Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study

Abstract

Background:

The human skin microbiome consists of colonizing and pathogen germs. The umbilical dimple is a humid environment prone to bacterial colonization and growth. In the laparoscopic era, the umbilicus has become the most common site of entrance into the peritoneum. The aim of this study was to describe the characteristics of umbilical microflora before antiseptic skin preparation.

Methods:

Descriptive single-center study. A series of patients who underwent laparoscopic/open and elective/urgent abdominal surgery over a 2-month period were included. Patients were admitted the same day or the day before surgery. Before antiseptic skin preparation, microbiological samples were taken from the umbilicus, left upper abdominal quadrant, and nostril. A delayed referral time (>30 minutes) of the skin swabs to the microbiology laboratory was an exclusion criterion.

Results:

Overall, 70 patients were included. The median age was 64 years (range 16–89) and a laparoscopic approach was used in 82.8% of cases. The most commonly performed operation was laparoscopic fundoplication for gastroesophageal reflux (25.8%). In the umbilicus, the most frequent colonizing bacteria were coagulase-negative Staphylococcus species and Corynebacterium. Opportunistic pathogens were found in 10 umbilical swabs compared with 8 in the left upper quadrant (14.2% versus 11.4%, p = .800). Overall, 50% of patients with umbilical opportunistic pathogens had a medium/high bacterial load compared with 62.5% in the left upper quadrant (p = .958). No postoperative surgical site infection was recorded in the study sample.

Conclusions:

Both the umbilicus and the left upper quadrant appear to be safe entry sites in laparoscopic surgery. Meticulous hygiene of these anatomical areas is strongly recommended before surgery regardless of the type of antiseptic solution and the short-term antibiotic prophylaxis. In-hospital preoperative showers may be unnecessary for well-educated patients.

Introduction

The human skin is physiologically populated by resident and transient microflora consisting of both nonpathogenic and pathogenic germs.^1,2 The umbilicus is prone to germ colonization because this area is often less well taken care of during body cleaning and can harbor a humid microenvironment.^3,4

In the laparoscopic era, the umbilicus has become the preferred entry site to the peritoneal cavity either with the Veress needle or the Hasson technique. Whether this may introduce a potential hazard for surgical site contamination and infection has been retrospectively analyzed in small studies with conflicting results.^5–7 Our aim was to describe the umbilical microbiome before antiseptic skin preparation.

Materials and Methods

This descriptive single-center study was approved by the Institutional Review Board. A cohort of patients who underwent laparoscopic/open and elective/urgent abdominal surgery at our tertiary care University hospital between March and April 2017 were included in the study. Written informed consent was obtained from all participants.

Patients were admitted the same day or the day before surgery. None of the patients had a shower with/without antiseptic agents after hospital admission. Culture swabs from the umbilicus, left upper abdominal quadrant skin (sample area: 5 × 5 cm), and nostrils were taken immediately before skin preparation in the operating room. Swabs were immediately sent to the microbiology laboratory in Stuart medium to prevent bacterial overgrowth. Delayed referral of skin swabs to the microbiology laboratory (>30 minutes) was an exclusion criterion. Age, gender, body–mass index, American Society of Anesthesiologists score, diabetes, cancer, coronary artery disease, concomitant medication (antibiotics, anticoagulants, and cortisol), previous laparotomy, indication for surgery, and type of surgical procedure were recorded. Surgical operations were classified as clean, clean-contaminated, and contaminated according to the U.S. Centers for Disease Control and Prevention (CDC) criteria.⁸ Postoperative surgical site infections (SSIs) were defined and classified according to CDC guidelines for prevention of SSIs.⁸

A Veress needle inserted in the umbilicus was routinely used to create the pneumoperitoneum and to access the abdominal cavity in laparoscopic procedures. Disinfection of the operative field was performed with povidone-iodine 5% solution. The umbilicus was the site of extraction of the surgical specimen enveloped in an Endo-Bag^® after cholecystectomy and appendectomy. Care was taken to protect the incision edges with towels in all open surgical procedures.

Patients were screened for aerobic and anaerobic bacteria and fungi in the umbilicus, for aerobic and fungi in abdominal skin, and for multidrug-resistant organisms such as carbapenemase-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA), using selective and differential chromogenic plates (bioMérieux, Marcy-l'étoile, France). Bacterial load was evaluated as colony-forming units per swab. Nasal swabs were analyzed for MRSA and methicillin-susceptible S. aureus (MSSA). Methicillin resistance was phenotypically confirmed by the Kirby–Bauer test with cefoxitin, 30 μg. Strain identification and susceptibility testing were performed with the automated platform Vitek2 compact (bioMérieux) system.

Patients were followed after hospital discharge and scheduled visits were planned at 7, 30, and 90 days postoperatively. The primary end point was to identify and quantify the microflora of the umbilicus before antiseptic skin preparation. The types of germs and bacterial load were then compared with other skin sites (left upper abdominal quadrant and nostrils). Colonizing flora was identified by looking for major bacterial groups that are normally resident in the moist environment (umbilicus) and dry environment (left upper abdominal quadrant skin).⁹ Opportunistic pathogens are defined by their capacity to cause disease when introduced into a susceptible body site or when hosted by immunologically compromised patients.¹⁰ The secondary end point was the incidence of postoperative SSIs.

Continuous data are described as median and range. Categorical variables are shown as frequencies and percentage. A two-sided chi-square test was used; P value less than .05 was considered statistically significant. Statistical analyses were performed using R, version 3.2.3.¹¹

Results

Seventy patients fulfilled the inclusion criteria. Demographics and clinical characteristics of the study sample are shown in Table 1. The majority of patients were males (57.1%) with a median age of 64 years (range 16–89) and all were Caucasians. An elective surgical procedure was performed in majority of patients (95.7%). Four patients (5.7%) had a recent hospitalization, and 2 (2.8%) had a recent antibiotic therapy for other reasons. All patients received prophylactic antibiotic therapy before the operation regardless of the type of operative procedure. The procedures were classified as clean (45.7%), clean-contaminated (48.6%), and contaminated (5.7%). A laparoscopic approach was performed in 58 patients (82.8%). Antireflux surgery (25.7%), cholecystectomy (20%), and esophagectomy for cancer were the three most commonly performed surgical procedures. There were no conversions from laparoscopy to laparotomy (Table 2).

Table 1.

Demographics and Clinical Characteristics of the Study Sample (n = 70)

Male gender, n (%)	40 (57.1)
Age years, median (range)	64 (15–89)
BMI (kg/m²), median (range)	22.5 (16.3–41.6)
ASA score, n (%)
1	6 (8.6)
2	44 (62.8)
3	20 (28.6)
4	0 (0)
Recent hospitalization, n (%)	4 (5.7)
Recent ATB therapy, n (%)	2 (2.9)
Diabetes, n (%)	6 (8.6)
Cortisol, n (%)	1 (1.4)
Cancer, n (%)	25 (35.7)
Previous CRT, n (%)	3 (4.3)
Coronary artery disease, n (%)	7 (10.0)

ASA, American Society of Anesthesiologists; ATB, antibiotic; BMI, body–mass index; CRT, chemoradiotherapy.

Table 2.

Surgical Procedures

	%	Elective (n)	Urgent (n)	Laparoscopy (n)	Laparotomy (n)
Antireflux surgery	25.7	18	0	18	0
Cholecystectomy	20.0	14	0	13	1
Esophagectomy	20.0	14	0	13	1
Explorative laparoscopy	8.6	6	0	6	0
Gastric resection	7.1	5	0	4	1
Groin hernia repair	5.7	4	0	1	3
Hemicolectomy	4.3	3	0	1	3
Heller myotomy	2.9	2	0	2	0
Lysis of adhesions	2.9	0	2	0	2
Appendectomy	1.4	0	1	1	0
Retroperitoneal mass excision	1.4	1	0	0	1

Regarding umbilical swabs, colonizing bacterial flora was found in 65 patients (92.8%) and most of them had two or more germs. The most common colonizing bacteria were coagulase-negative Staphylococcus (CONS) species and Corynebacterium species. Nine patients had concomitant colonizing and opportunistic pathogens, while one patient had just opportunistic pathogens (Pseudomonas). The most commonly isolated opportunistic bacteria were S. aureus (four strains, one of which was methicillin resistant). Four patients had negative bacterial cultures; colonizing and opportunistic genus and species from all patients are shown in Table 3.

Table 3.

Umbilical Microbiome: Number of Patients with Colonizing Bacteria and Opportunistic Pathogens

Colonizing bacteria	n	Opportunistic pathogens	Genus	Species
CONS	34	4	Morganella	n.i.
			Klebsiella	oxytoca
			Candida	albicans
			Staphylococcus	aureus ^a
CONS and Corynebacterium	13	1	Granulicatella	elegans
CONS and Propionibacterium	3	1	Staphylococcus	aureus ^b
CONS and Clostridium	1
CONS and Finegoldia	1	0
CONS and various anaerobic species	1	0
CONS and Corynebacterium and Bacillus	1	0
CONS and Corynebacterium and Clostridium	1	0
CONS and Corynebacterium and Actinomyces	1	0
CONS and Propionibacterium and Corynebacterium	1	0
Corynebacterium	6	1	Enterococcus	faecium
Corynebacterium	6	1	Staphylococcus	aureus ^a
Corynebacterium and Parvimonas	1	0
Propionibacterium	1	1	Staphylococcus	aureus ^a

		1	Pseudomonas	n.i.

Negative	4

Methicillin-susceptible (MSSA).

Methicillin-resistant (MRSA).

CONS, coagulase-negative Staphylococcus; n.i., not identified.

Regarding the left upper quadrant swabs, colonizing bacteria were found in 52 patients (74.3%). Majority of patients with colonizing flora had one single germ (CONS). Six patients had concomitant opportunistic pathogens (Acinetobacter lwoffii, Enterococcus faecium, Enterobacter aerogenes, Klebsiella oxytoca, and Streptococcus mitis), while two patients had just this type of bacterial flora (S. aureus, E. faecium, and Pseudomonas sp.). Sixteen patients had negative bacterial cultures; genus and species from all patients are shown in Table 4.

Table 4.

Left Upper Abdominal Quadrant Skin Microbiome: Number of Patients with Colonizing Bacteria and Opportunistic Pathogens

Colonizing bacteria	n	Opportunistic pathogen	Genus	Species
CONS	39	5	Acinetobacter	lwoffii
			Enterococcus	faecium
			Enterobacter	aerogenes
			Klebsiella	oxytoca
			Staphylococcus	aureus ^a
CONS and Corynebacterium	9	1	Streptococcus	mitis
CONS and Corynebacterium	9
CONS and Bacillus	2
CONS and Corynebacterium and Bacillus	2
		2	Enterococcus	faecium
			Pseudomonas	n.i.

Negative	16

Methicillin-susceptible (MSSA).

CONS, coagulase-negative Staphylococcus; n.i. not identified.

Four umbilical swabs were negative compared with 16 in the left upper quadrant (5.7% versus 22.8%, P = .008). Pathogen microflora was found in 10 umbilical and 8 left upper quadrant cultures (14.2% versus 11.4%, P = .800). Overall, 50% of patients with pathogen umbilical flora had a medium/high bacterial load compared with 62.5% in the left upper quadrant (P = .958) (Table 5). The prevalence of umbilical pathogens was similar in both males and females (60% versus 40%, P = .655); interestingly, none of the 4 patients with a history of a recent hospitalization (<30 days) had umbilical opportunistic pathogens.

Table 5.

Bacterial Load of Umbilical and Abdominal Quadrant Skin

	Umbilicus			Abdominal quadrant
	Bacterial load
	Low	Medium	High	Low	Medium	High
CONS	14		15	34
CONS andMorganella			1
CONS andMorganella			1
CONS andC. albicans			1
CONS andC. albicans	1
CONS andKlebsiella oxytoca			1	1
CONS andKlebsiella oxytoca	1					1
CONS and Staphylococcus aureus ^a	1			1
CONS and Staphylococcus aureus ^a	1			1
CONS andAcinetobacter lwoffii				1
CONS andAcinetobacter lwoffii				1
CONS and Enterococcus faecium						1
CONS and Enterococcus faecium						1
CONS and Enterobacter aerogenes				1
CONS and Enterobacter aerogenes				1
CONS and Corynebacterium	4	1	7	6		2
CONS and Corynebacterium andStreptococcus mitis					1
CONS and Corynebacterium andStreptococcus mitis						1
CONS + Corynebacterium +Granulicatella		1
CONS + Corynebacterium +Granulicatella			1
CONS and Propionibacterium			2
CONS and Propionibacterium and S. aureus ^b		1
CONS and Propionibacterium and S. aureus ^b		1
CONS andClostridium	1
CONS andClostridium			1
CONS and Bacillus				2
CONS and Finegoldia magna	1
CONS andVarious anaerobic species	1
CONS andVarious anaerobic species		1
CONS and Corynebacterium and Bacillus			1	2
CONS and Corynebacterium and Clostridium			1
CONS and Corynebacterium andActinomyces	1
CONS and Corynebacterium andActinomyces			1
CONS and Corynebacterium and Propionibacterium			1
Corynebacterium	1		3
Corynebacterium and Parvimonas			1
Corynebacterium and E. faecium			1
Corynebacterium and E. faecium			1
Corynebacterium and S. aureus ^a			1
Corynebacterium and S. aureus ^a			1
Propionibacterium and S. aureus ^a	1
Propionibacterium and S. aureus ^a			1
Pseudomonas spp			1			1
Enterococcus faecium						1

Opportunistic pathogens in bold type.

Low: <10² cfu/swab; Medium: 10³–10⁵ cfu/swab; High: >10⁵ cfu/swab.

Methicillin susceptible (MSSA).

Methicillin resistant (MRSA).

cfu, colony-forming units; CONS, coagulase-negative Staphylococcus.

Four patients had a nasal swab positive for S. aureus; MSSA was found in three of them and MRSA only in one case. There was no carbapenemase resistance, and these pathogens were not concomitantly found in the umbilical or left upper abdominal quadrant cultures. No instance of postoperative SSIs was recorded in any of the patients during the hospital stay and follow-up.

Discussion

A small prospective study from Japan revealed a surprising diversity of umbilical microbiome and identified pathogens that do not normally colonize human skin, including Enterococcus species, K. oxytoca, and Acinetobacter species.¹² The biodiversity of umbilical microbiota has been recently revisited by the Belly Button Diversity Project. The authors identified 1400 bacteria among the tested subjects, including 662 newly identified strains.^13,14

In conventional laparoscopic surgery, the umbilicus or left upper abdominal quadrant are common sites for inducing pneumoperitoneum with the Veress needle or the Hasson technique and for subsequent trocar placement. Reasons to choose the umbilicus as an elective entry site in the abdomen are both anatomical and cosmetic. It has been hypothesized that foreign body materials accumulate together with scales and seborrheic secretions in the umbilical dimple where they are compacted.^1,2,4 In addition, the umbilicus could be a difficult site to reach by antiseptic skin solutions. In this context, there is not much data regarding the physiological umbilical microbiome and the potential higher risk of SSIs after transumbilical port placement. Clinical implications of skin microflora colonization and postoperative SSIs have been investigated in retrospective studies. The umbilicus is associated with a higher infection rate compared with other trocar sites. The reason may be related to the larger diameter of the umbilical trocar and the need to enlarge the skin and fascia incision for specimen retrieval.⁷ Similarly, a 100% wound infection rate has been reported in trocar sites used for specimen retrieval, with no correlations with the umbilical microflora.⁶ More recently, a prospective study, including 93 patients, found that the majority of postoperative SSIs were caused by intra-abdominal contamination rather than by skin microflora. Interestingly, preoperative skin preparation with povidone-iodine (PVP-I) failed to completely eradicate the umbilical microflora in up to 25% of patients.⁵

In the present study, a large spectrum of both resident and transient germs was cultured in the umbilicus. In accordance with Grice and Segre, the most common colonizing bacteria were Corynebacteriaceae and CONS species.¹⁵ Interestingly, the percentage of anaerobes was consistent in the umbilicus. Our data also confirm the complexity of human skin bacterial flora, with wider heterogeneity in the moist environment that also harbors anaerobic bacteria (Clostridium species, Actinomyces species, Parvimonas micra, and Finegoldia magna, etc.); the prevalence of CONS, both in the umbilicus and in abdominal skin, supports the theory of a positive interaction between multiple not aureus and other cutaneous germs. The recovery of opportunistic pathogens seems unrelated to the body site, but it should be taken in strong consideration due to higher risk of hospital-acquired infections and carriage of antimicrobial resistance mechanisms.

We did not record any postoperative SSIs in our series. Current guidelines suggest different regimens of preoperative antibiotic prophylaxis according to the type of surgery, use of prosthetic material, grade of contamination, and patient comorbidities.¹⁶ However, a meta-analysis and a prospective randomized study found no difference in SSI rates among low-risk patients undergoing laparoscopic cholecystectomy with or without prophylactic antibiotics.^17,18

The ideal preoperative antiseptic skin preparation is controversial. Alcohol-based chlorhexidine gluconate (CHG) and PVP-I are the most commonly used solutions.¹⁹ A meta-analysis from six randomized controlled trials showed a statistically significant reduction of risk of SSIs with the use of alcohol-based CHG compared with PVP-I (odds ratio: 0.58; 95% confidence interval: 0.42–0.80). However, four of the six trials reported no SSI events in at least one of the study arms, and most studies reported the number of colony-forming units as the primary outcome and not SSIs.^20–25 Although CHG is widely accepted as a safe and relatively risk-free agent before elective surgery and has been strongly recommended by the CDC Hospital Infection Control Practices Advisory Committee report, there might be some unintended consequences associated with its preoperative use,^8,26 such as decreased skin immune function and alteration of local microbiome. In this direction, a recent retrospective study demonstrated an increased risk of SSIs related to the use of CHG baths in patients undergoing ventral hernia repair.²⁷ Finally, in addition to a proper surgical technique, the use of wound protector devices has been shown to be effective in reduction of overall and superficial SSIs in patients undergoing abdominal surgery.²⁸

A limitation of this study is the relatively small sample size. Since no SSIs were recorded, we were not able to make any inference regarding the relationship of microflora and infection development. In addition, no postoperative swabs were collected after local antisepsis and at the end of the surgical procedure. However, data were collected over a short period of time and the umbilical microbiome was compared with other anatomical sites.

Conclusions

Both umbilicus and left upper quadrant appear to be safe entry sites in laparoscopic surgery. Meticulous hygiene of these anatomical areas is strongly recommended before surgery regardless of the type of antiseptic solution and the short-term antibiotic prophylaxis. In-hospital preoperative showers may be unnecessary for well-educated patients.

Footnotes

Disclosure Statement

No competing financial interests exist.

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