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Bacterial repopulation after surgery & antibiotics
reservoirs within paranasal sinus biofilms, in intramucosal
sites, or within the nasopharynx.
8–10
Up to 75% of post-
ESS infections may be from bacterial isolates not present
at the time of surgery, suggesting that opportunistic de
novo bacteria are responsible for recalcitrant CRS, impli-
cating patient-specific alterations in immunity.
11
However,
it has also been hypothesized that bacterial repopulation
may arise from an extranasal source, including introduc-
tion from the skin or direct inoculation from water irriga-
tion bottles.
9,12
The goals of this study were to examine
changes in the sinus microbiome following ESS and initial
postoperative medical therapies in order to identify poten-
tial sources for postsurgical microbial repopulation.
Patients and methods
Study design and population
This cross-sectional study was approved by the Institutional
Review Board of the University of Colorado (COMIRB
protocol number 11–1442). The diagnosis of CRS was
made according to the 2007 Adult Sinusitis Guidelines,
and accordingly, CRS patients were initially managed med-
ically with a minimum trial of saline rinses, oral antibiotics,
and topical intranasal steroids.
13
Those with continued ev-
idence of disease who elected to undergo functional endo-
scopic sinus surgery (FESS)
14
were enrolled in the study.
The extent of surgery was determined by extent of dis-
ease and ranged from maxillary antrostomy with anterior
ethmoidectomy to complete bilateral surgery addressing
all paranasal sinuses. Meticulous mucosal-sparing surgi-
cal technique was used. Patients less than 18 years of age,
with antibiotic use within 1 month of surgery (systemic
or topical), or with cystic fibrosis, immunodeficiency, or
autoimmune diseases were excluded from the study. Post-
operatively, patients were routinely placed on sinus irriga-
tions and a 2-week course of oral antibiotics (amoxicillin-
clavulanate, or clarithromycin if penicillin-allergic). Bacte-
rial load was hypothesized to be the lowest after treatment
(FESS with irrigation at completion of surgery,
15
followed
by 2 weeks of postoperative antibiotics and saline rinses),
and then bacterial repopulation was expected to subse-
quently occur in the following weeks. As such, we com-
pared microbiota present at the time of surgery, 2 weeks
postoperatively, and 6 weeks postoperatively.
Sample collection
Subjects were recruited between November 2013 and
May 2014. All swabs were collected using CultureSwabs
(BD, Franklin Lakes, NJ), rotating at least 5 full turns
until fully saturated. Samples were collected at surgery
or in clinic during the 2-week and 6-week postoperative
appointments. At surgery, swabs were endoscopically
guided to the anterior nares and nasopharynx and, once
open, into the ethmoid sinus, with care taken to avoid
contamination by neighboring sites. At postoperative
visits, swabs were endoscopically guided to the ethmoid
cavity and sampled in an identical fashion. CultureSwabs
for DNA extraction were placed on ice upon collection
and frozen at
−
80
°
C until DNA extraction.
16S amplicon library construction
DNA was extracted from all samples using the
UltraClean
TM
DNA Isolation Kit (Mo Bio, Carlsbad, CA).
Bacterial profiles were determined by broad-range amplifi-
cation and sequence analysis of 16S rRNA genes following
previously described methods.
16,17
In brief, amplicons were
generated using primers that target approximately 340 base
pairs (bp) of the V1V2 variable region of the 16S rRNA
gene (primers 27FYM [Frank et al.
18
] and 338R,
19
modi-
fied by adding dual indexes and Illumina adapter sequences;
Illumina, San Diego, CA, USA). Illumina paired-end se-
quencing was performed on the MiSeq platform with ver-
sion v2.3.0.8 of the MiSeq Control Software and version
v2.3.32 of MiSeq Reporter, using a 600-cycle version 3
reagent kit (all from Illumina).
As described,
17
Illumina MiSeq paired-end se-
quences were sorted by sample via barcodes in the
paired reads with a Python script (Python Software
Foundation;
https://www.python.org).
The sorted
paired reads were merged using the phrap assembly
software.
20,21
Potential chimeras identified with Uchime
(usearch6.0.203_i86linux32)
22
using the Schloss and
Westcott
23
Silva reference sequences were removed from
subsequent analyses. This process generated 11,989,194
high-quality sequences for 69 samples (2 anterior nares
failed to amplify with 16S primers), with a median of
105,889 sequences/sample (IQR, 45,883 to 259,155). As-
sembled sequences were aligned and classified with SINA
(1.2.11)
24
using the 418,497 bacterial sequences in Silva
115NR99 (Quast et al.
25
) as reference configured to yield
the Silva taxonomy. Operational taxonomic units (OTUs)
were produced by clustering sequences with identical
taxonomic assignments. Relative abundances of OTUs
were calculated for each subject by dividing the sequence
counts observed for each OTU by the total number of
high-quality bacterial 16S rRNA sequences generated for
the subject. All sequence libraries had Good’s coverage
scores 99% at the rarefaction point of 15,000 sequences,
indicating that sequence coverage was excellent.
Statistical analysis
Similarity between the microbiomes of pairs of patient sam-
ples (ie, beta-diversity) was measured using the abundance-
based Morisita-Horn index (using the “vegdist” R com-
mand). Similarity/dissimilarity in community composition
(ie, beta-diversity) was assessed using a permutation-based
multiple analysis of variance (PERMANOVA) test, imple-
mented by the adonis function of the vegan R package.
26
Values of
p
were generated using 5000 label permutations,
with beta-diversity measured using the Morisita-Horn in-
dex. The R (v3.0.3,
http://cran.r-project.org)27
and Explicet
(v2.9.4,
http://www.explicet.org)28
software packages were
used for data display, analysis, and figure generation.
International Forum of Allergy & Rhinology, Vol. 6, No. 1, January 2016
121