Clinical Microbiology and Infection xxx (xxxx) xxx

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Clinical Microbiology and Infection

journal homepage: www.clinicalmicrobiologyandinfection.com

Original article

Predicting Pseudomonas aeruginosa susceptibility phenotypes from

whole genome sequence resistome analysis
~ o, Carla Lo
Sara Cortes-Lara, Ester del Barrio-Tofin *, Antonio Oliver**on behalf
 pez-Causape
of the GEMARA-SEIMC/REIPI Pseudomonas study Groupy
n, Hospital Universitario Son Espases, Instituto de Investigacio
Servicio de Microbiología and Unidad de Investigacio n Sanitaria Illes Balears (IdISBa), Palma
de Mallorca, Spain

a r t i c l e i n f o a b s t r a c t

Article history: Objectives: The aim was to develop and validate a Pseudomonas aeruginosa genotypic resistance score,
Received 15 November 2020 based on analysis of the whole genome sequence resistome, to predict antimicrobial susceptibility
Received in revised form phenotypes.
28 April 2021
Methods: A scoring system based on the analysis of mutation-driven resistance in 40 chromosomal genes
Accepted 5 May 2021
and horizontally acquired resistance (Resfinder) was developed for ceftazidime, ceftolozane/tazobactam,
Available online xxx
meropenem, ciprofloxacin and tobramycin. Resistance genes/mutations were scored from 0 (no effect) to
Editor: S. Malhotra-Kumar 1 (EUCAST clinical resistance). One hundred wild-type strains obtained from 51 different hospitals during
a 2017 multicentre study were fully sequenced and analysed in order to define a catalogue of natural
Keywords: polymorphisms in the 40 chromosomal resistance genes. The capacity of genotypic score to predict the
Antimicrobial resistance susceptibility phenotype was tested in 204 isolates randomly selected from the 51 hospitals (four from
Pseudomonas aeruginosa each hospital).
Resistome Results: The analysis of the 100 wild-type isolates yielded a catalogue of 455 natural polymorphisms in
Susceptibility testing
the 40 genes involved in mutational resistance. However, resistance mutations and high-risk clones
Whole genome sequence
(such as ST235) were also documented among a few wild-type isolates. Overall, the capacity of the
genotypic score (<0.5) for predicting phenotypic susceptibility (S þ I in the case of meropenem) was very
high (95e100%). In contrast, the capacity of the genotypic score to predict resistance (1) was far more
variable depending on the agent. Prediction of meropenem clinical resistance was particularly low (18/
39, 46.1%), whereas it classified clinical ceftolozane/tazobactam resistance in 100% (7/7) of cases.
Discussion: Although a margin for improvement was evidenced in this proof of concept study, an overall
good correlation between the genotypic resistance score and the susceptibility profile was documented.
Further refining of the scoring system, automatization and testing of large international cohorts should
follow. Sara Cortes-Lara, Clin Microbiol Infect 2021;▪:1
© 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All
rights reserved.

Introduction

The growing prevalence of nosocomial infections by multidrug-

* Corresponding author: Carla Lo pez-Causape, Servicio de Microbiología and
Unidad de Investigacio n, Hospital Universitario Son Espases, Instituto de Inves-
 n Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain.
tigacio
** Corresponding author: Antonio Oliver, Servicio de Microbiología and Unidad de
Investigacion, Hospital Universitario Son Espases, Instituto de Investigacio  n Sani-
taria Illes Balears (IdISBa), Palma de Mallorca, Spain.
E-mail addresses: Carla.lopez@ssib.es (C. Lopez-Causape ), antonio.oliver@ssib.es
(A. Oliver).
y
Members of GEMARA-SEIMC/REIPI Pseudomonas study Group are listed in the
Acknowledgements.
resistant (MDR)/extensively drug-resistant (XDR) Pseudomonas
aeruginosa strains is associated with significantly increased
morbidity and mortality [1]. This increasing threat results from the
extraordinary capacity of P. aeruginosa for developing resistance by
the selection of mutations in chromosomal genes and from the
growing prevalence of transferable resistance determinants,
frequently linked to epidemic high-risk clones [2,3].
Over the last decade whole genome sequencing (WGS) has proved
useful for the analysis of P. aeruginosa resistance mechanisms,

https://doi.org/10.1016/j.cmi.2021.05.011
1198-743X/© 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
2 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx

including both mutation-driven resistance (mutational resistome)
and horizontally acquired resistance [4e6]. Indeed, a major potential
use of WGS is the prediction of antimicrobial susceptibility pheno-
types, but the current state of the art is far from achieving this goal for
most bacterial pathogens and particularly for P. aeruginosa, given the
extraordinary diversity and complexity of mutation-driven resistance
in this microorganism [7e9]. In order to move forward in this field, in
this proof of concept study we developed and validated a resistance
genotype score, based on the analysis of the WGS resistome, to predict
the P. aeruginosa antimicrobial susceptibility phenotype for five
relevant antipseudomonal agents: ceftazidime, ceftolozane/tazo-
bactam, meropenem, ciprofloxacin and tobramycin. The approach
followed was based on two key milestones: the definition of wild-
type natural polymorphisms in chromosomal resistance genes and
the development of a catalogue of resistance mutations weighted
according to the expected impact in resistance levels.
Material and methods
Validation of the genotypic resistance scores
Once the resistance genotypic scores were developed, their ca-
pacity to predict the susceptibility phenotype was tested in 204
isolates randomly selected from the 51 participating hospitals (four
from each hospital). MICs for the above panel of antipseudomonal
antibiotics have been previously determined [4]. Isolates were
classified according to their antibiotic susceptibility profile into
susceptible to all agents (S), resistant to one or two families (modR),
MDR and XDR using previously established criteria [18,19].
Confirmation of genotypeephenotype discrepancies
Discrepant results between resistance genotype and phenotype
were confirmed by repeated MIC testing. Additionally, the expres-
sion of ampC or genes coding efflux pumps (mexB, mexD, mexF or
mexY) was evaluated as previously described [20] by reverse tran-
scription (RT)-PCR assays in cases of persisting genotypeephenotype
discrepant results.

Defining the P. aeruginosa genotypic resistance score

Phylogenetic analysis
Published data on clinical strains and in vitro resistance evolu-
tion experiments were used to define the genes potentially Multilocus sequence typing of all isolates was performed in silico
involved in mutation-driven and acquired resistance for ceftazi- using a web-based tool (https://cge.cbs.dtu.dk/services/MLST/).
dime, ceftolozane/tazobactam, meropenem, ciprofloxacin and
tobramycin [10e19]. The presence of acquired resistance de-
terminants and mutations within the chromosomal genes was then
scored for each antipseudomonal agent, ranging their effect on
antibiotic resistance from 0 (no effect) to 1 (clinical resistance,
EUCAST v9.0 clinical breakpoints). When scoring mutations within
chromosomal genes, the predicted effect of the specific mutation
on gene functionality was taken into consideration, thus for many
of the genes there is a double score. Likewise, the effect of muta-
tions known to increase susceptibility was considered. Acquired
resistance determinants were individually scored based on the
published literature. Score values under 0.5 points were intended
to predict phenotypic susceptibility and, conversely, score values
equal or above 1 should predict a resistance phenotype.

Defining P. aeruginosa natural polymorphisms

A total of 1445 isolates was used, including up to 30 consecutive

healthcare-associated non-duplicated P. aeruginosa isolates
collected from 51 different Spanish hospitals (covering all 17
Spanish regions) in October 2017 [4]. The study was approved by
the Research Committee of Hospital Universitario Son Espases.
MICs of ticarcillin, aztreonam, piperacillin/tazobactam, ceftazidime,
cefepime, imipenem, meropenem, ceftolozane/tazobactam, cefta-
zidime/avibactam, ciprofloxacin, amikacin, tobramycin and colisitin
were determined by broth microdilution using EUCAST v9.0 clinical
breakpoints for their interpretation in the previous study. Isolates
with a wild-type susceptibility profile were defined, according to
EUCAST epidemiological cut-off (ECOFF) values and/or MIC within
twofold dilutions of the reference strain PAO1, as those exhibiting
the following MICs (mg/L): ticarcillin 32, piperacillin/tazobactam
4, aztreonam 8, ceftazidime 4, cefepime 4, imipenem 2,
meropenem 1, ceftolozane/tazobactam 1, ceftazidime/avi-
bactam 2, ciprofloxacin 0.25, amikacin 4, tobramycin 2 and
colisitin 2. Up to 100 wild-type isolates were randomly selected
covering most of the participating hospitals (two or three isolates/
hospital) and fully sequenced on an Illumina Miseq® benchtop
sequencer in order to define the list of P. aeruginosa natural poly- Fig. 1. Minimum spanning tree showing the genetic relationship among the 100
morphisms (please see supplementary material). selected P. aeruginosa wild-type isolates.

Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx 3

Minimum spanning trees were constructed using the goeBURST
algorithm (http://www.phyloviz.net/). Core genome phylogenetic
reconstruction was performed with Parsnp (https://harvest.
readthedocs.io/en/latest/content/parsnp.html) and visualized us-
ing the iTOL tool (https://itol.embl.de/).
loss-of-function mutations were given full score values, whereas
amino acid changes were given only half. Table S1 shows the
complete list of genes and their scoring system for each antibiotic.
Moreover, a detailed complementary rational for the assessment of
scores is provided in the supplementary material.

Data availability Defining natural polymorphisms and resistome analysis in wild-type

Sequence files have been deposited in the European Nucleotide
Archive under study numbers PRJEB40140 and PRJEB31047.
Results
Developing a P. aeruginosa genotypic resistance score
After detailed review of existing literature, a total of 40 chro-
mosomal genes were selected and scored taking into account their
expected effect on resistance for each antibiotic: no effect (0), low-
level resistance, meaning that two mutations are required for
clinical resistance, (0.5) and clinical resistance (1). Well-
characterized gain-of-function mutations and clearly inactivating
strains
Most of the participating hospitals (43/51) had at least one
isolate fulfilling the wild-type phenotype stablished criteria among
the 30 isolates analysed per centre. A high genetic diversity back-
ground was documented among the wild-type isolates (Fig. 1), with
up to 81 different Sequence Types (STs) detected among the 100
isolates studied. Moreover, 68 isolates showed unique STs and 20
were ascribed to a non-previously described ST. Conversely, STs
classified as high-risk clones such as ST235, ST244, ST308 or ST654
were also detected. The complete characteristics of the studied
wild-type strains, including origin, ST, susceptibility data, genetic
variation in resistance genes and horizontally acquired resistance
determinants are shown in Table S2.

Fig. 2. Distribution of the natural polymorphisms encountered within the 100 P. aeruginosa wild-type isolates among the 40 selected genes involved in mutational resistance. The
number of isolates showing polymorphisms for each gene (x axis), as well the number of different polymorphisms detected for each gene (colour scale) is shown.

Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
4 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx
The analysis of genetic variation in chromosomal resistance
genes (Table S3 and Fig. 2) revealed a total of 455 different missense
mutations to be included in the list of P. aeruginosa natural poly-
morphisms. Natural polymorphisms were encountered in all
selected chromosomal genes except the PA4003 locus, coding for
the penicillin-binding protein PBP2. Natural polymorphisms were
also shown to rarely occur in genes coding for other penicillin-
binding proteins such as PBP3, PBP4 or PBP5. In contrast, some
genes such as those coding for AmpC, MexXY or MexCD-OprJ were
shown to be under strong evolutionary pressure as more than 25
different natural polymorphisms were described within these
genes and they were present in most of the wild-type isolates
(Table S3 and Fig. 2).
Apart from the listed polymorphisms, some amino acid changes
with unknown effect were detected in just one isolate or ST and no
more than one record was available at the NCBI database being,
therefore, classified as acquired mutations. Moreover, nonsense
mutations with a clear impact on antimicrobial resistance were
detected among some wild-type isolates, including in particular
mutations that reduce resistance (such as MexAB-OprM and
MexXY structural components) but also a few associated with
increased resistance (such as MexZ, NalC and MexS efflux pump
regulators or OprD) (Table S4). In addition to chromosomal muta-
tions, horizontally acquired resistance determinants strA and strB
were detected in one of the isolates and aadA6 in another
(Table S2).
Once natural polymorphisms were defined and filtered from the
resistome analysis of the wild-type isolates, the genotypic scores
for ceftazidime, ceftolozane/tazobactam, meropenem, ciprofloxa-
cin and tobramycin were calculated. As shown in Table 1, full
discrepancy was detected in just two isolates, for which an inacti-
vating mutation in mexS determined a clinical resistance score of 1
for ciprofloxacin, despite showing a wild-type phenotype. How-
ever, despite the presence of the mexS inactivating mutation, RT-
PCR failed to demonstrate increased mexF transcription, explain-
ing the discrepancy between the resistance genotype and the
phenotype. Additionally, three to five wild-type isolates showed
scores 0.5 and < 1 (low level genotypic resistance) for ceftazi-
dime, meropenem, ciprofloxacin or tobramycin.
Testing of the resistance genotypic score among clinical strains
The developed genotypic scores were validated in a set of 204
isolates, four from each of 51 hospitals. In contrast to the wild-type
collection, most encountered STs have been previously defined
(189/204, 92.7%) and most isolates were determined to belong to
shared STs (118/204, 57.8%). Up to 78 isolates belonged to high-risk
clones, with ST175, ST244 and ST253 the most frequent STs, with 17,
15 and 11 isolates, respectively. Clonal relatedness among the
validation set isolates and with the wild-type collection are shown
in Fig. 3.
Table 1
Distribution of the resistance genotype scores values for the 100 wild-type
P. aeruginosa
Antibiotic No. of isolates
Score <0.5 Score 0.5 to <1 Score 1
TAZ 96 4 0
TOL/TZ 100 0 0
MER 96 4 0
CIP 93 5 2
TOB 97 3 0
TAZ, ceftazidime; TOL/TZ, ceftolozane/tazobactam; MER, meropenem; CIP, cipro-
floxacin; TOB, tobramycin.
Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
Up to 45% (92/204) of the isolates were susceptible to all tested
antimicrobials, whereas 6.9% (14/204) and 15.2% (31/204) were
classified as MDR (nonXDR) and XDR. Resistance rates were highest
for ciprofloxacin (75/204, 36.8%) and lowest for ceftolozane/tazo-
bactam (7/204, 3.4%). For ceftazidime and tobramycin resistance
rates of 14.2% (29/204) and 13.2% (27/204) were documented.
Meropenem was the only agent tested showing a EUCAST I (sus-
ceptible with increased exposure category (139/204 (68.1%) S, 44/
204 (21.6%) I, 21/204 (10.3%) R).
The mutational and acquired resistome was investigated in all
204 P. aeruginosa isolates; nevertheless, the GAL03-003 isolate was
considered to be not assessable because it was demonstrated to be
an outlier isolate in the phylogenetic reconstructions (Fig. 3). After
filtering natural polymorphisms, the genotypic scores were calcu-
lated and obtained results are represented in Fig. 4 and summa-
rized in Table 2.
For ceftazidime, the genotypic score was able to predict the
phenotypic susceptibility in most of the isolates (129/132, 97.7%)
whereas failed predicting resistance in 27.6% (8/29) of them. The
three resistant isolates for which the ceftazidime genotypic score
predicted full susceptibility exhibited MIC values  32 mg/L (Fig. 4,
Table S2); however, despite resequencing we did not find any
resistance mechanism that could explain the phenotype. On the
contrary, the eight isolates for which the score predicted resistance
harboured amino acid changes within some of the AmpC regula-
tors; thus AmpC expression levels were determined confirming its
overexpression (95- to 2241-fold respect wild-type PAO1) in four of
the eight isolates (ARA03-004, CAT06-005, CAT06-008 and GAL02-
006) (Table S2). On the other hand, as shown in Table 2, the
developed score was able to predict the phenotypic susceptibility
(scores <0.5, 100% (177/177) susceptible) and resistance (scores 1,
100% (7/7) resistant) in all isolates for ceftolozane/tazobactam.
Meropenem assessment was complicated by the existence of an
I category (MICs 4e8) that microbiologically correlates with a non-
wild-type population (low-level resistance). In any case, good cor-
relation was also documented since only 3/125 (2.4%) of the isolates
showing a score of <0.5 were phenotypically resistant. Conversely,
scores 1 resulted in fully susceptible (S) phenotypes in 15.4% (6/
39) of the cases, but in all of them mutations clearly involved in
antibiotic resistance were present (Table S2). On the other hand, the
genotypic score completely failed to predict the I category, i.e.
isolates with low level resistance frequently showed scores ranging
from 0.5 to 1).
In the case of tobramycin, the developed genotypic score
perfectly predicted the susceptible phenotype (score <0.5 resulted
in 100% (153/153) susceptibility) however failed predicting resis-
tance in four isolates of 31 (12.9%) of isolates with a score 1
(Table 2, Fig. 4). Remarkably, in two of these isolates an acquired
aminoglycoside modifying enzyme (aacA4) was detected
(Table S2).
Finally, for ciprofloxacin, a good correlation between the geno-
typic scores and the phenotypes were documented (>95%) (Table 2,
Fig. 4). Again, well-known resistance mutations were encountered
among genotypically resistant isolates exhibiting a susceptible
phenotype (Table S2).
Discussion
We developed and validated a genotypic score for the prediction
of P. aeruginosa phenotypic susceptibility to five relevant anti-
pseudomonal agents. The differential contribution of the approach
followed was based in a detailed analysis of the mutational resis-
tome. The mutational resistome of bacterial pathogens is composed
by the repertoire of potential mutations that modulate antibiotic
resistance [21]. The mutational resistome of P. aeruginosa is indeed
 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx 5

Fig. 3. Core-genome phylogenetic reconstruction of the 304 P. aeruginosa sequenced isolates and PAO1, PA14 and PA7 reference strains. Clinical isolates are labelled according to the
following format: region-hospital code-isolate identification, STs and resistance profiles are indicated.

Fig. 4. Distribution of genotypic scores versus SIR EUCAST categories for the 204 analysed P. aeruginosa clinical isolates.

Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
6 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx

Table 2
Sensitivity of the resistance genotype score to predict phenotypic susceptibility and resistance in the 204 clinical isolates studied

Antibiotic % (n) S/I/R score <0.5 % (n) S/I/R score 0.5 - <1 % (n) S/I/R score 1

TAZ 97.7 (129/132)/2.3 (3/132) 88.1 (37/42)/11.9 (5/42) 27.6 (8/29)/72.4 (21/29)
TOL/TZ 100 (177/177)/0 (0/177) 100 (19/19)/0 (0/19) 0 (0/7)/100 (7/7)
MER 86.5 (108/125)/11.1 (14/125)/2.4 (3/125) 60.5 (23/38)/39.5 (15/38)/0 (0/38) 15.4 (6/39)/38.5 (15/39)/46.1 (18/39)
CIP 95.5 (107/112)/4.5 (5/112) 73.9 (17/23)/26.1 (6/23) 5.9 (4/68)/94.1 (64/68)
TOB 100 (153/153)/0 (0/153) 100 (19/19)/0 (0/19) 12.9 (4/31)/87.1 (27/31)

TAZ, ceftazidime; TOL/TZ, ceftolozane/tazobactam; MER, meropenem; CIP, ciprofloxacin; TOB, tobramycin.

particularly relevant (a major cause of antimicrobial resistance) and
complex (a large number of genes involved) [9]. A set of 40 chro-
mosomal genes was defined for analysing mutational resistance,
along with horizontally acquired determinants. A major require-
ment for defining the mutational resistome is to differentiate
relevant mutations from natural polymorphisms in resistance
genes. For this purpose we analysed the genomes of 100 wild-type
isolates and defined a catalogue of up to 455 natural poly-
morphisms in the 40 analysed genes. However, the analysis of wild-
type strains also revealed in a few cases mutations with a clear
impact on antimicrobial resistance, including especially mutations
that reduce resistance (such as those leading to the inactivation of
efflux pumps) but also a few associated with increase resistance
(such as mutation in efflux pump regulators or the porin OprD).
Indeed, the presence of resistance mutations is occasionally noted
among susceptible isolates, exemplified by previously documented
oprD inactivating mutations among imipenem susceptible isolates
[22]. Likewise, high-risk clones such as ST235 which are typically
linked to MDR/XDR profiles [2,3] were detected in the collection of
wild-type isolates, pointing out that the detection of these strains
may not always be linked to antimicrobial resistance.
In order to avoid overestimating resistance, the genotypic score
developed did not only subtract natural polymorphisms, but also
took into consideration the expected level of resistance (low-level
vs. clinical) as well as the presence of mutations increasing anti-
microbial susceptibility or compensating resistance. Overall, the
capacity of the genotypic score (<0.5) for predicting phenotypic
susceptibility was very high (95e100%). Detailed analysis of the few
isolates genotypically scored as susceptible but showing pheno-
typic resistance could eventually lead to the discovery of yet un-
noticed resistance mechanisms. That could be the case for two
isolates showing resistance to both ceftazidime and meropenem
but with a fully wild-type genotypic score. In contrast to suscep-
tibility, the capacity of the genotypic score to predict resistance
(1) was far more variable depending on the agent. Prediction of
meropenem clinical resistance (R) was particularly low, likely
reflecting the difficulties for weighting the impact on meropenem
resistance level of mechanisms such as OprD inactivation or efflux
pumps and AmpC overexpression [23]. In contrast, the genotypic
score perfectly classified clinical ceftolozane/tazobactam resis-
tance, either linked to horizontally acquired b-lactamases or spe-
cific AmpC mutations.
The approach followed could certainly be complementary to
approaches based on machine learning. A recent study used ma-
chine learning for predicting resistance and susceptibility to four of
the tested antipseudomonal agents (ceftazidime, meropenem,
ciprofloxacin and tobramycin) from WGS and transcriptome anal-
ysis with sensitivity ranging from 81% to 94% [24]. Merging both
approaches could eventually increase the accuracy of the pre-
dictions. Indeed, avoiding discordant interlaboratory bioinformatic
predictions of resistance was found to be a major challenge in a
previous survey [25].
Our study has some limitations. First, due to the single country
nature of the study, despite including over 50 different hospitals,
the genotypic score developed should be tested in an international
cohort in the next steps. Likewise, the scoring system needs to be
further refined, including both the catalogue of the natural poly-
morphisms and the panel of resistance genes analysed. Finally, the
scoring of mutation-driven and horizontally acquired resistance
was made manually, which is time consuming and requires
expertise on P. aeruginosa resistance mechanisms; ongoing
automatization of the scoring system in a web platform would
significantly improve the usefulness of this tool. Likewise, the
resistance genotype analysis will benefit from future inclusion of
other new relevant antipseudomonal agents such as ceftazidime/
avibactam, that shows mutational resistance features resembling
either ceftazidime or ceftolozane/tazobactam depending on the
type of mutation [26,27] as well as a differential horizontally ac-
quired resistance profile.
Author contributions
S.C.-L. and E.B.-T. performed research and analysed data. C.L.-C.
and A.O. designed research, analysed data and wrote the
manuscript.
Transparency declaration
A.O. has received grants and consulting and speaker fees from
MSD, Pfizer and Shionogi. All other authors have nothing to declare.
This work was supported by Plan Nacional de IþDþi 2013-2016 and
n General de Redes y Cen-
Instituto de Salud Carlos III, Subdireccio
 n Cooperativa, Ministerio de Economía, Indus-
tros de Investigacio
tria y Competitividad, Spanish Network for Research in Infectious
Diseases (REIPI RD16/0016) and grants PI18/00076 and PI21/00017
co-financed by European Development Regional Fund ERDF “A way
to achieve Europe”, Operative program Intelligent Growth 2014-
2020.
Acknowledgements
Members of GEMARA-SEIMC/REIPI Pseudomonas study Group:
n Bou, Laura Zamorano, Irina
Luis Martínez-Martínez, Germa
S
anchez-Diener, Fa tima Gala n, Irene Gracia, Manuel Antonio
nchez, Laura Vin ~ uela, Ma
Rodríguez, Lina Martín, Juan Manuel Sa
 pez-
Victoria García, Jose Antonio Lepe, Javier Aznar, Inma Lo
ndez, Cristina Seral, Francisco Javier Castillo-García, Ana
Herna
pez-Calleja, Carmen Aspiroz, Pedro de la Iglesia, Susana
Isabel Lo
 n, Elena Riera, María Cruz Pe rez, Carmen Gallegos, Jorge
Ramo
Calvo, María Dolores Quesada, Cristina Pitart, Francesc Marco,

Yannick Hoyos, Juan Pablo Horcajada, Nieves Larrosa, Juan Jose
lez, Fe Tubau, Silvia Capilla, Mar Olga Pe rez-Moreno, Ma Jose 
Gonza
Centelles, Emma Padilla, Alba Rivera, Beatriz Mirelis, Raquel Elisa
s, María del Pilar Ortega,
Rodríguez-Tarazona, Noelia Arenal-Andre

Gregoria Megías, Inmaculada García, Cristina Colmenarejo, Jose
lez, Nora Mariela Martínez, B
Carlos Gonza arbara Gomila, Salvador
~ o, Jose Andres Agulla, Alejan-
Giner, Nuria Tormo, Eugenio Gardun
dro Seoane, Julia Pita, Isabel Paz Vidal, David Mauricio Guzm an,

Please cite this article as: Cortes-Lara S et al., Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence
resistome analysis, Clinical Microbiology and Infection, https://doi.org/10.1016/j.cmi.2021.05.011
 S. Cortes-Lara et al. / Clinical Microbiology and Infection xxx (xxxx) xxx
Marta García, María Luisa Pe rez del Molino, Gema Barbeito, Fer-
 Manuel Azcona-Gutie rrez, Yolanda Sa enz, Jose
 J Antimicrob Chemother 2018;73:658e63.
nando Artiles, Jose
Antonio Oteo, Ana Gonzalez, Jennifer Villa, Fernando Chaves, Emilia
 n, Nelly Daniela Zurita, Desire
Cercenado, Teresa Alarco  Gijo
n, Irene
n, María Isabel Sanchez,
Merino, María Isabel Morosini, Rafael Canto
Laura Moreno, Genoveva Yagüe, Jose  Leiva, Jose Luis Barrios, Andre
s
Canut, Jesús Oteo.
This work was partially presented at 2020 ECCMID (abstract
number 1073).
Appendix A. Supplementary data
Supplementary data to this article can be found online at
https://doi.org/10.1016/j.cmi.2021.05.011.
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