RESUMEN
Outer membrane porins in Gram-negative bacteria facilitate antibiotic influx. In Klebsiella pneumoniae, modifications in the porin OmpK36 are implicated in increasing resistance to carbapenems. An analysis of large K. pneumoniae genome collections, encompassing major healthcare-associated clones, revealed the recurrent emergence of a synonymous cytosine-to-thymine transition at position 25 (25c > t) in ompK36. We show that the 25c > t transition increases carbapenem resistance through depletion of OmpK36 from the outer membrane. The mutation attenuates K. pneumoniae in a murine pneumonia model, which accounts for its limited clonal expansion observed by phylogenetic analysis. However, in the context of carbapenem treatment, the 25c > t transition tips the balance toward treatment failure, thus accounting for its recurrent emergence. Mechanistically, the 25c > t transition mediates an intramolecular messenger RNA (mRNA) interaction between a uracil encoded by 25t and the first adenine within the Shine-Dalgarno sequence. This specific interaction leads to the formation of an RNA stem structure, which obscures the ribosomal binding site thus disrupting translation. While mutations reducing OmpK36 expression via transcriptional silencing are known, we uniquely demonstrate the repeated selection of a synonymous ompK36 mutation mediating translational suppression in response to antibiotic pressure.
Asunto(s)
Antibacterianos , Proteínas Bacterianas , Carbapenémicos , Klebsiella pneumoniae , Porinas , Resistencia betalactámica , Animales , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/clasificación , Proteínas Bacterianas/genética , Carbapenémicos/farmacología , Carbapenémicos/uso terapéutico , Modelos Animales de Enfermedad , Infecciones por Klebsiella/tratamiento farmacológico , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Ratones , Pruebas de Sensibilidad Microbiana , Mutación , Filogenia , Neumonía Bacteriana/tratamiento farmacológico , Neumonía Bacteriana/microbiología , Porinas/clasificación , Porinas/genética , ARN Mensajero/metabolismo , Resistencia betalactámica/genéticaRESUMEN
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.
Asunto(s)
Infecciones por Klebsiella , Klebsiella pneumoniae , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Ácido Aspártico , Proteínas Bacterianas/metabolismo , Células Clonales , Humanos , Infecciones por Klebsiella/tratamiento farmacológico , Infecciones por Klebsiella/microbiología , Pruebas de Sensibilidad Microbiana , Porinas/genética , Porinas/metabolismo , beta-Lactamasas/genética , beta-Lactamasas/metabolismoRESUMEN
Antimicrobial susceptibility testing (AST) from blood culture (BC) may take several days, limiting the eventual impact on antimicrobial stewardship. Hence, rapid AST systems represent a valuable support in shorting the time-to-response. In this work, the Quantamatrix dRASTTM system (dRAST) was evaluated for rapid AST on 100 monomicrobial BCs (50 Gram-negatives and 50 Gram-positives), including several isolates with clinically relevant resistance mechanisms. AST results were provided in 6-hours, on average. Compared to Micronaut (Merlin) system based on broth microdilution, dRAST exhibited an overall categorical agreement of 92.5 %, essential agreement of 89.0 %, and mean bias of 15.9 %. Category overestimation (potentially leading to unnecessary high-dosage treatment or to exclude active agents) and category underestimation (potentially leading to underdosing or using ineffective agents) were observed in 4.3 % and 3.1 % of cases, respectively. Even though several issues were reported, results confirmed the potential contribution of dRAST to shorten the BCs clinical microbiology workflow and management.
Asunto(s)
Antibacterianos , Cultivo de Sangre , Pruebas de Sensibilidad Microbiana , Pruebas de Sensibilidad Microbiana/métodos , Humanos , Cultivo de Sangre/métodos , Antibacterianos/farmacología , Bacterias Gramnegativas/efectos de los fármacos , Bacterias Gramnegativas/aislamiento & purificación , Bacterias Grampositivas/efectos de los fármacos , Bacterias Grampositivas/aislamiento & purificación , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacteriemia/microbiología , Factores de TiempoRESUMEN
Detection of SARS-CoV-2 in bronchoalveolar lavage (BAL) is considered as a promising alternative method to detect COVID-19 infection. STANDARD™ M10 SARS-CoV-2 assay on 150 negative and 50 positives BAL samples for SARS-CoV-2 showed 96 % sensitivity, 100 % specificity compared to Allplex™ SARS-CoV-2 assay and a 31.25 genomic copies/mL limit of detection.
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Alzheimer's disease (AD) is a neurodegenerative process responsible for almost 70% of all cases of dementia. The clinical signs consist in progressive and irreversible loss of memory, cognitive, and behavioral functions. The main histopathological hallmark is the accumulation of amyloid-ß (Aß) peptide fibrils in the brain. To date, the origin of Aß has not been determined. Recent studies have shown that the gut microbiota produces Aß, and dysbiotic states have been identified in AD patients and animal models of AD. Starting from the hypothesis that maintaining or restoring the microbiota's eubiosis is essential to control Aß's production and deposition in the brain, we used a mixture of probiotics and prebiotics (symbiotic) to treat APPPS1 male and female mice, an animal model of AD, from 2 to 8 months of age and evaluated their cognitive performances, mucus secretion, Aß serum concentration, and microbiota composition. The results showed that the treatment was able to prevent the memory deficits, the reduced mucus secretion, the increased Aß blood levels, and the imbalance in the gut microbiota found in APPPS1 mice. The present study demonstrates that the gut-brain axis plays a critical role in the genesis of cognitive impairment, and that modulation of the gut microbiota can ameliorate AD's symptomatology.
Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Disfunción Cognitiva , Modelos Animales de Enfermedad , Microbioma Gastrointestinal , Ratones Transgénicos , Prebióticos , Probióticos , Animales , Péptidos beta-Amiloides/metabolismo , Disfunción Cognitiva/terapia , Enfermedad de Alzheimer/terapia , Femenino , Ratones , Masculino , Presenilina-1/genética , Eje Cerebro-Intestino , Precursor de Proteína beta-Amiloide/genética , Encéfalo/metabolismo , CogniciónRESUMEN
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7â¯% of samples, while 51.4â¯%, 22.8â¯% and 8.6â¯% resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
Asunto(s)
COVID-19 , ARN Viral , SARS-CoV-2 , Sensibilidad y Especificidad , Aguas Residuales , Aguas Residuales/virología , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , ARN Viral/genética , ARN Viral/aislamiento & purificación , COVID-19/diagnóstico , COVID-19/virología , Humanos , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodosRESUMEN
Broncho-alveolar lavage (BAL) is indicated in cases of uncertain diagnosis but high suspicion of Sars-Cov-2 infection allowing to collect material for microbiological culture to define the presence of coinfection or super-infection. This prospective study investigated the correlation between chest computed tomography (CT) findings, Covid-19 Reporting and Data System score, and clinical outcomes in Coronavirus disease 2019 (Covid-19) patients who underwent BAL with the aim of predicting outcomes such as lung coinfection, respiratory failure, and hospitalization length based on chest CT abnormalities. Study population included 34 patients (range 38-90 years old; 20 males, 14 females) with a positive nucleic acid amplification test for Covid-19 infection, suitable BAL examination, and good quality chest CT scan in the absence of lung cancer history. Pulmonary coinfections were found in 20.6% of patients, predominantly caused by bacteria. Specific correlations were found between right middle lobe involvement and pulmonary co-infections. Severe lung injury (PaO2/FiO2 ratio of 100-200) was associated with substantial involvement of right middle, right upper, and left lower lobes. No significant correlation was found between chest CT findings and inflammatory markers (C-reactive protein, procalcitonin) or hospitalization length of stay. Specific chest CT patterns, especially in right middle lobe, could serve as indicators for the presence of co-infections and disease severity in noncritically ill Covid-19 patients, aiding clinicians in timely interventions and personalized treatment strategies.
Asunto(s)
COVID-19 , Tomografía Computarizada por Rayos X , Humanos , COVID-19/complicaciones , COVID-19/diagnóstico por imagen , Masculino , Femenino , Persona de Mediana Edad , Anciano , Adulto , Tomografía Computarizada por Rayos X/métodos , Anciano de 80 o más Años , Estudios Prospectivos , Lavado Broncoalveolar/métodos , SARS-CoV-2 , Coinfección , Pulmón/diagnóstico por imagen , Unidades de Cuidados Intensivos/estadística & datos numéricosRESUMEN
Background: Among multidrug-resistant (MDR) bacteria able to threaten human health, carbapenem-resistant Enterobacterales (CRE) have become a major public health threat globally. National and international guidelines point out the importance of active routine surveillance policies to prevent CRE transmission. Therefore, defining lines of intervention and strategies capable of containing and controlling the spread of CRE is considered determinant. CRE screening is one of the main actions to curb transmission and control outbreaks, outlining the presence and also the prevalence and types of carbapenemase enzymes circulating locally. Objective: The purpose of this study was to outline the epidemiology of CRE colonization in Italy, detecting CRE-colonized patients at admission and during hospitalization, before and during the first year of COVID-19. Materials and methods: A total of 11,063 patients admitted to seven different hospitals (Bologna, Catania, Florence, Genoa, Naples, Palermo, and Turin) in Intensive Care Units (ICU) and other wards (non-ICU) located in the North, Center, and South of Italy were enrolled and screened for CRE carriage at admission (T0) and during the first 3 weeks of hospitalization (T1-T3). The study spanned two periods, before (September 2018-Septemeber 2019, I observational period) and during the COVID-19 pandemic (October 2019-September 2020, II observational period). Results: Overall, the prevalence of CRE-colonized patients at admission in ICU or in other ward, ranged from 3.9 to 11.5%, while a percentage from 5.1 to 15.5% of patients acquired CRE during hospital stay. There were large differences between the I and II period of study according to the different geographical areas and enrolling centers. Overall, comparison of prevalence of CRE-positive patients showed a significant increased trend between I and II observational periods both in ICU and non-ICU wards, mostly in the Southern participating centers. KPC-producing Klebsiella pneumoniae was the most frequent CRE species-carbapenemase combination reported in this study. In particular, the presence of KPC-producing K. pneumoniae was reported in period I during hospitalization in all the CRE-positive patients enrolled in ICU in Turin (North Italy), while in period II at admission in all the CRE-positive patients enrolled in ICU in Catania and in 58.3% of non-ICU CRE-positive patients in Naples (both centers in South Italy). Conclusion: The prevalence of CRE in Italy highly increased during the COVID-19 pandemic, mostly in the Southern hospital centers. KPC-producing K. pneumoniae was the most frequent colonizing CRE species reported. The results of our study confirmed the crucial value of active surveillance as well as the importance of multicenter studies representing diverse geographical areas even in endemic countries. Differences in CRE colonization prevalence among centers suggest the need for diversified and center-specific interventions as well as for strengthening efforts in infection prevention and control practices and policies.
Asunto(s)
COVID-19 , Enterobacteriaceae Resistentes a los Carbapenémicos , Infecciones por Enterobacteriaceae , Humanos , Carbapenémicos/farmacología , Carbapenémicos/uso terapéutico , COVID-19/epidemiología , Italia/epidemiología , Pandemias , Prevalencia , Infecciones por Enterobacteriaceae/epidemiologíaRESUMEN
The rapid detection of carbapenemase-producing microorganisms is crucial for clinical and infection control purposes. Here we evaluated Revogene®Carba C assay on 154 carbapenemase-producing and -nonproducing Gram-negatives. Up to 8 samples per 70 minutes were processed by Revogene®Carba C assay which showed excellent performances with 100% sensitivity, 99.5% specificity,100% NPV, and 97.8% positive predictive value.
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Proteínas Bacterianas , beta-Lactamasas , Proteínas Bacterianas/genética , Humanos , Sensibilidad y Especificidad , beta-Lactamasas/genéticaRESUMEN
OBJECTIVES: To evaluate the activity of meropenem-amikacin and meropenem-colistin combinations with checkerboard broth microdilution (CKBM) compared with isothermal microcalorimetry (ITMC) assays against a multi-centric collection of multi-drug-resistant Gram-negative clinical isolates; and to compare the fractional inhibitory concentration (FIC) index and time to results of CKBM and ITMC. METHODS: A collection of 333 multi-drug-resistant Gram-negative clinical isolates showing reduced susceptibility to meropenem (121 Klebsiella pneumoniae, 14 Escherichia coli, 130 Pseudomonas aeruginosa and 68 Acinetobacter baumannii) isolated from different centres (Florence, Madrid, Rotterdam and Stockholm) was included in the study. The antimicrobial activity of meropenem-amikacin and meropenem-colistin combinations was evaluated with CKBM and ITMC. FIC index results were interpreted as synergistic/additive and indifferent for values ≤0.5/0.5
Asunto(s)
Amicacina , Colistina , Amicacina/farmacología , Antibacterianos/farmacología , Colistina/farmacología , Farmacorresistencia Bacteriana Múltiple , Sinergismo Farmacológico , Escherichia coli , Klebsiella pneumoniae , Meropenem/farmacología , Pruebas de Sensibilidad MicrobianaRESUMEN
Recurrent infection by Clostridioides difficile has recently been treated by fecal microbiota transplantation (FMT). As viable SARS-CoV-2 was recovered from stool of asymptomatic individuals, the FMT procedure could be a potential risk of SARS-CoV-2 transmission, thus underlying the need to reliably detect SARS-CoV-2 in stool. Here, we performed a multicentric study to explore performances of two commercially available assays for detection of SARS-CoV-2 RNA in stool of potential FMT donors. In three hospitals, 180 stool samples were spiked with serial 10-fold dilutions of a SARS-CoV-2 inactivated lysate to evaluate the Seegene Allplex™ SARS-CoV-2 (SC2) and SARS-CoV-2/FluA/FluB/RSV (SC2FABR) Assays for the detection of viral RNA in stool of FMT donors. The results revealed that both assays detected down to 2 TCID50/mL with comparable limit of detection values, SC2 showing more consistent target positivity rate than SC2FABR. Beyond high amplification efficiency, correlation between CT values and log concentrations of inactivated viral lysates showed R2 values ranging from 0.88 to 0.90 and from 0.87 to 0.91 for the SC2 and SC2FABR assay, respectively. The present results demonstrate that both methods are highly reproducible, sensitive, and accurate for SARS-CoV-2 RNA detection in stool, suggesting a potential use in FMT-donor screening.
RESUMEN
OBJECTIVE: When using high-throughput batched diagnostic platforms based on RT-PCR for SARS-CoV-2 detection, avoidance of the conventional nucleic acid extraction step can help to reduce the turnaround time and increase processivity. This approach can also spare reagents and plasticware, which have experienced a shortage during the initial waves of the pandemic, reducing the overall testing costs. METHODS: This study evaluated the performance of extraction-free protocols based on simple dilution of the specimen in sterile RNAse free water (with or without a heating step) in comparison to standard RNA extraction protocols, using two commercial kits for molecular detection of SARS-CoV-2 (Allplex™ SARS-CoV-2 assay and Allplex™ SARS-CoV-2/FluA/FluB/RSV assay) in nasopharyngeal swabs (NPS). RESULTS: Compared with conventional protocols, extraction-free protocols based on sample dilution without a heating step exhibited a lower analytical sensitivity: 74.0% and 82.1% with the Allplex™ SARS-CoV-2 assay (tested with 139 NPS samples) and the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay (tested with 69 NPS samples), with a mean increase of Ct values of +2.04 and +1.32, respectively. Most false negative results were observed with sampled low viral load. Including a step of heat exposure did not improve but actually decreased the analytical sensitivity of the assay. CONCLUSIONS: Results confirmed that extraction-free protocols could be a faster and cheaper approach to SARS-CoV-2 detection in NPS samples, which could improve processivity of diagnostic platforms.
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COVID-19 , SARS-CoV-2 , Prueba de COVID-19 , Humanos , ARN Viral/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Sensibilidad y EspecificidadRESUMEN
Three assays for SARS-CoV-2 antigen detection in nasopharyngeal swabs (Lumipulse® G SARS-CoV-2 Ag [LPG], STANDARDTM F COVID-19 Ag FIA [STF] and AFIAS COVID-19 Ag [AFC] were evaluated. Compared to RT-PCR, LPG, AFC and STF showed a variable sensitivity (87.9%, 37.5%, and 35.7%, respectively) and an overall high specificity (> 95%).
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Prueba Serológica para COVID-19 , COVID-19/diagnóstico , Pruebas en el Punto de Atención , SARS-CoV-2/aislamiento & purificación , Antígenos Virales/análisis , Humanos , Inmunoensayo , Nasofaringe/virología , SARS-CoV-2/inmunología , Sensibilidad y EspecificidadRESUMEN
Irrigant solutions commonly used for the treatment of endodontic infections can be inhibited by both organic and inorganic substances. The aim of this study was to evaluate the in vitro antimicrobial activity of the novel irrigant HybenX® and 2.5% and 5% sodium hypochlorite against Enterococcus faecalis, in presence of dentine powder (DP) or bovine serum albumin 20% (BSA) as inhibitory agents. An E. faecalis American Type Culture Collection (ATCC) 29212 suspension was added to the irrigants (Hybenx® or NaOCl) and one or two different inhibitors (BSA and DP) either after one-hour pre-incubation at 35 ± 1 °C or not. The antimicrobial activity of HybenX® against E. faecalis was already proved at 15 min and was neither affected by BSA nor by DP or combinations thereof. NaOCl 2.5% showed an effective antimicrobial activity starting from 15 min and this activity was partially inhibited by BSA and BSA plus DP combination within one hour when pre-incubation occurred. NaOCl 5% showed antimicrobial activity within 15 min, which was inhibited within one hour only in the presence of both BSA and DP regardless of the pre-incubation period. HybenX® could represent a good alternative to common irrigants for the treatment of E. faecalis endodontic infections, showing a rapid antimicrobial activity not inhibited by organic and inorganic inhibitors.