•Pseudomonas aeruginosa global clones associated with MDR/XDR phenotypes are denoted high-risk clones.•High-risk clones are a growing threat in hospitals worldwide.•Worldwide top 10 high-risk clones ...include ST235, ST111, ST233, ST244, ST357, ST308, ST175, ST277, ST654 and ST298.•ST235 is the most prevalent high-risk clone, associated with multiple acquired β-lactamases and higher virulence.•Deeper understanding of factors driving the success of high-risk clones is required for global strategies to combat them.
Pseudomonas aeruginosa global clones associated with multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes, denominated high-risk clones, are a growing threat in hospitals worldwide. Here we provide a 2020 update on nosocomial MDR/XDR high-risk P. aeruginosa clones. According to their prevalence, global spread and association with MDR/XDR profiles and regarding extended-spectrum β-lactamases (ESBLs) and carbapenemases, the worldwide top 10 P. aeruginosa high-risk clones includes ST235, ST111, ST233, ST244, ST357, ST308, ST175, ST277, ST654 and ST298. ST235 is certainly the most relevant high-risk clone, showing a worldwide dissemination associated with over 60 different β-lactamase variants, including multiple carbapenemases from classes A and B. Moreover, ST235 shows a highly virulent phenotype associated with a high mortality rate, likely due to the production of the ExoU cytotoxin. ST111 and ST233 are also worldwide disseminated MDR/XDR clones, particularly linked to VIM-2 metallo-β-lactamase (MBL), whereas ST244 is a very prevalent clone not always associated with MDR/XDR profiles. ST357, ST308 and ST298 are also exoU+ and are therefore potentially associated with higher virulence. In contrast, ST175, prevalent in some European countries, shows a MDR/XDR phenotype frequently caused by specific chromosomal mutations and is associated with lower virulence. Finally, ST277 is highly prevalent in Brazil and is specifically associated with the SPM MBL. A deeper understanding of the underlying factors driving the success of high-risk clones, including the reported increased capacity for acquiring exogenous determinants, increased spontaneous mutation rates or greater ability to develop biofilms, is required to develop global strategies to combat them.
One of the most striking features of
is its outstanding capacity for developing antimicrobial resistance to nearly all available antipseudomonal agents through the selection of chromosomal mutations, ...leading to the failure of the treatment of severe hospital-acquired or chronic infections. Recent whole-genome sequencing (WGS) data obtained from
assays on the evolution of antibiotic resistance,
monitoring of antimicrobial resistance development, analysis of sequential cystic fibrosis isolates, and characterization of widespread epidemic high-risk clones have provided new insights into the evolutionary dynamics and mechanisms of
antibiotic resistance, thus motivating this review. Indeed, the analysis of the WGS mutational resistome has proven to be useful for understanding the evolutionary dynamics of classical resistance pathways and to describe new mechanisms for the majority of antipseudomonal classes, including β-lactams, aminoglycosides, fluoroquinolones, or polymixins. Beyond addressing a relevant scientific question, the analysis of the
mutational resistome is expected to be useful, together with the analysis of the horizontally-acquired resistance determinants, for establishing the antibiotic resistance genotype, which should correlate with the antibiotic resistance phenotype and as such, it should be useful for the design of therapeutic strategies and for monitoring the efficacy of administered antibiotic treatments. However, further experimental research and new bioinformatics tools are still needed to overcome the interpretation limitations imposed by the complex interactions (including those leading to collateral resistance or susceptibility) between the 100s of genes involved in the mutational resistome, as well as the frequent difficulties for differentiating relevant mutations from simple natural polymorphisms.
It is well established that antibiotic treatment selects for resistance, but the dynamics of this process during infections are poorly understood. Here we map the responses of Pseudomonas aeruginosa ...to treatment in high definition during a lung infection of a single ICU patient. Host immunity and antibiotic therapy with meropenem suppressed P. aeruginosa, but a second wave of infection emerged due to the growth of oprD and wbpM meropenem resistant mutants that evolved in situ. Selection then led to a loss of resistance by decreasing the prevalence of low fitness oprD mutants, increasing the frequency of high fitness mutants lacking the MexAB-OprM efflux pump, and decreasing the copy number of a multidrug resistance plasmid. Ultimately, host immunity suppressed wbpM mutants with high meropenem resistance and fitness. Our study highlights how natural selection and host immunity interact to drive both the rapid rise, and fall, of resistance during infection.
Abstract
Objectives
To determine the susceptibility profiles and the resistome of Pseudomonas aeruginosa isolates from European ICUs during a prospective cohort study (ASPIRE-ICU).
Methods
723 ...isolates from respiratory samples or perianal swabs of 402 patients from 29 sites in 11 countries were studied. MICs of 12 antibiotics were determined by broth microdilution. Horizontally acquired β-lactamases were analysed through phenotypic and genetic assays. The first respiratory isolates from 105 patients providing such samples were analysed through WGS, including the analysis of the resistome and a previously defined genotypic resistance score. Spontaneous mutant frequencies and the genetic basis of hypermutation were assessed.
Results
All agents except colistin showed resistance rates above 20%, including ceftolozane/tazobactam and ceftazidime/avibactam. 24.9% of the isolates were XDR, with a wide intercountry variation (0%–62.5%). 13.2% of the isolates were classified as DTR (difficult-to-treat resistance). 21.4% of the isolates produced ESBLs (mostly PER-1) or carbapenemases (mostly NDM-1, VIM-1/2 and GES-5). WGS showed that these determinants were linked to high-risk clones (particularly ST235 and ST654). WGS revealed a wide repertoire of mutation-driven resistance mechanisms, with multiple lineage-specific mutations. The most frequently mutated genes were gyrA, parC, oprD, mexZ, nalD and parS, but only two of the isolates were hypermutable. Finally, a good accuracy of the genotypic score to predict susceptibility (91%–100%) and resistance (94%–100%) was documented.
Conclusions
An overall high prevalence of resistance is documented European ICUs, but with a wide intercountry variability determined by the dissemination of XDR high-risk clones, arguing for the need to reinforce infection control measures.
Pseudomonas aeruginosa causes severe infections, particularly in healthcare settings and immunocompromised patients in whom MDR and XDR isolates are more prevalent. The aim of this study is to ...validate a method based on MALDI-TOF spectra analysis for early detection of the ST175 high-risk clone (HRC).
The MALDI-TOF spectra of the first 10 P. aeruginosa clinical isolates from each of the 51 participating Spanish hospitals were analyzed (n=506). Resistance profiles were determined by broth microdilution, and clonal epidemiology was assessed by PFGE analysis and multilocus sequence typing (MLST) in a previous study.
Among all the isolates, 14.2% were XDR and 26.9% were non-susceptible to meropenem, while rates of resistance to ceftolozane/tazobactam (3.6%) and colistin (5.7%) were low. Up to 41.7% of all XDR isolates belonged to the ST175 clone, and most of them were only susceptible to ceftolozane/tazobactam and colistin. However, most of the resistance to ceftolozane/tazobactam among isolates belonging to this HRC was observed in carbapenemase-producing isolates. A model based on the presence of two MALDI-TOF biomarker peaks at m/z 6911 and 7359 yielded a negative predictive value (NPV) and a positive predictive value (PPV) of 99.8% and 91.9%, respectively, and sensitivity and specificity values of 97.1% and 99.4%, respectively.
MALDI-TOF spectra analysis using a model based on the presence of two biomarker peaks proved to maintain high sensitivity and specificity for early detection of the ST175 HRC in a large collection of isolates from all Spanish regions. These data support the use of this model in a clinical setting; however, the consequences of detection of the ST175 HRC, such as choice of empirical antibiotic therapy, must be consistent with local epidemiology and the prevalence of certain resistance patterns of this HRC, such as carbapenemase production, in a given geographical area.
P. aeruginosa causa infecciones graves, particularmente asociadas a cuidados sanitarios y en pacientes inmunodeprimidos, donde los aislamientos MDR o XDR son más frecuentes. El objetivo de este estudio es validar el método basado en el análisis de espectros MALDI-TOF para la detección precoz del clon de alto riesgo ST175.
Se analizaron los espectros de MALDI-TOF de los primeros 10 aislados clínicos de P. aeruginosa pertenecientes a cada uno de los 51 hospitales españoles participantes (n=506). En un trabajo previo se determinaron los perfiles de resistencia mediante microdilución en caldo y se estableció su relación clonal mediante electroforesis en campo pulsante (PFGE) y multilocus sequence typing (MLST).
Del total de los aislamientos el 14,2% fueron XDR y el 26,9% resultaron ser no sensibles a meropenem, mientras que la resistencia al ceftolozano-tazobactam (3,6%) y la colistina (5,7%) fue baja. Hasta el 41,7% de todos los aislamientos XDR pertenecieron al clon ST175 y la mayoría de ellos solo resultaron ser sensibles a ceftolozano-tazobactam y a colistina. No obstante, la mayor parte de la resistencia a ceftolozano-tazobactam observada entre los aislados pertenecientes a este clon de alto riesgo se debió a la producción de carbapenemasas. El modelo basado en la presencia de dos picos de biomarcadores MALDI-TOF en m/z 6911 y 7359 obtuvo un valor predictivo negativo y positivo (VPN/VPP) del 99,8/91,9% y valores de sensibilidad y especificidad del 97,1/99,4%, respectivamente.
El análisis de los espectros de MALDI-TOF utilizando el modelo basado en la presencia de dos picos de biomarcadores ha demostrado poseer una alta sensibilidad y especificidad para la detección precoz del clon de alto riesgo ST175 en una gran colección de aislados clínicos representando todo el territorio español. Estos datos, por tanto, respaldan el uso de este modelo en el entorno clínico; no obstante, las consecuencias derivadas de la detección del ST175, como la elección de un tratamiento antibiótico empírico, deben ser acordes a la epidemiología local y a la prevalencia de ciertos patrones de resistencia de este clon de alto riesgo en una determinada área geográfica, como puede ser la producción de carbapenemasas.
In the context of difficult-to-treat carbapenem-resistant
infections, we evaluated imipenem, meropenem, and doripenem combinations against eleven carbapenemase-producing
isolates. According to the ...widespread global distribution of high-risk clones and carbapenemases, four representative isolates were selected: ST175 (OXA-2/VIM-20), ST175 (VIM-2), ST235 (GES-5), and ST111 (IMP-33), for efficacy studies using a sepsis murine model. Minimum inhibitory concentration (mg/L) ranges were 64-256 for imipenem and 16-128 for meropenem and doripenem. In vitro, imipenem plus meropenem was synergistic against 72% of isolates and doripenem plus meropenem or imipenem against 55% and 45%, respectively. All combinations were synergistic against the ST175, ST235, and ST155 clones. In vivo, meropenem diminished the spleen and blood bacterial concentrations of four and three isolates, respectively, with better efficacy than imipenem or doripenem. The combinations did not show efficacy compared with the more active monotherapies, except for imipenem plus meropenem, which reduced the ST235 bacterial spleen concentration. Mortality decreased with imipenem plus meropenem or doripenem for the ST175 isolate. Results suggest that carbapenem combinations are not an alternative for severe infections by carbapenemase-producing
. Meropenem monotherapy showed in vivo efficacy despite its high MIC, probably because its dosage allowed a sufficient antimicrobial exposure at the infection sites.
A ceftolozane-tazobactam- and ceftazime-avibactam-resistant Pseudomonas aeruginosa isolate was recovered after treatment (including azithromycin, meropenem, and ceftolozane-tazobactam) from a patient ...that had developed ventilator-associated pneumonia after COVID-19 infection. Whole-genome sequencing revealed that the strain, belonging to ST274, had acquired a nonsense mutation leading to truncated carbapenem porin OprD (W277X), a 7-bp deletion (nt213Δ7) in NfxB (negative regulator of the efflux pump MexCD-OprJ), and two missense mutations (Q178R and S133G) located within the first large periplasmic loop of MexD. Through the construction of
mutants and complementation assays with wild-type
, it was evidenced that resistance to the novel cephalosporin-β-lactamase inhibitor combinations was caused by the modification of MexD substrate specificity.
To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe ...social restrictions and tourism travels.
Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations.
Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (
= 25) since July 2021.
Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.
Resistance development to novel cephalosporin-β-lactamase inhibitor combinations during ceftazidime treatment of a surgical infection by
was investigated. Both initial (97C2) and final (98G1) ...isolates belonged to the high-risk clone sequence type (ST) 235 and were resistant to carbapenems (
), fluoroquinolones (GyrA-T83I, ParC-S87L), and aminoglycosides (
). 98G1 also showed resistance to ceftazidime, ceftazidime-avibactam, and ceftolozane-tazobactam. Sequencing identified
in 97C2, but 98G1 contained a 3-bp insertion leading to the duplication of the key residue D149 (designated OXA-539). Evaluation of PAO1 transformants producing cloned OXA-2 or OXA-539 confirmed that D149 duplication was the cause of resistance. Active surveillance of the emergence of resistance to these new valuable agents is warranted.
•Cutaneous scarification of anthrax lesions was associated with increased mortality.•The high percentage of pediatric cases found in Cubal is a cause for concern.•Severe anthrax treatment was ...challenging because of the limited therapeutic options.•There is a need to improve anthrax awareness among health care workers.•Community and traditional healers must be aware of the risks of skin scarification.
Bacillus anthracis infection is a worldwide zoonosis that affects the most vulnerable population and has a high mortality rate without treatment, especially in non-cutaneous presentations. Cutaneous scarification is still common in some regions of the world for the treatment of certain diseases as part of traditional medicine. We describe a series of cutaneus anthrax from a rural setting in Angola where cutaneus scarification is common.
This is a retrospective observational study describing a series of cutaneous anthrax cases from Cubal (Angola), many of whom were treated with skin scarification before admission. A total of 26 cases were diagnosed from January 2010 to December 2018. None of the cases were confirmed and eight (30.8%) were probable cases according to the Centers for the Disease Control and Prevention anthrax case definition. The median age was 11 (4.7-30.5) years, 17 (65.4%) had lesions on the head, face, or neck and 15 (57.7%) were treated with cutaneous scarification. Nine (34.6%) patients died. Traditional cutaneous scarification was significantly associated with cutaneous superinfection, respiratory, systemic involvement, and death.
Our case series points to increased complications and worse outcome of cutaneous anthrax disease if treated with skin scarification.
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