In vitro activity of ceftazidime-avibactam, cefiderocol, meropenem-vaborbactam and imipenem-relebactam

PLOS ONE
RESEARCH ARTICLE
In vitro activity of ceftazidime/avibactam,

cefiderocol, meropenem/vaborbactam and
imipenem/relebactam against clinical strains
of the Stenotrophomonas maltophilia complex
Braulio Josué Méndez-Sotelo ID1☯, Mónica Delgado-Beltrán2☯, Melissa Hernández-Durán3,
Claudia Adriana Colı́n-Castro ID3, José Esquivel-Bautista4, Sandra Angélica Ortega-Oliva4,
Jossue Ortiz-Álvarez5, Rodolfo Garcı́a-Contreras6, Rafael Franco-Cendejas7*, Luis
Esau Lopez Jacome ID3,8*
a1111111111 1 Infectious Diseases Division, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City,
a1111111111 Mexico, 2 Infectious Diseases Department, Instituto Nacional de Cancerologı́a, Mexico City, Mexico,
a1111111111 3 Clinical Microbiology Laboratory, Infectious Diseases Division, Instituto Nacional de Rehabilitación Luis
a1111111111 Guillermo Ibarra Ibarra, Mexico City, Mexico, 4 Centro Nacional de Referencia de Inocuidad y Bioseguridad
Agroalimentaria, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Tecámac,
a1111111111 Mexico State, Mexico, 5 Programa “Investigadoras e Investigadores por México”, Consejo Nacional de
Humanidades, Ciencias y Tecnologı́as (CONAHCYT), Mexico City, Mexico, 6 Medicine Faculty, Bacteriology
Laboratory, Microbiology and Parasitology Department, Universidad Nacional Autónoma de México, Mexico
City, Mexico, 7 Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Biomedical Research
Subdirection, Mexico City, Mexico, 8 Chemistry Faculty, Biology Department, Universidad Nacional
OPEN ACCESS Autónoma de México, Mexico City, Mexico
Citation: Méndez-Sotelo BJ, Delgado-Beltrán M, ☯ These authors contributed equally to this work.
Hernández-Durán M, Colı́n-Castro CA, Esquivel- * esaulopezjacome@quimica.unam.mx (LELJ); raffcend@yahoo.com (RF-C)
Bautista J, Ortega-Oliva SA, et al. (2024) In vitro
activity of ceftazidime/avibactam, cefiderocol,
meropenem/vaborbactam and imipenem/
relebactam against clinical strains of the
Abstract
Stenotrophomonas maltophilia complex. PLoS
ONE 19(4): e0298577. https://doi.org/10.1371/
journal.pone.0298577 Background
Editor: Marwan Osman, Yale University School of Infections caused by Stenotrophomonas maltophilia and related species are increasing
Medicine, UNITED STATES worldwide. Unfortunately, treatment options are limited, whereas the antimicrobial resis-
Received: November 24, 2023 tance is increasing.
Accepted: January 28, 2024
Methods
Published: April 18, 2024
We included clinical isolates identified as S. maltophilia by VITEK 2 Compact. Ceftazidime/
Peer Review History: PLOS recognizes the
benefits of transparency in the peer review avibactam, meropenem/vaborbactam, imipenem/relebactam, cefiderocol, quinolones, and
process; therefore, we enable the publication of tetracycline family members were evaluated by broth microdilution method and compared
all of the content of peer review and author with first-line treatment drugs. Minimum inhibitory concentrations (MICs) were reported for
responses alongside final, published articles. The
all antibiotics. We sequenced the Whole Genome of cefiderocol resistant strains (CRSs)
editorial history of this article is available here:
https://doi.org/10.1371/journal.pone.0298577 and annotated their genes associated with cefiderocol resistance (GACR). Presumptive
phylogenetic identification employing the 16S marker was performed.
Copyright: © 2024 Méndez-Sotelo et al. This is an
open access article distributed under the terms of
the Creative Commons Attribution License, which Results
permits unrestricted use, distribution, and
reproduction in any medium, provided the original One hundred and one clinical strains were evaluated, sulfamethoxazole and trimethoprim,
author and source are credited. levofloxacin and minocycline showed susceptibilities of 99.01%, 95.04% and 100%
PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 1 / 15

PLOS ONE In vitro activity of new molecules against clinical strains of Stenenotrophomonas maltophilia
Data Availability Statement: All relevant data are respectively. Ceftazidime was the antibiotic with the highest percentage of resistance in all
within the paper. The Whole Genome Shotgun samples (77.22%). Five strains were resistant to cefiderocol exhibiting MIC values � 2 μg/
project has been deposited at DDBJ/ENA/GenBank
under the accession numbers JAWJTG000000000,
mL (4.95%). The β-lactamase inhibitors meropenem/vaborbactam and imipenem/relebac-
JAWJTH000000000, JAWJTI000000000, tam, failed to inhibit S. maltophilia, preserving both MIC50 and MIC90 �64 μg/mL. Ceftazi-
JAWJTJ000000000 and JAWJTK000000000. The dime/avibactam restored the activity of ceftazidime decreasing the MIC range. Tigecycline
version described in this article are available under
had the lowest MIC range, MIC50 and MIC90. Phylogeny based on 16S rRNA allowed to
accession numbers JAWJTG010000000,
JAWJTH010000000, JAWJTI010000000, identify to cefiderocol resistant strains as putative species clustered into Stenotrophomonas
JAWJTJ010000000 and JAWJTK010000000. maltophilia complex (Smc). In these strains, we detected GARCs such as Mutiple Drug
Funding: The author(s) received no specific Resistance (MDR) efflux pumps, L1-type β-lactamases, iron transporters and type-1
funding for this work. fimbriae.
Competing interests: The authors have declared
that no competing interests exist. Conclusion
Antimicrobial resistance to first-line treatment is low. The in vitro activity of new β-lactamase
inhibitors against S. maltophilia is poor, but avibactam may be a potential option. Cefiderocol
could be considered as a potential new option for multidrug resistant infections. Tetracy-
clines had the best in vitro activity of all antibiotics evaluated.
Introduction
Stenotrophomonas maltophilia is an aerobic, Gram-negative, non-fermenting rod capable of
oxidizing glucose and maltose. It has a remarkable ability to adhere and form biofilms, allow-
ing it to survive in a variety of aqueous environments, both natural and artificial settings. This
Gram-negative rod is persistent in medical devices such as intravascular catheters, implantable
devices, and mechanical ventilation circuits [1]. Previously considered as a microorganism of
low virulence, it is now recognized as an opportunistic pathogen that can affect immunocom-
promised patients in hospital settings [2]. In addition, recent studies have demonstrated its
pathogenic potential in immunocompetent individuals as successful [3]. S. maltophilia is clus-
tered with other Stenotrophomonas genomospecies that share elevated levels of identity in 16S
gene sequence conservation, forming the Stenotrophomonas maltophilia complex (Smc) [4,5].
Risk factors associated with invasive S. maltophilia infection include prolonged hospitaliza-
tion in the intensive care unit, invasive procedures, mechanical ventilation, vascular access,
prolonged exposure to antibiotics or corticosteroids, immunosuppression and solid organ or
hematopoietic cell transplantation. In multivariate analyses, prolonged use of antibiotics
(mainly carbapenems) was reported to be one of the major risk factors for developing S. malto-
philia infections [6,7].
S. maltophilia is intrinsically resistant to several antibiotics, representing challenge for treat-
ment. The antimicrobial resistance mechanisms described involve a combination of resistance
mediated by plasmids [8], integrons [9], antibiotic-modifying enzymes, efflux pumps, and
decreased membrane permeability [10,11]. The most reported [12] is the expression of two
inducible chromosomal ß-lactamases L1 (a class B3 metallo-ß-lactamase) inhibiting carbape-
nems and L2 (class A cephalosporinase), which confers resistance to broad-spectrum cephalo-
sporins and aztreonam, and can also be inactivated by clavulanic acid and avibactam [12].
Infections caused by S. maltophilia are increasing worldwide, the Antimicrobial Surveil-
lance Program SENTRY study from 1997–2016 reported that it was the 6th cause of hospital-
acquired pneumonia in intensive care units in the United States; in addition, in Latin America,

of the total isolates 56.8% belong to bacteremia, 34.8% to hospital-acquired pneumonia, and
6.8% to skin and soft tissue infections, with a mortality of 14–69% when an inadequate antibi-
otic was administered [13].
There are limited treatment options for infections caused by S. maltophilia, and CLSI (The
Clinical & Laboratory Standards Institute) susceptibility breakpoints have only been described
for ticarcillin/clavulanate (TIM), ceftazidime (CAZ), cefiderocol (FDC), minocycline (MIN),
levofloxacin (LVX), trimethoprim-sulfamethoxazole (SXT) and chloramphenicol (CHL) [14],
and for SXT and FDC in EUCAST (The European Committee on Antimicrobial Susceptibility
Testing) [15]. The first-line treatment option remains SXT, which has an estimated susceptibil-
ity of 79–96% [10]. The SENTRY program reported that from 2009 to 2012, 96.3% of patients
with S. maltophilia pneumonia had adequate susceptibility to SXT [16], although there are
concerns about the increase of resistance in certain regions and the few alternatives in case of
resistance [17].
CAZ and TIM are β-lactam antibiotics with significant activity against S. maltophilia. How-
ever, recent studies have shown a worrying increase in resistance rates of more than 30% for
these antibiotics [18]. In comparison, the fluoroquinolones have shown a more favorable sus-
ceptibility profile when compared to CAZ and TIM, making them a suitable alternative treat-
ment for SXT. However, it is important to note that an increase in resistance to LVX has been
reported in some countries, particularly in the Asia-Pacific regions, reaching up to 30% [19].
Doxycycline (DO), tigecycline (TGC), and MIN have consistently shown good activity against
S. maltophilia in numerous studies conducted over different time periods, sample types, and
geographic regions. These antibiotics have shown susceptibility rates of up to 96% and can be
considered viable treatment options for S. maltophilia infections [20].
The development of new β-lactamase inhibitors has opened the possibility of investigating
new treatments against several microorganisms, such as S. maltophilia. Some studies with the
new inhibitors showed that the addition of aztreonam (ATM) to CAZ with avibactam (AVI)
improved in vitro activity from 82 to 97% [21], while Biagi et al published in 2020, AVI
restored ATM susceptibility to 98%, compared to 61%, 71%, and 15% with clavulanate, rele-
bactam, and vaborbactam, respectively [18].
FCD, a novel antibiotic consisting of cephalosporins linked to siderophores, has attracted
considerable interest because of multidrug-resistant Gram-negative infections. One of its main
advantages is its stability against both serine and metallo β-lactamases, making it a promising
option in the fight against antibiotic resistance [22]. In vitro, studies have demonstrated high
susceptibility rates of FDC against S. maltophilia, with some reports indicating almost 100%
susceptibility [23]. However, clinical experience with FDC for S. maltophilia infections
remains limited and is based primarily on experimental animal models.
Our aim was to describe the minimum inhibitory concentrations (MICs) of first and sec-
ond-line antibiotics, as well as the new β-lactamase inhibitors, against invasive S. maltophilia
isolates. By determining the MIC values, we aimed to provide valuable insights into the poten-
tial efficacy of these antimicrobial agents against S. maltophilia, thus helping to guide appropri-
ate treatment strategies for infections caused by this pathogen.
Results
Clinical strains
A total of 219 confirmed clinical strains of S. maltophilia were collected during the study
period. Of these, 118 (53.8%) were excluded from the analysis for various reasons: two were
environmental samples, 32 were swab samples, 14 strains were recovered from catheter tips,
one from sonication of prosthetic joint material, four had missing information in electronic

Fig 1. Isolates selection algorithm.

https://doi.org/10.1371/journal.pone.0298577.g001
medical records, 19 were from urine cultures, and 46 were repeated isolates. As a result, we
included 101 clinical specimens (Fig 1 and S1 Table).
Susceptibility patterns
The isolates showed high susceptibility rates of 99.01%, 95.04%, and 100% to SXT, LVX, and
MIN, respectively. There were no differences in SXT breakpoints between CLSI and EUCAST,
as only one strain was found to be resistant according to both systems (also resistant to CAZ).
During the period of 2015–2016, we identified 3 LVX-resistant isolates (3%) and 2 isolates
with intermediate susceptibility (2%). Notably, all these LVX-resistant isolates were also found
to be resistant to CAZ. Among all samples assessed, CAZ exhibited the highest percentage of
resistance, with a rate of 77.22% (Table 1).
Table 1. In vitro activities of selected agents against clinical S. maltophilia isolates.

Antibiotics MIC (μg/mL)
0.06 125 0.25 0.5 1 2 4 8 16 32 �64
CAZ 0 0 0 0 0 0 5 6 12 18 60
SXT 7 15 26 39 11 2 0 1 0 0 0
LVX 0 3 12 16 48 17 2 3 0 0 0
MIN 3 27 32 25 7 7 0 0 0 0 0
FDC 2 22 34 26 12 2 3 0 0 0 0
MEV 0 0 0 1 0 0 0 0 0 0 100
IMR 0 0 0 0 0 0 0 0 0 1 100
CZA 0 0 0 0 0 1 8 14 19 19 40
TGC 0 1 13 53 22 7 5 0 0 0 0
MIC, minimal inhibitory concentration; CAZ, ceftazidime; SXT, trimethoprim-sulfamethoxazole; LVX, levofloxacin; MIN, minocycline; FDC, cefiderocol; MEV,
meropenem-vaborbactam; IMR, imipenem-relebactam; CZA, ceftazidime-avibactam; TGC, tigecycline.
https://doi.org/10.1371/journal.pone.0298577.t001

Table 2. MIC50, MIC90, ranges of MIC and susceptibilities of selected agents for S. maltophilia isolates from clinical specimens.
Antibiotics MIC (μg/mL) Susceptibilitya
n = 101 (%)
Range MIC50 MIC90 S I R
SXT 0.06–8 0.5 1 100 (99.01) - 1 (0.99)
MIN 0.06–2 0.25 1 101 (100) 0 0
CAZ 4–64 32 64 11 (10.8) 12 (12) 78 (77)
LVX 0.125–8 1 2 96 (95) 2 (1.98) 3 (2.97)
FDC 0.06–4 0.25 1 96 (95) - 5 (4.95)
MEV 0.5–64 64 64 NA NA NA
IMR 32–64 64 64 NA NA NA
CZA 2–64 16 64 NA NA NA
TGC 0.125–1 0.5 1 NA NA NA
MIC, minimal inhibitory concentration; S, susceptible; I, intermediate; R, resistant; NA, not applicable.
CAZ, ceftazidime; SXT, trimethoprim-sulfamethoxazole; LVX, levofloxacin; MIN, minocycline; FDC, cefiderocol; MEV, meropenem-vaborbactam; IMR, imipenem-
relebactam; CZA, ceftazidime-avibactam; TGC, tigecycline.
a
Susceptibilities of the isolates to the antimicrobial agents tested were determined according to the MIC interpretive breakpoints recommended by the CLSI.
The MIC, MIC50 and MIC90 ranges of antibiotics that did not have CLSI approved suscepti-
bility breakpoints are described in Table 2. Both meropenem/vaborbactam (MEV) and imipe-
nem/relebactam (IMR) showed no inhibitory activity against S. maltophilia, as indicated by
their high MIC50 and MIC90values, both �64 μg/mL. However, a single strain showed low
MIC values for these antibiotics (Table 2).
In the case of ceftazidime (CAZ), the addition of avibactam (CZA) resulted in an overall
decrease in MIC50 and MIC90 compared to CAZ alone. Specifically, CAZ exhibited MIC50 =
32 μg/mL and MIC90 = 64 μg/mL, whereas CZA exhibited MIC50 = 16 μg/mL and
MIC90 = 64 μg/mL, indicating a significant reduction (p<0.001). Resemble to MIN, tigecy-
cline (TGC) had the lowest range of MIC values, with both MIC50 and MIC90 falling within a
favorable range (Table 2).
The annual susceptibility pattern for first-line antibiotics in the treatment of S. maltophilia
infection SXT, LVX and CAZ is shown in Fig 2. It can be noted that LVX and SXT have
Fig 2. Percentage of susceptibility per year of S. maltophilia to ceftazidime, levofloxacin, and trimethoprim-
sulfamethoxazole.

Table 3. In vitro activities to other antibiotics of cefiderocol resistant S. maltophilia isolates.

Isolate Susceptibilitya MIC (μg/mL)
SXT LVX MIN CAZ CZA MEV IMR TGC
Isolate 1 S S S R >64 64 64 0.5
Isolate 2 S S S R 16 64 64 1
Isolate 3 S S S R 64 64 64 0.5
Isolate 4 S S S R 64 64 64 0.5
Isolate 5 R S S R 64 64 64 4
MIC, minimal inhibitory concentration; S, susceptible; I, intermediate; R, resistant.

a
Susceptibilities were determined according to the MIC interpretive breakpoints recommended by the CLSI. CAZ, ceftazidime; SXT, trimethoprim-sulfamethoxazole;
LVX, levofloxacin; MIN, minocycline; MEV, meropenem-vaborbactam; IMR, imipenem-relebactam; CZA, ceftazidime-avibactam; TGC, tigecycline.
maintained their susceptibility pattern above 73% in the last 10 years, while CAZ has never
reached a susceptibility higher than 25%.
Cefiderocol-Resistant Stenotrophomonas strains

Finally, five samples defined as CRSS with MIC for FDC � 2 μg/mL; of these strains, all were
susceptible to LVX and MIN; also had a MIC lower than 4 μg/mL to TGC. We found only one
CRSS resistant to SXT. One CRSS had a MIC for CZA of 16/4 μg/mL, the other four CRSS had
a MIC � 64 μg/mL. All CRSS that were resistant to CAZ with a MIC � 16 μg/mL showed
MIC � 16μg/mL for CZA, MEV and IMR as well (Table 3).
A total of 14 GACRs were detected in the partial genome assembly of the five SRSS (Fig 3).
The heat map plot shows a heterogeneous inclusion of GACRs among the SRSS. All GACRs
were identified in the strain C960, while strain C1657 showed the lowest level of AREs. The
transporters tolQ, tonB and smeT involved in the regulation of the multidrug resistance
(MDR) efflux pump were found in all strains, as well as the core metabolic proteins cysk1 and
panD. Also, two components belonging to MDR (smeE and smeF) were detected in the five
SRSS, but smeD was absent in C960 and C2852 but present in the rest of the strains. The β-lac-
tamase L1 was identified in four strains but not in C1657.
Fig 3. Presence/absence plot of Genes Associated to Cefiderocol Resistance (GACR) detected in the genome of Cefiderocol-
Resistant Stenotrophomonas Strains (CRSS). The panel on the right rise represents the functional type of the GACR. Legends on the x-
axis represent the proteins annotated. Legends of the y-axis represents the strain ID. Colored boxes represented the GACR detected in
the strains. White boxes represent the GACR absents.

Fig 4. ML phylogenetic tree of the 16S rRNA sequences. The ID of the sequences from type strains are displayed into the brackets. The
CRSS position in marked in bold and pink color into the tree. Numbers on the nodes and branches represent the Ultrafast Bootstrap
values of 2000 replicates. Scale bar represents the number of nucleotide differences between branches.
Phylogenetic reconstructions showed that all SRSS were clustered into the Smc. Pairwise
comparison of the 16S gene showed that C960, C2852, C2866 and C4267 were related to Steno-
trophomonas septilia and Stenotrophomonas geniculata (99.2%), but C1657 showed <90%
identity similarity (S1 Fig). However, the phylogeny and the pairwise comparison showed dis-
cordances among them, since that C2852 was closely related to Stenotrophomonas africana,
C1657 to Xanthomonas retroflexus, but C4297, C960, and C2866 were clustered in indepen-
dent branches, suggesting that these strains could be designated as novel Stenotrophomonas
species (Fig 4).
Discussion
Infections caused by Stenotrophomonas maltophilia and related species remain challenging to
treat due to limited options resulting from both intrinsic and acquired antimicrobial resis-
tance. The introduction of β-lactamase inhibitors has helped to expand the treatment options
for certain multidrug-resistant Gram-negative infections. However, it is important to note that
currently none of the recently available commercial β-lactamase inhibitors have demonstrated
approved activity against S. maltophilia [23].
In our analysis, we examined a total of 101 clinical specimens. When comparing our results
to similar studies conducted in our country, specifically the work by Cruz-Cordova et al.,
which focused on an outbreak in a tertiary care hospital in Mexico City, we noted some dispar-
ities. Their findings revealed high resistance to SXT (76%) and tetracycline (TET) (80%) in 21
isolated samples [24]. Another study conducted by Velázquez-Acosta et al. analyzed 171 clini-
cal samples of bacteremia and pneumonia in a tertiary-care oncology center. They reported a
5.2% (9/171) resistance rate for SXT, in contrast to our findings, and 20% were resistant to
LVX [25]. Additionally, studies conducted in Latin America have shown susceptibility rates
for SXT of up to 94.4% and 87.8% for LVX [16].

We found that isolates of S. maltophilia obtained from invasive samples remain sufficiently
susceptible to first-line antibiotics such as SXT and LVX. This susceptibility has been stable for
10 years. However, between 2015 and 2016 we noticed a decline in LVX susceptibility, which
fell to 73%. The reduction in susceptibility was not linked with an outbreak but instead was
attributed to numerous factors. We found that we imported two strains from other hospitals
because the Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra is a third level
center, some cases came to our institution from the first instance and many other patients
were referred from other hospitals. Once the patient arrives, we perform the microbiological
protocol to know their colonization status with which the patient arrives. In this way, we may
correlate the cases of importation of those residents ones. One of the strains was intermediate
to LVX, and the last two were from patients with prolonged antibiotic exposure. These differ-
ences in resistance patterns among assorted studies emphasize the importance of monitoring
for local resistance rates and understanding regional differences in antimicrobial resistance.
Continuous monitoring and individualized approaches to antibiotic selection based on local
susceptibility patterns, are essentials, as emphasized in previous studies [26].
Among the antibiotics evaluated in vitro, MIN and TGC displayed the highest overall activ-
ity. Despite TGC not having approved breakpoints, further investigation is warranted for its
potential use in in vivo scenarios. On the other hand, CAZ exhibited a high percentage of resis-
tance (77.22%) and is not recommended as an alternative treatment option. In fact, the Infec-
tious Diseases Society of America (IDSA) guidelines advise against using CAZ as a treatment
option, even if it seems susceptible in the antibiogram. This is because of the presence of
intrinsic L1 and L2 β-lactamases, which are known to make CAZ ineffective [27]. As expected,
clinical isolates that were resistant to CZA were also resistant to CAZ alone. It is worth noting
that although CZA significantly decreased the MIC50 and MIC90 (p<0.001), there are no estab-
lished breakpoints in the CLSI/EUCAST guidelines [28]. In a previous study by Moriceau et al,
CZA demonstrated superior results compared to CAZ alone in terms of the proportion of sus-
ceptible isolates (66.7% vs. 38.9%, p<0.01) and MIC50 (2 μg/mL vs. 12 μg/mL, p<0.05) [29].
However, this option still appears appealing and mandates additional scrutiny and assessment.
MEV and IMR showed no activity against S. maltophilia strains, indicating their inherent
resistance. Therefore, they should not be considered as alternative treatment options [30].
It is noteworthy that none of the clinical isolates that exhibited resistance to any of the ß-
lactamase inhibitors had previous drug exposure.
Regarding tetracycline family results, it is noteworthy that all isolates showed susceptibility
to MIN and TGC had MICs <4 μg/mL therefore could be used as a potential option in case of
multidrug resistance. However, TGC’s usage in severe clinical cases is often limited due to ris-
ing trends in clinical failure, mortality, and adverse events [31], even though it shows in vitro
activity against S. maltophilia. Several real-world studies have reported gastrointestinal symp-
toms as a common adverse event associated with TGC administration [31]. Therefore, it is
important to exercise caution when contemplating the use of TGC as a treatment for severe S.
maltophilia infections, and it is recommended in the IDSA guideline [32] to consider com-
bined options. TGC possesses a lateral lipophilic group that enables it to circumvent the pri-
mary resistance mechanisms of second-generation tetracyclines, specifically efflux pumps and
ribosomal protection proteins. This property allows for its utility in MIN-resistant S. maltophi-
lia infections [33]. Nevertheless, a ventilator-associated pneumonia multicenter retrospective
study documented by Zha et al. showed that the clinical outcomes of patients treated with
TGC were worse in comparison to that of fluoroquinolones [34]. MIN may serve as a viable
option for oral treatment given its superior susceptibility activity, high distribution volume,
high-dose regimen (200 mg twice daily) probability of target attainment across MIC distribu-
tion [35], and its well-known automated system testability [36].

Five strains, named CRSS (C960, C1657, C2852, C2866, and C4297) showed MICs >2 μg/
mL for FDC, which accurately targets S. maltophilia. However, the lack of clinical evidence
makes it difficult to determine breakpoints [37]. Stracquadanio et al. conducted an in vitro
assessment of FDC MICs in 127 clinical isolates. Results showed that FDC had the lowest MIC
values and achieved complete efficacy when compared to colistin, CZA, and ceftolozane/tazo-
bactam. This results suggest that FDC may be a highly effective treatment for S. maltophilia
infections [38]. Recently, the resistance of S. maltophilia resistance to FDC has been attributed
to various mechanisms such as mutations in the siderophore receptor, mutations affecting
porin and efflux pump expression/function, and mutations in the membrane transporter and
fimbriae adhesion sites. Therefore, performing genomic sequencing of these strains could be
valuable in identifying their resistance mechanism [39].
Since five strains exhibited FDC resistance, we opted to perform WGS of the CRSS for iden-
tifying GACR. Previous studies shows that at least 14 components have been associated with
FDC resistance [39,40]. Although β-lactam resistance is primarily conferred by the presence of
beta lactamases, the presence of mutations in tonB, a membrane receptor, may be responsible
for conferring FDC resistance to S. maltophilia by preventing the active transport of cefidero-
col-siderophore conjugates [11,41,42]. Other factors, including iron transporters, type-1 fim-
briae, MDR and core metabolic proteins, have been directly or indirectly correlated with FDC
resistance in S. maltophilia [40,43]. Presumably, mutations in the transcriptional regulator
smeT are linked to FDC resistance, enabling increased expression of smeDEF [40,43]. Muta-
tions in other membrane proteins that allow for the active transport of siderophore conjugates
with FDC, such as tolQ or transporters like smlt1418, as well as Type-1 fimbriae, also have
been linked to FDC resistance [39]. Even mutations in elements involved in amino acid and
fatty acid metabolism, such as cysk1, panD, smlt3318, and tesB, can contribute to FDC resis-
tance [40]. Indeed, we suspect there are several mechanisms that may contribute to FDC resis-
tance in our strains. However, further studies are necessary to clarify the precise mechanism
by which Stenotrophomonas spp., confer resistance to FDC.
Currently, the species identification based on phenotypic methods is not decisive and lack
of accuracy. Therefore, we have decided to perform a presumptive phylogenetic identification
of the SRSS. The phylogenetic and pairwise comparisons of 16S-rRNA (>98.5%) suggest that
four SRSS can be recognized as members of the Smc species, but the identity percentage for
C1657 (<90%) indicates that it may be a new species according to the species designation cri-
teria based on the 16S-rRNA identity percentage [44]. S. maltophilia, Stenotrophomonas septi-
lia, and Stenotrophomonas africana are the only three reported species recognized as human
opportunistic pathogens [4,45–47]. Therefore, our research indicates that a greater number of
Stenotrophomonas spp., participate in nosocomial infections. During this study, we carefully
refrained from assigning a definitive species name to our SRSS. The phylogenetic analysis of
16s-rRNA is insubstantial for species identification for the genus Stenotrophomonas [48].
Nonetheless, due comparative identity percentage among species belonging Smc is very similar
and maintain high levels 16S gene sequence conservation [4,5], the identification based on this
marker is not resolute yet.
Therefore, we plan to conduct a more rigorous taxonomic analysis based on phylogenomic
and comparative genomics in a future study to refine and obtain a more species identification.
It is crucial to recognize that our current study has several limitations. First, our study only
collected and analyzed data from a single center, potentially limiting the generalization of our
findings to other settings. To improve the epidemiological context and achieve a more com-
prehensive understanding, we suggest establishing a future network dedicated to studying this
specific gram-negative rod. Second, we did not evaluate the susceptibility to monobactams. It
would be advantageous to incorporate ATM susceptibility testing in upcoming research to

enable us to compare the effectiveness of various inhibitors in the presence of ATM. Lin Q.
et al performed a comparable analysis and examined the potency of ATM-Avibactam, show-
casing its potential as a treatment option [21]. Conversely, a crucial aspect of our study is that
we assessed the activity of novel ß-lactams, such as FDC, and new β-lactamase inhibitors.
Assessing the in vitro activity of these new beta-lactams and beta-lactamase inhibitors is critical
in expanding our arsenal for therapy and overcoming the challenges posed by antimicrobial
resistance.
Conclusion
Resistance to first-line antibiotics SXT, LVX, and MIN is low, making them viable therapeutic
alternatives in our institution. TGC and FDC exhibit the most potent in vitro activity com-
pared to the other antibiotics tested, indicating their potential use in future clinical trials. Addi-
tionally, exploring the resistance mechanisms of non-susceptible strains to FDC is of interest.
AVI restored CAZ’s activity and decreased its MIC range by one dilution. This positions it as a
viable option for comparison with other antibiotics, including monobactams.
Material and methods

Ethics statements
The research committee approved the current protocol assigning the number 2022/054. No
individuals were recruited, animals or cell lines were used; therefore, no ethics committee
approval or informed consents were required.
Strains collection
We included all strains of S. maltophilia isolated from invasive specimens, including blood cul-
tures, lower respiratory tract samples, abscesses, and tissue biopsies, over a ten-year period
from January 2012 to January 2022. Duplicated samples were excluded, and only recovered
isolates were considered for analysis. Sample collection and processing were performed at the
Clinical Microbiology Laboratory of the Instituto Nacional de Rehabilitación Luis Guillermo
Ibarra Ibarra in Mexico City. All isolates were stored at -70˚C and then inoculated onto sheep
blood agar prior to their use. Identification was confirmed through phenotypic characteristics,
standard biochemical tests, and the Vitek 2 System (bioMérieux, Marcy 0 Étoile, France).
Minimal inhibitory concentrations determination

The evaluated antibiotics and inhibitors were LVX, SXT, FDC (MedChem Express1, Mon-
mouth Junction, New Jersey, USA), vaborbactam, avibactam, relebactam (Cayman Chemical
Company1, Ann Arbor, Michigan, USA), and meropenem (MEM), imipenem (IMP), CAZ,
TGC and MIN (Sigma Aldrich1, Saint Louis, Missouri, USA).
Broth microdilution was performed according to the recommendations of the CLSI guide-
lines [14]. The type strains Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC BAA-
1705 (KPC producer) and Enterobacter cloacae ATCC BAA-2408 (NDM producer) were used
for quality control of selected antibiotics. Breakpoints were defined according to the M100
from CLSI 2023 for SXT, LVX, CAZ, FDC and MIN [28]. For agents without a reported MIC,
the MIC was defined as the lowest concentration that inhibits bacterial growth. MIC values
were reported as MIC50, MIC90 and MIC range. Results of descriptive analysis were reported
in descriptive statistics as percentages and frequencies. To compare the susceptibility of CAZ
and ceftazidime/avibactam (CZA), non-parametric statistics were performed with the Wil-
coxon sign test for paired samples; a p-value of � 0.05 was defined as significant.

Whole Genome Sequencing (WGS)

Five Cefiderocol-Resistant Stenotrophomonas strains (CRSS) were chosen for WGS to under-
stand the resistance mechanism associated with FDC. Genomic DNA was extracted using the
DNeasy Blood & Tissue (QIAGEN, Germantown, Maryland, USA), according to the manufac-
turer’s instructions. After extraction, DNA quality and quantity were determined using the
Qubit 3.0 fluorometer (Invitrogen, Thermo Fisher Scientific Waltham, Massachusetts, USA)
and the Nanodrop One/One spectrophotometer (Thermo Fisher Scientific, Waltham, Massa-
chusetts, USA). DNA samples were stored at -20˚C, until use. Library preparation was per-
formed according to the manufacturer’s instructions using the Illumina DNA Prep (Illumina,
San Diego, California, USA) for the labelling and cleaning steps and IDT for Illumina DNA/
RNA UD Indexes (Illumina, San Diego, California, USA) for the indexing step. Library quality
control was performed using the Qubit 3.0 fluorometer (Invitrogen, Thermo Fisher Scientific
Waltham, Massachusetts, USA) and the 4200 Tapestation System (Agilent, Santa Clara, Cali-
fornia, USA). Sequencing of pooled and normalized libraries was performed using the MiSeq
Reagent Kit V2 (300 cycles) on the Illumina MiSeq (Illumina, San Diego, California, USA)
platform in a paired end configuration. Samples were sequenced at the Centro Nacional de
Referencia de Inocuidad y Bioseguridad Agroalimentaria. Servicio Nacional de Sanidad,
Inocuidad y Calidad Agroalimentaria.
Bioinformatic analysis
Quality metrics analysis for the generated WGS raw reads generated was performed using
FastQC version 0.11.9 [49]. Raw reads were trimmed using Trimmomatic version 0.39
(parameters: LEADING 3; TRAILING 3; SLIDINGWINDOW 4:20) to remove contamina-
tions, artifacts, and reads with low Phred quality in the raw reads [50]. The genome was assem-
bled with SPAdes version 3.12.0 [51] by using default parameters, combined with the—careful
and—cov-cutoff auto options to reduce mismatches errors during assembly. Contigs less than
200 pb in length were removed using setk-seq version 1.3 (https://github.com/lh3/seqtk/).
Quality metrics evaluation of assembled contigs was performed using QUAST version 5.2.0
[52]. Encoding nucleotide sequences and their translated amino acid sequences were predicted
and annotated using Prokka version 1.14.6 [53].
Genes Associated with Cefiredocol Resistance (GACR) were annotated and identified using
ABRIcate version 1.10.1 (https://github.com/tseemann/abricate), using the Comprehensive
Antibiotic Resistance Database (CARD) database. Presumptive species assignment and identi-
fication was performed by phylogenetic evaluation based on the analysis of the 16S rRNA
gene. The 16S gene sequences belonging to Stenotrophomonas type strains were downloaded
from the DSMZ-German Collection of Microorganisms and Cell Cultures (https://www.dsmz.
de/dsmz) [54] and the National Institute for the Biotechnological Information (NCBI)
(https://www.ncbi.nlm.nih.gov) [55]. The 16S sequences belonging to CRSS were extracted by
using barrnap version 0.9 (https://github.com/tseemann/barrnap). A multiple alignment was
performed using MUSCLE v3.8.31 [56]. The maximum-likelihood (ML) phylogenetic tree was
constructed by using IQ-TREE v2.1.2 [57], by using the TN + F + I evolutionary model and an
ultrafast bootstrap statistical support of the branches with 2000 replicates. The phylogeny was
visualized and edited using iTOL v6 [58]. Pairwise comparisons to determine the percentage
of identity among 16S gene sequences were calculated using MatGat software [59].
Supporting information
S1 Fig. Heatmap of pairwise comparison among 16S rRNA sequences. Degraded panel on
the right side reflects the visual representation of identity percentage from the lowest value

(0% in blue) to the highest value (100% in dark red). Numbers into the boxes represent the
numerical value of the identity percentages.
(PPTX)
S1 Table. Strains included in the study with isolation date and type of microbiological sam-
ple.
(XLSX)
Acknowledgments
To SENASICA and WHO Collaborating Centre on Antimicrobial Resistance in Foodborne
and Environmental Bacteria (MEX-33), especially Mayrén Zamora Nava and Cindy Fabiola
Hernández Pérez, and all the sequencing and bioinformatics staff for helping us to sequence
our samples.
Author Contributions
Conceptualization: Rafael Franco-Cendejas, Luis Esau Lopez Jacome.
Formal analysis: Braulio Josué Méndez-Sotelo, Mónica Delgado-Beltrán, Melissa Hernández-
Durán, Claudia Adriana Colı́n-Castro, José Esquivel-Bautista, Sandra Angélica Ortega-
Oliva, Jossue Ortiz-Álvarez, Rodolfo Garcı́a-Contreras, Rafael Franco-Cendejas, Luis Esau
Lopez Jacome.
Methodology: Mónica Delgado-Beltrán, Melissa Hernández-Durán, Claudia Adriana Colı́n-
Castro, José Esquivel-Bautista, Sandra Angélica Ortega-Oliva, Jossue Ortiz-Álvarez.
Supervision: Rafael Franco-Cendejas, Luis Esau Lopez Jacome.
Writing – original draft: Braulio Josué Méndez-Sotelo.
Writing – review & editing: Mónica Delgado-Beltrán, Jossue Ortiz-Álvarez, Rodolfo Garcı́a-
Contreras, Rafael Franco-Cendejas, Luis Esau Lopez Jacome.
References
1. Strateva T, Trifonova A, Sirakov I, Borisova D, Stancheva M, Keuleyan E, et al. Analysis of biofilm for-
mation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study
(2011–2022). Acta Microbiol Immunol Hung. 2023; 70: 11–21. https://doi.org/10.1556/030.2023.01920
PMID: 36640262
2. Dimopoulos G, Garnacho-Montero J, Paramythiotou E, Gutierrez-Pizarraya A, Gogos C, Adriansen-
Pérez M, et al. Upraising Stenotrophomonas maltophilia in Critically Ill Patients: A New Enemy? Diag-
nostics. 2023;13. https://doi.org/10.3390/diagnostics13061106 PMID: 36980413
3. Adegoke AA, Stenström TA, Okoh AI. Stenotrophomonas maltophilia as an emerging ubiquitous patho-
gen: Looking beyond contemporary antibiotic therapy. Frontiers in Microbiology. Front Microbiol; 2017.
https://doi.org/10.3389/fmicb.2017.02276 PMID: 29250041
4. Patil PPB, Kumar S, Midha S, Gautam V, Patil PPB. Taxonogenomics reveal multiple novel genomos-
pecies associated with clinical isolates of Stenotrophomonas maltophilia. Microb Genomics. 2018;4.
https://doi.org/10.1099/mgen.0.000207 PMID: 30084764
5. Ochoa-Sánchez LE, Vinuesa P. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct
Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Com-
plex. Front Microbiol. 2017;8. https://doi.org/10.3389/fmicb.2017.01548 PMID: 28861062
6. Wang Y, Wang Y, Rong H, Guo Z, Xu J, Huang X. Risk factors of lower respiratory tract infection caused
by Stenotrophomonas maltophilia: Systematic review and meta-analysis. Frontiers in Public Health.
Frontiers Media SA; 2023. https://doi.org/10.3389/fpubh.2022.1035812 PMID: 36703851
7. Osawa K, Shigemura K, Kitagawa K, Tokimatsu I, Fujisawa M. Risk factors for death from Stenotropho-
monas maltophilia bacteremia. J Infect Chemother. 2018; 24: 632–636. https://doi.org/10.1016/j.jiac.
2018.03.011 PMID: 29673561

8. Maravić A, Skočibušić M, Fredotović Ž, Cvjetan S, Šamanić I, Puizina J. Characterization of Environ-

mental CTX-M-15-Producing Stenotrophomonas maltophilia. Antimicrob Agents Chemother. 2014; 58:
6333–6334. https://doi.org/10.1128/AAC.03601-14 PMID: 25092701
9. Ebrahim-Saraie HS, Heidari H, Soltani B, Mardaneh J, Motamedifar M. Prevalence of antibiotic resis-
tance and integrons, sul and Smqnr genes in clinical isolates of Stenotrophomonas maltophilia from a
tertiary care hospital in Southwest Iran. Iran J Basic Med Sci. 2019; 22: 872–877. https://doi.org/10.
22038/ijbms.2019.31291.7540 PMID: 31579442
10. Brooke JS. Stenotrophomonas maltophilia: An emerging global opportunistic pathogen. Clinical Micro-
biology Reviews. Clin Microbiol Rev; 2012. pp. 2–41. https://doi.org/10.1128/CMR.00019-11 PMID:
22232370
11. Mojica MF, Humphries R, Lipuma JJ, Mathers AJ, Rao GG, Shelburne SA, et al. Clinical challenges
treating Stenotrophomonas maltophilia infections: An update. JAC-Antimicrobial Resistance. JAC Anti-
microb Resist; 2022. https://doi.org/10.1093/jacamr/dlac040 PMID: 35529051
12. Chang YT, Lin CY, Chen YH, Hsueh PR. Update on infections caused by Stenotrophomonas maltophi-
lia with particular attention to resistance mechanisms and therapeutic options. Frontiers in Microbiology.
Front Microbiol; 2015. https://doi.org/10.3389/fmicb.2015.00893 PMID: 26388847
13. Gales AC, Seifert H, Gur D, Castanheira M, Jones RN, Sader HS. Antimicrobial Susceptibility of acine-
tobacter calcoaceticus-acinetobacter baumannii complex and stenotrophomonas maltophilia clinical
isolates: Results from the SENTRY Antimicrobial Surveillance Program (1997–2016). Open Forum
Infect Dis. 2019; 6: S34–S46. https://doi.org/10.1093/ofid/ofy293 PMID: 30895213
14. Clinical and Laboratory Standards Institute. M100. Performance standards for antimicrobial susceptibil-
ity testing; approved guideline. 32th ed. In: 2022. 2022 p. 352.
15. Committee E. EUCAST: Clinical breakpoints and dosing of antibiotics. In: European Committee on Anti-
microbial Susceptibility Testing [Internet]. 2022 [cited 24 Oct 2023]. Available: https://www.eucast.org/
clinical_breakpoints.
16. Sader HS, Farrell DJ, Flamm RK, Jones RN. Antimicrobial susceptibility of Gram-negative organisms
isolated from patients hospitalised with pneumonia in US and European hospitals: Results from the
SENTRY Antimicrobial Surveillance Program, 2009–2012. Int J Antimicrob Agents. 2014; 43: 328–334.
https://doi.org/10.1016/j.ijantimicag.2014.01.007 PMID: 24630306
17. Dadashi M, Hajikhani B, Nazarinejad N, Noorisepehr N, Yazdani S, Hashemi A, et al. Global prevalence
and distribution of antibiotic resistance among clinical isolates of Stenotrophomonas maltophilia: A sys-
tematic review and meta-analysis. Journal of Global Antimicrobial Resistance. Frontiers Media SA;
2023. https://doi.org/10.1016/j.jgar.2023.02.018 PMID: 36906172
18. Biagi M, Lamm D, Meyer K, Vialichka A, Jurkovic M, Patel S, et al. Activity of Aztreonam in Combination
with Avibactam, Clavulanate, Relebactam, and Vaborbactam against Multidrug-Resistant Stenotropho-
monas maltophilia. Antimicrob Agents Chemother. 2020;64. https://doi.org/10.1128/AAC.00297-20
PMID: 32928733
19. Chawla K, Vishwanath S, Munim FC. Nonfermenting gram-negative bacilli other than pseudomonas
aeruginosa and acinetobacter spp. causing respiratory tract infections in a tertiary care center. J Glob
Infect Dis. 2013; 5: 144–148. https://doi.org/10.4103/0974-777X.121996 PMID: 24672175
20. Biagi M, Tan X, Wu T, Jurkovic M, Vialichka A, Meyer K, et al. Activity of potential alternative treatment
agents for stenotrophomonas maltophilia isolates nonsusceptible to levofloxacin and/or Trimethoprim-
sulfamethoxazole. J Clin Microbiol. 2020;58. https://doi.org/10.1128/JCM.01603-19 PMID: 31748318
21. Lin Q, Zou H, Chen X, Wu M, Ma D, Yu H, et al. Avibactam potentiated the activity of both ceftazidime
and aztreonam against S. maltophilia clinical isolates in vitro. BMC Microbiol. 2021;21. https://doi.org/
10.1186/s12866-021-02108-2 PMID: 33618662
22. Tamma PD, Goodman KE, Harris AD, Tekle T, Roberts A, Taiwo A, et al. Comparing the outcomes of
patients with carbapenemase-producing and non-carbapenemase- producing carbapenem-resistant
enterobacteriaceae bacteremia. Clin Infect Dis. 2017; 64: 257–264. https://doi.org/10.1093/cid/ciw741
PMID: 28013264
23. Hsueh SC, Lee YJ, Huang YT, Liao CH, Tsuji M, Hsueh PR. In vitro activities of cefiderocol, ceftolo-
zane/tazobactam, ceftazidime/avibactam and other comparative drugs against imipenem-resistant
Pseudomonas aeruginosa and Acinetobacter baumannii, and Stenotrophomonas maltophilia, all asso-
ciated with bloodstream. J Antimicrob Chemother. 2019; 74: 380–386. https://doi.org/10.1093/jac/
dky425 PMID: 30357343
24. Cruz-Córdova A, Mancilla-Rojano J, Luna-Pineda VM, Escalona-Venegas G, Cázares-Domı́nguez V,
Ormsby C, et al. Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotropho-
monas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital. Front Cell
Infect Microbiol. 2020;10. https://doi.org/10.3389/fcimb.2020.00050 PMID: 32133303

25. Velázquez-Acosta C, Zarco-Márquez S, Jiménez-Andrade MC, Volkow-Fernández P, Cornejo-Juárez

P. Stenotrophomonas maltophilia bacteremia and pneumonia at a tertiary-care oncology center: a
review of 16 years. Support Care Cancer. 2018; 26: 1953–1960. https://doi.org/10.1007/s00520-017-
4032-x PMID: 29307014
26. Flores-Treviño S, Gutiérrez-Ferman JL, Morfı́n-Otero R, Rodrı́guez-Noriega E, Estrada-Rivadeneyra
D, Rivas-Morales C, et al. Stenotrophomonas maltophilia in Mexico: Antimicrobial resistance, Biofilm
formation and clonal diversity. J Med Microbiol. 2014; 63: 1524–1530. https://doi.org/10.1099/jmm.0.
074385-0 PMID: 25165124
27. Gibb J, Wong DW. Antimicrobial Treatment Strategies for Stenotrophomonas maltophilia: A Focus on
Novel Therapies. Antibiotics. 2021; 10: 1226. https://doi.org/10.3390/antibiotics10101226 PMID:
34680807
28. Institute C and LS. CLSI. M100. Performance Standards for Antimicrobial Susceptibility Testing;
Twenty-Second Informational Supplement. 33rd ed. Clinical and Laboratory Standars Institute; 2023.
29. Moriceau C, Eveillard M, Lemarié C, Chenouard R, Pailhoriès H, Kempf M. Stenotrophomonas malto-
philia susceptibility to ceftazidime-avibactam combination versus ceftazidime alone. Med Mal Infect.
2020; 50: 305–307. https://doi.org/10.1016/j.medmal.2020.01.003 PMID: 32014291
30. Brooke JS. New strategies against Stenotrophomonas maltophilia: A serious worldwide intrinsically
drug-resistant opportunistic pathogen. Expert Review of Anti-Infective Therapy. Expert Rev Anti Infect
Ther; 2014. pp. 1–4. https://doi.org/10.1586/14787210.2014.864553 PMID: 24308713
31. Yaghoubi S, Zekiy AO, Krutova M, Gholami M, Kouhsari E, Sholeh M, et al. Tigecycline antibacterial
activity, clinical effectiveness, and mechanisms and epidemiology of resistance: narrative review. Euro-
pean Journal of Clinical Microbiology and Infectious Diseases. Eur J Clin Microbiol Infect Dis; 2022. pp.
1003–1022. https://doi.org/10.1007/s10096-020-04121-1 PMID: 33403565
32. Tamma PD, Aitken SL, Bonomo RA, Mathers AJ, van Duin D, Clancy CJ. Infectious Diseases Society
of America 2023 Guidance on the Treatment of Antimicrobial Resistant Gram-Negative Infections. Clin
Infect Dis. 2023 [cited 24 Oct 2023]. https://doi.org/10.1093/cid/ciad428 PMID: 37463564
33. Bassetti M, Echols R, Matsunaga Y, Ariyasu M, Doi Y, Ferrer R, et al. Efficacy and safety of cefiderocol
or best available therapy for the treatment of serious infections caused by carbapenem-resistant Gram-
negative bacteria (CREDIBLE-CR): a randomised, open-label, multicentre, pathogen-focused, descrip-
tive, phase 3 trial. Lancet Infect Dis. 2021; 21: 226–240. https://doi.org/10.1016/S1473-3099(20)30796-
9 PMID: 33058795
34. Zha L, Zhang D, Pan L, Ren Z, Li X, Zou Y, et al. Tigecycline in the Treatment of Ventilator-Associated
Pneumonia Due to Stenotrophomonas maltophilia: A Multicenter Retrospective Cohort Study. Infect
Dis Ther. 2021; 10: 2415–2429. https://doi.org/10.1007/s40121-021-00516-5 PMID: 34374953
35. Kullar R, Wenzler E, Alexander J, Goldstein EJC. Overcoming Stenotrophomonas maltophilia Resis-
tance for a More Rational Therapeutic Approach. Open Forum Infect Dis. 2022;9. https://doi.org/10.
1093/ofid/ofac095 PMID: 35415194
36. LaPlante KL, Dhand A, Wright K, Lauterio M. Re-establishing the utility of tetracycline-class antibiotics
for current challenges with antibiotic resistance. Ann Med. 2022; 54: 1686–1700. https://doi.org/10.
1080/07853890.2022.2085881 PMID: 35723082
37. Bassetti M, Graziano E, Berruti M, Giacobbe DR. The role of fosfomycin for multidrug-resistant gram-
negative infections. Curr Opin Infect Dis. 2019;32. https://doi.org/10.1097/QCO.0000000000000597
PMID: 31567411
38. Maraolo AE, Corcione S, Grossi A, Signori A, Alicino C, Hussein K, et al. The Impact of Carbapenem
Resistance on Mortality in Patients With Klebsiella Pneumoniae Bloodstream Infection: An Individual
Patient Data Meta-Analysis of 1952 Patients. Infect Dis Ther. 2021; 10: 541–558. https://doi.org/10.
1007/s40121-021-00408-8 PMID: 33586088
39. Karakonstantis S, Rousaki M, Kritsotakis EI. Cefiderocol: Systematic Review of Mechanisms of Resis-
tance, Heteroresistance and In Vivo Emergence of Resistance. Antibiotics. Antibiotics (Basel); 2022.
https://doi.org/10.3390/antibiotics11060723 PMID: 35740130
40. Werth BJ, Ashford NK, Penewit K, Waalkes A, Holmes EA, Bryan A, et al. Evolution of cefiderocol resis-
tance in Stenotrophomonas maltophilia using in vitro serial passage techniques. JAC-Antimicrobial
Resist. 2022;4. https://doi.org/10.1093/jacamr/dlac011 PMID: 35156034
41. Noinaj N, Guillier M, Barnard TJ, Buchanan SK. TonB-Dependent Transporters: Regulation, Structure,
and Function. Annu Rev Microbiol. 2010; 64: 43–60. https://doi.org/10.1146/annurev.micro.112408.
134247 PMID: 20420522
42. Soriano A, Mensa J. Mechanism of action of cefiderocol. Rev Española Quimioter. 2022; 35: 16–19.
https://doi.org/10.37201/req/s02.02.2022 PMID: 36193980

43. Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, et al. Clinically relevant
mutations in core metabolic genes confer antibiotic resistance. Science (80-). 2021;371. https://doi.org/
10.1126/science.aba0862 PMID: 33602825
44. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition.
Proc Natl Acad Sci. 2009; 106: 19126–19131. https://doi.org/10.1073/pnas.0906412106 PMID:
19855009
45. Patil PP, Midha S, Kumar S, Patil PB. Genome sequence of type strains of genus Stenotrophomonas.
Front Microbiol. 2016;7. https://doi.org/10.3389/fmicb.2016.00309 PMID: 27014232
46. Gautam V, Patil PP, Bansal K, Kumar S, Kaur A, Singh A, et al. Description of Stenotrophomonas sepi-
lia sp. nov., isolated from blood culture of a hospitalized patient as a new member of Stenotrophomonas
maltophilia complex. New Microbes New Infect. 2021; 43: 100920. https://doi.org/10.1016/j.nmni.2021.
100920 PMID: 34457314
47. Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, et al. The phylogenetic landscape
and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Com-
mun. 2020; 11: 2044. https://doi.org/10.1038/s41467-020-15123-0 PMID: 32341346
48. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads
based on 16S rRNA sequence. Int J Syst Evol Microbiol. 2000; 50: 1563–1589. https://doi.org/10.1099/
00207713-50-4-1563 PMID: 10939664
49. Andrews Simon. Babraham Bioinformatics—FastQC A Quality Control tool for High Throughput
Sequence Data. Soil. 2020. pp. 47–81. Available: https://www.bioinformatics.babraham.ac.uk/projects/
fastqc/.
50. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinfor-
matics. 2014; 30: 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 PMID: 24695404
51. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome
Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012; 19: 455–477.
https://doi.org/10.1089/cmb.2012.0021 PMID: 22506599
52. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies.
Bioinformatics. 2013; 29: 1072–1075. https://doi.org/10.1093/bioinformatics/btt086 PMID: 23422339
53. Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based
framework for NGS analysis in microbiology. Bioinformatics. 2014; 30: 1928–1929. https://doi.org/10.
1093/bioinformatics/btu135 PMID: 24618473
54. DSMZ GmbH. German Collection of Microorganisms and Cell Cultures, Komagataeibacter xylinus.
2013 [cited 25 Oct 2023]. Available: https://www.dsmz.de/dsmz.
55. NIH. National Center for Biotechnology Information. 2019. pp. 1723–1723. https://doi.org/10.1007/978-
3-662-48986-4_301184
56. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic
Acids Res. 2004; 32: 1792–1797. https://doi.org/10.1093/nar/gkh340 PMID: 15034147
57. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A Fast and Effective Stochastic Algo-
rithm for Estimating Maximum-Likelihood Phylogenies. Mol Biol Evol. 2015; 32: 268–274. https://doi.
org/10.1093/molbev/msu300 PMID: 25371430
58. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and
annotation. Nucleic Acids Res. 2021; 49: W293–W296. https://doi.org/10.1093/nar/gkab301 PMID:
33885785
59. Campanella JJ, Bitincka L, Smalley J. MatGAT: an application that generates similarity/identity matrices
using protein or DNA sequences. BMC Bioinformatics. 2003; 4: 29. https://doi.org/10.1186/1471-2105-
4-29 PMID: 12854978

In vitro activity of ceftazidime-avibactam, cefiderocol, meropenem-vaborbactam and imipenem-relebactam

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

In vitro activity of ceftazidime-avibactam, cefiderocol, meropenem-vaborbactam and imipenem-relebactam

Uploaded by

Copyright:

Available Formats

PLOS ONE

In vitro activity of ceftazidime/avibactam,

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 1 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 2 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 3 / 15

Fig 1. Isolates selection algorithm.

Table 1. In vitro activities of selected agents against clinical S. maltophilia isolates.

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 4 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 5 / 15

Table 3. In vitro activities to other antibiotics of cefiderocol resistant S. maltophilia isolates.

MIC, minimal inhibitory concentration; S, susceptible; I, intermediate; R, resistant.

Cefiderocol-Resistant Stenotrophomonas strains

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 6 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 7 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 8 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 9 / 15

Material and methods

Minimal inhibitory concentrations determination

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 10 / 15

Whole Genome Sequencing (WGS)

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 11 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 12 / 15

8. Maravić A, Skočibušić M, Fredotović Ž, Cvjetan S, Šamanić I, Puizina J. Characterization of Environ-

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 13 / 15

25. Velázquez-Acosta C, Zarco-Márquez S, Jiménez-Andrade MC, Volkow-Fernández P, Cornejo-Juárez

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 14 / 15

PLOS ONE | https://doi.org/10.1371/journal.pone.0298577 April 18, 2024 15 / 15

You might also like