Difficult-to-treat (DTR) Pseudomonas aeruginosa harboring Verona-Integron metallo-ß-lactamase (blaVIM): infection management and molecular analysis.

Pseudomonas aeruginosa harboring Verona Integron-encoded metallo-ß-lactamase enzymes (VIM-CRPA) have been associated with infection outbreaks in several parts of the world. In the US, however, VIM-CRPA remain rare. Starting in December 2018, we identified a cluster of cases in our institution. Herein, we present our epidemiological investigation and strategies to control/manage these challenging infections. This study was conducted in a large academic healthcare system in Miami, FL, between December 2018 and January 2022. Patients were prospectively identified via rapid molecular diagnostics when cultures revealed carbapenem-resistant P. aeruginosa. Alerts were received in real time by the antimicrobial stewardship program and infection prevention teams. Upon alert recognition, a series of interventions were performed as a coordinated effort. A retrospective chart review was conducted to collect patient demographics, antimicrobial therapy, and clinical outcomes. Thirty-nine VIM-CRPA isolates led to infection in 21 patients. The majority were male (76.2%); the median age was 52 years. The majority were mechanically ventilated (n = 15/21; 71.4%); 47.6% (n = 10/21) received renal replacement therapy at the time of index culture. Respiratory (n = 20/39; 51.3%) or bloodstream (n = 13/39; 33.3%) were the most common sources. Most infections (n = 23/37; 62.2%) were treated with an aztreonam-avibactam regimen. Six patients (28.6%) expired within 30 days of index VIM-CRPA infection. Fourteen isolates were selected for whole genome sequencing. Most of them belonged to ST111 (12/14), and they all carried blaVIM-2 chromosomally. This report describes the clinical experience treating serious VIM-CRPA infections with either aztreonam-ceftazidime/avibactam or cefiderocol in combination with other agents. The importance of implementing infection prevention strategies to curb VIM-CRPA outbreaks is also demonstrated.

Large scale sampling of Mexican maize landraces for the presence of transgenes.

The presence and levels of transgenic maize in Mexico and the effect this could have on local landraces or closely related species such as teosinte has been the subject of several previous reports, some showing contrasting results. Cultural, social and political factors all affect maize cultivation in Mexico and although since 1998 there has been a moratorium on the commercial cultivation of transgenic maize, Mexico imports maize, mainly from the USA where transgenic cultivars are widely grown. Additionally extensive migration between rural areas in Mexico and the USA and customs of seed exchange between farmers may also play an unintentional role in the establishment of transgenic seed. A comprehensive study of all Mexican maize landraces throughout the country is not feasible, however this report presents data based on analysis of 3204 maize accessions obtained from the central region of Mexico (where permits have never been authorized for cultivation of transgenic maize) and the northern region (where for a short period authorization for experimental plots was granted). The results of the study confirm that transgenes are present in all the geographical areas sampled and were more common in germplasm obtained in the northern region. However, there was no evidence that regions where field trials had been authorized showed higher levels of transgene presence or that the morphology of seed lots harboring transgenic material was significantly modified in favor of expected transgenic phenotypes.

Antibiotic prescription errors: the relationship with clinical competence in junior medical residents.

BACKGROUND: A large portion of prescribing errors can be attributed to deficiencies in medication knowledge. These errors are preventable and most often occur at the time of prescription. Antimicrobials are the drug class most common incorrectly prescribed. OBJECTIVE: To characterize the relationship between clinical competence and antibiotic prescription errors. We also investigated the frequency and severity of antibiotic prescription errors to identify items and attributes of clinical competence which are correlated with the antibiotic prescription error ratio. METHOD: A cross-sectional study was applied to assess clinical competence of junior medical residents in two reference academic hospitals and a regional hospital in Mexico City. It was conducted during February 2019. We used an infectious disease Objective Structured Clinical Examination (OSCE) to assess clinical competence and a measure of frequency, and severity of antibiotic prescription errors. RESULTS: The number of eligible participants was ~ 255 (hospital meeting attendance), and the number of residents in this study were 51 (~ 20%), 31 were female (60.8%). The mean OSCE score was 0.692 ± 0.073. The inter-item (Cronbach's alpha = 0.927) and inter-station internal consistency was adequate (Cronbach's alpha = 0.774). The G coefficient in generalizability theory analysis was 0.84. The antibiotic prescription error ratio was 45.1% ± 7%. The most frequent category of severity of antibiotic prescription errors was category E (errors that may contribute to or result in temporary harm to the patient and require intervention), 235 (65.2%). We observed a negative and significant correlation between clinical competence and antibiotic prescription errors (r = -0.33, p < 0.05, CI95% -0.57 to -0.07), which remained significant after controlling for the effect of gender and time since graduation from medical school (r = -0.39, p < 0.01, CI95% -0.625 to -0.118). Using exploratory factor analysis we identified two factors, which explained 69% of the variance in clinical competence, factor 1 evaluated socio-clinical skills and factor 2 evaluated diagnostic-therapeutic skills. Factor 2 was correlated with antibiotic prescription error ratio (r = -0.536, p < 0.001). CONCLUSIONS: We observed a negative correlation between clinical competence and antibiotic prescription error ratio in graduated physicians who have been accepted in a medical specialty. The therapeutic plan, which is a component of the clinical competence score, and the prescription skills had a negative correlation with antibiotic prescription errors. The most frequent errors in antibiotic prescriptions would require a second intervention.

Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis.

During the ripening process, the pericarp of chili pepper (Capsicum spp.) fruits accumulates large amounts of carotenoids. Although the carotenoid biosynthesis pathway in the Capsicum genus has been widely studied from different perspectives, the transcriptional regulation of genes encoding carotenoid biosynthetic enzymes has not been elucidated in this fruit. We analyzed RNA-Seq transcriptomic data from the fruits of 12 accessions of Capsicum annuum during the growth, development, and ripening processes using the R package named Salsa. We performed coexpression analyses between the standardized expression of genes encoding carotenoid biosynthetic enzymes (target genes (TGs)) and the genes of all expressed transcription factors (TFs). Additionally, we analyzed the promoter region of each biosynthetic gene to identify putative binding sequences for each selected TF candidate. We selected 83 TFs as putative regulators of the carotenogenic structural genes. From them, putative binding sites in the promoters of the carotenoid-biosynthesis-related structural genes were found for only 54 TFs. These results could guide the search for transcription factors involved in the regulation of the carotenogenic pathway in chili pepper fruits and might facilitate the collection of corresponding experimental evidence to corroborate their participation in the regulation of this biosynthetic pathway in Capsicum spp.

Comparison of the clinical and ultrasound evaluation of haemophilic arthropathy in children.

BACKGROUND: Joint ultrasound examination using the HEAD-US method in the detection of early arthropathy is poorly studied in our country. OBJECTIVE: To compare the clinical and ultrasound evaluation of the joints in haemophilia. METHOD: Longitudinal, prospective and descriptive study with paediatric patients with haemophilia A and B evaluated with the HJHS 2.1 scale and ultrasound with a linear transducer of 8 to 12 MHz. Elbows, knees and ankles joints were evaluated bilaterally, with HEAD-US protocol. RESULTS: 69 paediatric patients were included of which 48 with severe haemophilia A (weight: 40.1 kg). On the HJHS scale, a greater involvement was observed in the left knee (0.49), and less in the right ankle (0.05). With the HEAD-US scale, the most affected was the right knee (0.78). There is a significant relationship in the involvement of the right knee evaluated with the HEAD-US scale in the presence of inhibitor. CONCLUSIONS: Weight above the 50th percentile is an independent risk factor for joint bleeding complications, while age and type of haemophilia do not appear to be related. The HEAD-US method is a useful and accessible tool for early detection of arthropathy and hemarthrosis.

ANTECEDENTES: La exploración articular por ultrasonido mediante el método HEAD-US en la detección de la artropatía temprana ha sido poco estudiada en nuestro país. OBJETIVO: Comparar la evaluación clínica y por ultrasonido de las articulaciones en niños con hemofilia. MÉTODOS: Estudio longitudinal, prospectivo y descriptivo con pacientes pediátricos con hemofilia A y B valorados con la escala HJHS 2.1 y ultrasonido con transductor lineal de 8 a 12 MHz. Se evaluaron las articulaciones de codos, rodillas y tobillos de forma bilateral, con el método HEAD-US. RESULTADOS: Se incluyeron 69 pacientes; de ellos, 48 con hemofilia A grave (peso: 40.1 kg). En la escala HJHS se observó mayor afectación en la rodilla izquierda (0.49) y menor en el tobillo derecho (0.05). Con la escala HEAD-US, la más afectada fue la rodilla derecha (0.78). Existe una relación significativa en la afectación de la rodilla derecha evaluada con la escala HEAD-US en presencia de inhibidor. CONCLUSIONES: El peso superior al percentil 50 es un factor de riesgo independiente de complicaciones por sangrado articular, mientras que la edad y el tipo de hemofilia no parecen relacionados. El método HEAD-US es una herramienta útil y accesible para la detección temprana de artropatía y hemartrosis.

Elevated MICs of Susceptible Antipseudomonal Cephalosporins in Non-Carbapenemase-Producing, Carbapenem-Resistant Pseudomonas aeruginosa: Implications for Dose Optimization.

The present study evaluated the in vitro potency of ceftazidime and cefepime among carbapenem-resistant Pseudomonas aeruginosa isolates collected as part of a global surveillance program and assessed the pharmacodynamic implications using previously published population pharmacokinetics. When susceptible, MICs resulted at the high end of distribution for both ceftazidime and cefepime, thus 6 g/day was required to achieve optimal pharmacodynamic profiles. These findings should be considered in the clinic and for the application of CLSI susceptibility breakpoints.

Association between cycle threshold (Ct ) values and clinical and laboratory data in inpatients with COVID-19 and asymptomatic health workers.

In-house assays for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative reverse-transcription polymerase chain reaction (qRT-PCR), are feasible alternatives, particularly in developing countries. Cycle threshold (Ct ) values obtained by qRT-PCR were compared with clinical and laboratory data from saliva of inpatients with COVID-19 and asymptomatic health workers (AHW) were studied. Saliva specimens from 58 inpatients confirmed by qRT-PCR for SARS-CoV-2 using nasopharyngeal specimens, and 105 AHW were studied by qRT-PCR using three sets of primers for the N (N1, N2, and N3) gene of SARS-CoV-2, according to the CDC Diagnostic Panel protocol, showing a positivity of 88% for inpatients and 8% for AHW. Bivariate analysis revealed an association between Ct < 38.0 values for N2 and mechanical ventilation assistance among patients (p = .013). In addition, values of aspartate-transaminase, lactate dehydrogenase, and ferritin showed significant correlations with Ct values of N1 and N3 genes in inpatients. Therefore, our results show that Ct values correlate with some relevant clinical data for inpatients with COVID-19.

The ERACE-PA Global Surveillance Program: Ceftolozane/tazobactam and Ceftazidime/avibactam in vitro Activity against a Global Collection of Carbapenem-resistant Pseudomonas aeruginosa.

The cephalosporin-ß-lactamase-inhibitor-combinations, ceftolozane/tazobactam and ceftazidime/avibactam, have revolutionized treatment of carbapenem-resistant Pseudomonas aeruginosa (CR-PA). A contemporary assessment of their in vitro potency against a global CR-PA collection and an assessment of carbapenemase diversity are warranted. Isolates determined as CR-PA by the submitting site were collected from 2019-2021 (17 centers in 12 countries) during the ERACE-PA Global Surveillance Program. Broth microdilution MICs were assessed per CLSI standards for ceftolozane/tazobactam, ceftazidime/avibactam, ceftazidime, and cefepime. Phenotypic carbapenemase testing was conducted (modified carbapenem inactivation method (mCIM)). mCIM positive isolates underwent genotypic carbapenemase testing using the CarbaR, the CarbaR NxG, or whole genome sequencing. The MIC50/90 was reported as well as percent susceptible (CLSI and EUCAST interpretation). Of the 807 isolates, 265 (33%) tested carbapenemase-positive phenotypically. Of these, 228 (86%) were genotypically positive for a carbapenemase with the most common being VIM followed by GES. In the entire cohort of CR-PA, ceftolozane/tazobactam and ceftazidime/avibactam had MIC50/90 values of 2/ > 64 and 4/64 mg/L, respectively. Ceftazidime/avibactam was the most active agent with 72% susceptibility per CLSI compared with 63% for ceftolozane/tazobactam. For comparison, 46% of CR-PA were susceptible to ceftazidime and cefepime. Against carbapenemase-negative isolates, 88 and 91% of isolates were susceptible to ceftolozane/tazobactam and ceftazidime/avibactam, respectively. Ceftolozane/tazobactam and ceftazidime/avibactam remained highly active against carbapenem-resistant P. aeruginosa, particularly in the absence of carbapenemases. The contemporary ERACE-PA Global Program cohort with 33% carbapenemase positivity including diverse enzymology will be useful to assess therapeutic options in these clinically challenging organisms with limited therapies.

Genome-Wide Identification and Analysis of the MYB Transcription Factor Gene Family in Chili Pepper (Capsicum spp.).

The MYB transcription factor family is very large and functionally diverse in plants, however, only a few members of this family have been reported and characterized in chili pepper (Capsicum spp.). In the present study, we performed genome-wide analyses of the MYB family in Capsicum annuum, including phylogenetic relationships, conserved domain, gene structure organization, motif protein arrangement, chromosome distribution, chemical properties predictions, RNA-seq expression, and RT-qPCR expression assays. A total of 235 non-redundant MYB proteins were identified from C. annuum, including R2R3-MYB, 3R-MYB, atypical MYB, and MYB-related subclasses. The sequence analysis of CaMYBs compared with other plant MYB proteins revealed gene conservation, but also potential specialized genes. Tissue-specific expression profiles showed that CaMYB genes were differentially expressed, suggesting that they are functionally divergent. Furthermore, the integration of our data allowed us to propose strong CaMYBs candidates to be regulating phenylpropanoid, lignin, capsaicinoid, carotenoid, and vitamin C biosynthesis, providing new insights into the role of MYB transcription factors in secondary metabolism. This study adds valuable knowledge about the functions of CaMYB genes in various processes in the Capsicum genus.

Compacta: a fast contig clustering tool for de novo assembled transcriptomes.

BACKGROUND: RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these transcripts. However, for unknown genomes, de novo assembly of RNA-Seq reads must be performed to generate a set of contigs that represents the transcriptome. These contig sets contain multiple transcripts, including immature mRNAs, spliced transcripts and allele variants, as well as products of close paralogs or gene families that can be difficult to distinguish. Thus, tools are needed to select a set of less redundant contigs to represent the transcriptome for downstream analyses. Here we describe the development of Compacta to produce contig sets from de novo assemblies. RESULTS: Compacta is a fast and flexible computational tool that allows selection of a representative set of contigs from de novo assemblies. Using a graph-based algorithm, Compacta groups contigs into clusters based on the proportion of shared reads. The user can determine the minimum coverage of the contigs to be clustered, as well as a threshold for the proportion of shared reads in the clustered contigs, thus providing a dynamic range of transcriptome compression that can be adapted according to experimental aims. We compared the performance of Compacta against state of the art clustering algorithms on assemblies from Arabidopsis, mouse and mango, and found that Compacta yielded more rapid results and had competitive precision and recall ratios. We describe and demonstrate a pipeline to tailor Compacta parameters to specific experimental aims. CONCLUSIONS: Compacta is a fast and flexible algorithm for the determination of optimum contig sets that represent the transcriptome for downstream analyses.

KPC-3-Producing Serratia marcescens Outbreak between Acute and Long-Term Care Facilities, Florida, USA.

We describe an outbreak caused by Serratia marcescens carrying blaKPC-3 that was sourced to a long-term care facility in Florida, USA. Whole-genome sequencing and plasmid profiling showed involvement of 3 clonal lineages of S. marcescens and 2 blaKPC-3-carrying plasmids. Determining the resistance mechanism is critical for timely implementation of infection control measures.

Successful Treatment of Invasive Fungal Infection Due to Highly Resistant Aspergillus calidoustus in an Allogeneic Hematopoietic Cell Transplant Recipient.

Invasive aspergillosis (IA) is the most common invasive fungal infection following a hematopoietic cell transplant, with emerging cryptic species exhibiting resistance to commonly used antifungals such as azoles. These species have been increasingly found after the introduction of anti-mold prophylaxis. We report a case of a 56-year-old female with primary myelofibrosis whose allogeneic hematopoietic cell transplant was complicated by disseminated fungal infection (skin, lung) due to Aspergillus calidoustus, a cryptic specie. Treatment of Aspergillus species remains challenging as these cryptic species are usually resistant to azoles including voriconazole which is the first line of treatment of IA. Infection was successfully treated with surgical excision and combination antifungal therapy based on in vitro susceptibility and synergy testing. Therapy included isavuconazole, a drug that has been shown to be non-inferior to voriconazole in the treatment of invasive mold infections.

Transcriptional landscapes of Axolotl (Ambystoma mexicanum).

The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.

Linezolid- and Vancomycin-resistant Enterococcus faecium in Solid Organ Transplant Recipients: Infection Control and Antimicrobial Stewardship Using Whole Genome Sequencing.

BACKGROUND: Vancomycin-resistant enterococci are an important cause of healthcare-associated infections and are inherently resistant to many commonly used antibiotics. Linezolid is the only drug currently approved by the US Food and Drug Administration to treat vancomycin-resistant enterococci; however, resistance to this antibiotic appears to be increasing. Although outbreaks of linezolid- and vancomycin-resistant Enterococcus faecium (LR-VRE) in solid organ transplant recipients remain uncommon, they represent a major challenge for infection control and hospital epidemiology. METHODS: We describe a cluster of 4 LR-VRE infections among a group of liver and multivisceral transplant recipients in a single intensive care unit. Failure of treatment with linezolid in 2 cases led to a review of standard clinical laboratory methods for susceptibility determination. Testing by alternative methods including whole genome sequencing (WGS) and a comprehensive outbreak investigation including sampling of staff members and surfaces was performed. RESULTS: Review of laboratory testing methods revealed a limitation in the VITEK 2 system with regard to reporting resistance to linezolid. Linezolid resistance in all cases was confirmed by E-test method. The use of WGS identified a resistant subpopulation with the G2376C mutation in the 23S ribosomal RNA. Sampling of staff members' dominant hands as well as sampling of surfaces in the unit identified no contaminated sources for transmission. CONCLUSIONS: This cluster of LR-VRE in transplant recipients highlights the possible shortcomings of standard microbiology laboratory methods and underscores the importance of WGS to identify resistance mechanisms that can inform patient care, as well as infection control and antibiotic stewardship measures.

"Double carbapenem" and oral fosfomycin for the treatment of complicated urinary tract infections caused by blaNDM -harboring Enterobacteriaceae in kidney transplantation.

Infections with carbapenemase-producing carbapenem-resistant Enterobacteriaceae represent an emergent problem worldwide. Treatment of infections caused by New Delhi metallo-beta-lactamase (NDM)-harboring Enterobacteriaceae is particularly challenging as it frequently involves the use of nephrotoxic agents, which is problematic in kidney transplant recipients and non-renal transplant patients with marginal kidney function. We present two cases of urinary tract infections caused by NDM-harboring Enterobacteriaceae successfully treated with a combination of "double carbapenem" and oral fosfomycin.

Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation.

Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation-responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.

Invasive Rhinosinusitis Caused by Lasiodiplodia theobromae in an Allogeneic Hematopoietic Cell Transplant Recipient Case Report and Review of Literature.

Lasiodiplodia theobromae is a known plant pathogen in tropical and subtropical areas. Few cases have been reported in humans (usually keratitis and endophthalmitis) with only two cases of fungal sinusitis in immunocompromised and immunocompetent patients published to date. We report a case of invasive sinusitis secondary to L. theobromae in an allogeneic hematopoietic cell transplant recipient successfully treated with surgical debridement and triazole antifungals with a review of available literature.

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates.

BACKGROUND: Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two. RESULTS: Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome. CONCLUSIONS: lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

Dynamics of the chili pepper transcriptome during fruit development.

BACKGROUND: The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. RESULTS: RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueño 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. CONCLUSIONS: In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.