at the site of colorectal surgery

2020 ◽  
Author(s):  
Jennifer Holder-Murray ◽  
Andrew Yeh ◽  
Matthew Rogers ◽  
Brian Firek ◽  
Brandon Mahler ◽  
...  
Keyword(s):  
Colorectal Surgery ◽  
Subcutaneous Fat ◽  
Gastrointestinal Surgery ◽  
Alpha Diversity ◽  
Surgical Site Infections ◽  
Perioperative Period ◽  
Early Postoperative Period ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Elective Colorectal Surgery

Abstract Objective: To characterize perioperative changes of the skin microbiome in patients undergoing elective colorectal surgery and to determine this relationship with surgical site infections (SSIs).Summary of Background Data: Despite the prevalence and significance of SSIs, their pathogenesis remains poorly understood. Although the complexity of the human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to the incidence of SSIs. Methods: Skin swabs of the abdominal wall and chest wall from 60 study subjects were collected before and after colorectal surgery, in addition to intraoperative samples including subcutaneous fat and colonic contents. Bacterial 16S rRNA gene sequences were sequenced and analyzed. Results: Alpha diversity on the skin decreased in the perioperative period but later recovered at the postoperative clinic visit. Alpha diversity of the subcutaneous fat increased significantly between the beginning and end of these operations, with an increase in abundance of gut microbes also seen within luminal contents after colon resection. In the early postoperative period, the abundance of Enterobacteriaceae increased at the site of surgical incision, with a concomitant decrease in commensals including Corynebacterium and Propionibacterium. Only one patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was later cultured from wound drainage at the time of SSI diagnosis. Conclusions: In most patients, we observed a transient postoperative loss of skin commensals at the surgical site, which were replaced by potential pathogens and anaerobes from the gut. We postulate that real time monitoring of the skin microbiome, in parallel with improved knowledge with the gut microbiome and gastrointestinal surgery, could provide actionable findings about the pathogenesis of SSIs.

scholarly journals Time-Dependent Displacement of Commensal Skin Microbes by Pathogens at the Site of Colorectal Surgery

2020 ◽  
Author(s):  
Jennifer Holder-Murray ◽  
Andrew Yeh ◽  
Matthew B Rogers ◽  
Brian Firek ◽  
Brandon Mahler ◽  
...  
Keyword(s):  
Colorectal Surgery ◽  
Alpha Diversity ◽  
Surgical Site Infections ◽  
Clinic Visit ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Healthy Human ◽  
Culture Independent ◽  
Skin Commensals

Abstract Background Although the healthy human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to surgical site infections (SSIs). Our objective in this study was to characterize temporal and spatial variation in the skin microbiota of patients undergoing colorectal surgery and determine if dysbiosis contributes to SSIs. Methods Sixty one adults scheduled to undergo elective colon or rectal resection were identified by convenience sampling. By analyzing bacterial 16S rRNA gene sequences isolated from clinical samples, we used a culture-independent strategy to monitor perioperative changes in microbial diversity of fecal samples and the skin. Results A total of 990 samples from 61 patients were analyzed. Alpha diversity on the skin decreased after surgery but later recovered at the postoperative clinic visit. In most patients, we observed a transient postoperative loss of skin commensals (Corynebacterium and Propionibacterium) at the surgical site, which were replaced by potential pathogens and intestinal anaerobes (eg, Enterobacteriaceae). These changes were not observed on skin that was uninvolved in the surgical incision (chest wall). One patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was also cultured from wound drainage. Conclusions We observed reproducible perioperative changes in the skin microbiome following surgery. The low incidence of SSIs in this cohort precluded analysis of associations between dysbiosis and infection. We postulate that real-time monitoring of the skin microbiome could provide actionable findings about the pathogenesis of SSIs.

Meta-analysis of the efficacy of ertapenem in preventing SSIs after elective colorectal surgery

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
C Vicentini ◽  
A Corradi ◽  
S Corcione ◽  
F G De Rosa ◽  
C M Zotti
Keyword(s):  
Colorectal Surgery ◽  
Antimicrobial Prophylaxis ◽  
Meta Analysis ◽  
Carbapenem Resistance ◽  
Surgical Site Infections ◽  
Resistant Isolate ◽  
Elective Colorectal Surgery ◽  
Surgical Antibiotic Prophylaxis ◽  
Surgical Antimicrobial Prophylaxis ◽  
Reported Data

Abstract Background The efficacy of standard surgical antimicrobial prophylaxis (SAP) regimens in preventing surgical site infections (SSIs) after colorectal surgery is declining, along with rising rates of intestinal colonization with antimicrobial resistant (AMR) Enterobacteriaceae and Bacteroides spp. Ertapenem has been approved by the FDA and EMA for SAP in this context, however it has not been used extensively for this indication out of concern for increasing carbapenem-resistance rates. A limited number of studies have investigated the efficacy of ertapenem in preventing SSIs after colorectal surgery, comparing ertapenem with different agents or combinations of agents. Methods A systematic review was conducted following the PRISMA checklist. PubMed, Embase and Cochrane databases were searched for studies measuring the efficacy of ertapenem in preventing SSIs following elective colorectal procedures. Studies were considered eligible if they reported extractable data on the proportion of SSIs and/or on the proportion of AMR pathogens isolated from SSIs. Data from all ertapenem study arms were extracted. A random effects meta-analysis was performed to estimate the overall proportion of SSI. Results Of 1109 identified studies, 5 met the inclusion criteria and were included in the meta-analysis, totalling 3176 participants. The pooled proportion of SSI was 0.10 (95% CI 0.05-0.18; I2=96%; τ2=0.6323; p ≤ 0.01). Only one study reported data on carbapenem resistance: out of 124 isolates from 30 patients, 1 gram negative carbapenem-resistant isolate was identified. Conclusions The pooled proportion of SSI using ertapenem as SAP found in this study is in line with the proportion of SSI using standard SAP found by a recent meta-analysis (Gandra, 2019). According to this analysis, the benefit of ertapenem does not outweigh the risk of further promoting AMR, although results should be interpreted with caution due to the high heterogeneity among included studies. Key messages According to this study, the efficacy of ertapenem in preventing surgical site infections after elective colorectal surgery is comparable to the efficacy of standard surgical antibiotic prophylaxis. The emergence of carbapenem resistance after surgical prophylaxis with ertapenem should be further investigated through longer term studies before widespread use for this indication.

scholarly journals Role of oral antibiotics for prophylaxis against surgical site infections after elective colorectal surgery

2017 ◽  
Vol 9 (12) ◽  
pp. 246-255 ◽  
Author(s):  
Shamir O Cawich ◽  
Sachin Teelucksingh ◽  
Samara Hassranah ◽  
Vijay Naraynsingh
Keyword(s):  
Colorectal Surgery ◽  
Surgical Site Infections ◽  
Oral Antibiotics ◽  
Elective Colorectal Surgery

scholarly journals A contribution to the larval amphibian microbiome: characterization of bacterial microbiome of Ichthyophis bannanicus (Order: Gymnophiona) and comparison with the other two amphibian orders

2021 ◽  
Author(s):  
Amrapali Rajput ◽  
Shipeng Zhou ◽  
Madhava Meegaskumbura
Keyword(s):  
Gut Microbiome ◽  
Alpha Diversity ◽  
The Other ◽  
Rrna Gene ◽  
Scaling Analysis ◽  
Skin Microbiome ◽  
Sequencing Platform ◽  
Bacterial Phyla ◽  
Faecal Samples ◽  
Skin Samples

It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.

scholarly journals Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

2019 ◽  
Author(s):  
C Pepe-Ranney ◽  
C Keyser ◽  
J Trimble ◽  
B Bissinger
Keyword(s):  
North Carolina ◽  
Community Assembly ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Skin Microbiome ◽  
Microbiome Composition ◽  
Pests And Diseases ◽  
Sub Saharan ◽  
Surrounding Soil

AbstractFarmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

Surveillance of surgical site infections in elective colorectal surgery. Results of the VINCat Program (2007–2010)

2012 ◽  
Vol 30 ◽  
pp. 20-25 ◽  
Author(s):  
Miquel Pujol ◽  
Enric Limón ◽  
Joaquín López-Contreras ◽  
Montserrat Sallés ◽  
Feliu Bella ◽  
...  
Keyword(s):  
Colorectal Surgery ◽  
Surgical Site Infections ◽  
Elective Colorectal Surgery
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