Bloodstream infections: trends and evolution of incidence and etiology in a 12-year period (2010-2021)

INTRODUCTION

The epidemiological evolution of bloodstream infections (BSIs) in the last decade is not clearly defined. Our aim was to analyze the changes in the workload in our institution and to describe the evolution of the incidence and etiology of BSIs in a 12-year period, including the COVID-19 pandemic.

METHODS

All blood cultures received in the laboratory of a tertiary general hospital between 2010 and 2021 were analyzed. Bloodstream infection episodes refer to each episode of bacteremia or fungemia in each patient. Incidence rates per 1000 admissions and per 100,000 population were calculated.

RESULTS

No significant changes in the incidence of BSI episodes/1000 admissions were observed (mean, 31.1), while estimated population-based incidences showed declining trends (mean, 182.8/100,000 inhabitants). There was a slight increase in BSI episodes per 1000 admissions caused by Gram-negatives (mean, 16.6/1000 admissions) and E. coli was the most frequent pathogen (mean, 8.5/1000 admissions). There was no significant rise in episodes caused by ESBL- and carbapenemase-producing E. coli or K. pneumoniae, with a decline in those caused by methicillin-resistant S. aureus. A spike in BSI episodes, fungal BSIs and catheter-related infections was detected in 2020, during the COVID-19 outbreak.

CONCLUSIONS

No clear increase in the incidence of BSI episodes was detected in our center over this period. Gram-negatives are the most frequent etiology, with no clear rise in antimicrobial resistance phenotypes. The COVID-19 pandemic accounted for a small increase in BSI episodes in 2020, probably related to the increase of catheter-related infections.

Antifungal resistance in Candida spp within the intra-abdominal cavity: study of resistance acquisition in patients with serial isolates

OBJECTIVES

Antifungal susceptibility testing is mostly conducted on blood-cultured Candida spp isolates. Because the intra-abdominal cavity has been highlighted as a hidden echinocandin-resistant C. glabrata reservoir, we assessed whether testing sequential isolates from a given patient might increase the chances of detecting antifungal resistance.

METHODS

Intra-abdominal initial and sequential isolates from the same species from patients included in the CANDIdaemia in MADrid study (January 2019 to June 2022) were studied. We assessed antifungal susceptibility to amphotericin B, azoles, anidulafungin, micafungin, and ibrexafungerp using European Committee on Antimicrobial Susceptibility Testing (EUCAST) methodology and molecularly characterized resistant isolates.

RESULTS

We collected 308 isolates (C. albicans [n = 179/308; 58.1%], C. glabrata [n = 101/308; 32.8%], C. tropicalis [n = 17/308; 5.5%], and C. parapsilosis [n = 11/308; 3.6%]) from 112 patients distributed as incident (n = 125/308) and sequential (n = 183/308). Per patient resistance rates of fluconazole (13.4% [15/112] vs. 8% [9/112]); 5.4% proportions difference (95% CI, -2.7% to 13.5%, p 0.09) and echinocandins (8.9% [10/112] vs. 1.8% [2/112]); 7.1% proportions difference (95% CI; 1.2-12.9%; p 0.01) were higher when considering all available isolates than only incident isolates. Resistance was detected in 18 of 112 patients and would have been overlooked in 11 of 18 (61.1%) patients if only incident isolates had been studied. Of the patients who harboured fluconazole or echinocandin-resistant isolates, 14 of 15 and 8 of 10 had received or were receiving fluconazole or echinocandins, respectively.

DISCUSSION

Testing sequential Candida isolates from intra-abdominal samples is required to detect antifungal resistance, particularly to echinocandins, in patients whose incident isolates turned out to be susceptible. Furthermore, patients with echinocandin-resistant infections had frequently used echinocandins and had common secondary resistance acquisition.

Trends in antifungal resistance in Candida from a multicenter study conducted in Madrid (CANDIMAD study): fluconazole-resistant C. parapsilosis spreading has gained traction in 2022

We previously conducted a multicenter surveillance study on Candida epidemiology and antifungal resistance in Madrid (CANDIMAD study; 2019-2021), detecting an increase in fluconazole-resistant Candida parapsilosis. We here present data on isolates collected in 2022. Furthermore, we report the epidemiology and antifungal resistance trends during the entire period, including an analysis per ward of admission. Candida spp. incident isolates from blood cultures and intra-abdominal samples from patients cared for at 16 hospitals in Madrid, Spain, were tested with the EUCAST E.Def 7.3.2 method against amphotericin B, azoles, micafungin, anidulafungin, and ibrexafungerp and were molecularly characterized. In 2022, we collected 766 Candida sp. isolates (686 patients; blood cultures, 48.8%). Candida albicans was the most common species found, and Candida auris was undetected. No resistance to amphotericin B was found. Overall, resistance to echinocandins was low (0.7%), whereas fluconazole resistance was 12.0%, being higher in blood cultures (16.0%) mainly due to fluconazole-resistant C. parapsilosis clones harboring the Y132F-R398I ERG11p substitutions. Ibrexafungerp showed in vitro activity against the isolates tested. Whereas C. albicans was the dominant species in most hospital wards, we observed increasing C. parapsilosis proportions in blood. During the entire period, echinocandin resistance rates remained steadily low, while fluconazole resistance increased in blood from 6.8% (2019) to 16% (2022), mainly due to fluconazole-resistant C. parapsilosis (2.6% in 2019 to 36.6% in 2022). Up to 7 out of 16 hospitals were affected by fluconazole-resistant C. parapsilosis. In conclusion, rampant clonal spreading of C. parapsilosis fluconazole-resistant genotypes is taking place in Madrid.

Microbiome profile and calprotectin levels as markers of risk of recurrent Clostridioides difficile infection

Introduction

Clostridioides difficile infection (CDI) is the main cause of nosocomial diarrhoea in developed countries. Recurrent CDI (R-CDI), which affects 20%-30% of patients and significantly increases hospital stay and associated costs, is a key challenge. The main objective of this study was to explore the role of the microbiome and calprotectin levels as predictive biomarkers of R-CDI.

Methods

We prospectively (2019-2021) included patients with a primary episode of CDI. Clinical data and faecal samples were collected. The microbiome was analysed by sequencing the hypervariable V4 region of the 16S rRNA gene on an Illumina Miseq platform.

Results

We enrolled 200 patients with primary CDI, of whom 54 developed R-CDI and 146 did not. We analysed 200 primary samples and found that Fusobacterium increased in abundance, while Collinsella, Senegalimassilia, Prevotella and Ruminococcus decreased in patients with recurrent versus non-recurrent disease. Elevated calprotectin levels correlated significantly with R-CDI (p=0.01). We built a risk index for R-CDI, including as prognostic factors age, sex, immunosuppression, toxin B amplification cycle, creatinine levels and faecal calprotectin levels (overall accuracy of 79%).

Discussion

Calprotectin levels and abundance of microbial genera such as Fusobacterium and Prevotella in primary episodes could be useful as early markers of R-CDI. We propose a readily available model for prediction of R-CDI that can be applied at the initial CDI episode. The use of this tool could help to better tailor treatments according to the risk of R-CDI.

A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic

BACKGROUND

COVID-19 diagnosis lies on the detection of SARS-CoV-2 on nasopharyngeal specimens by RT-PCR. The Xpert-Xpress SARS-CoV-2 assay provides results in less than one hour from specimen reception, which makes it suitable for clinical/epidemiological circumstances that require faster responses. The analysis of a COVID-19 outbreak suspected in the neonatology ward from our institution showed that the Ct values obtained for the targeted genes in the Xpert assay were markedly different within each specimen (N Ct value > 20 cycles above the E Ct value).

RESULTS

We identified the mutation C29200T in the N gene as responsible for an impairment in the N gene amplification by performing whole genome sequencing of the specimens involved in the outbreak (Omicron variant). Subsequently, a retrospective analysis of all specimens sequenced in our institution allowed us to identify the same SNP as responsible for similar impairments in another 12 cases (42% of the total cases reported in the literature). Finally, we found that the same SNP emerged in five different lineages independently, throughout almost all the COVID-19 pandemic.

CONCLUSIONS

We demonstrated for the first time the impact of this SNP on the Xpert assay, when harbored by new Omicron variants. We extend our observation period throughout almost all the COVID-19 pandemic, offering the most updated observations of this phenomenon, including sequences from the seventh pandemic wave, until now absent in the reports related to this issue. Continuous monitoring of emerging SNPs that could affect the performance of the most commonly used diagnostic tests, is required to redesign the tests to restore their correct performance.

The Gastrointestinal Tract Is Pinpointed as a Reservoir of Candida albicans, Candida parapsilosis, and Candida tropicalis Genotypes Found in Blood and Intra-Abdominal Samples

BACKGROUND

Candida spp., as part of the microbiota, can colonise the gastrointestinal tract. We hypothesised that genotyping Candida spp. isolates from the gastrointestinal tract could help spot genotypes able to cause invasive infections.

MATERIALS/METHODS

A total of 816 isolates of C. albicans (n = 595), C. parapsilosis (n = 118), and C. tropicalis (n = 103) from rectal swabs (n = 754 patients) were studied. Genotyping was conducted using species-specific microsatellite markers. Rectal swab genotypes were compared with previously studied blood (n = 814) and intra-abdominal (n = 202) genotypes.

RESULTS

A total of 36/754 patients had the same Candida spp. isolated from blood cultures, intra-abdominal samples, or both; these patients had candidemia (n = 18), intra-abdominal candidiasis (n = 11), both clinical forms (n = 1), and non-significant isolation (n = 6). Genotypes matching the rectal swab and their blood cultures (84.2%) or their intra-abdominal samples (92.3%) were found in most of the significant patients. We detected 656 genotypes from rectal swabs, 88.4% of which were singletons and 11.6% were clusters. Of these 656 rectal swab genotypes, 94 (14.3%) were also detected in blood cultures and 34 (5.2%) in intra-abdominal samples. Of the rectal swab clusters, 62.7% were previously defined as a widespread genotype.

CONCLUSIONS

Our study pinpoints the gastrointestinal tract as a potential reservoir of potentially invasive Candida spp. genotypes.

Clinical impact of time to results from the microbiology laboratory in bloodstream infections caused by carbapenemase-producing Enterobacterales (TIME-CPE STUDY)

OBJECTIVES

To evaluate the impact of time to results (TTR) on the outcome of patients with carbapenemase-producing Enterobacterales bloodstream infections (CPE-BSI).

METHODS

Times-series study conducted from January 2014 to December 2021, selecting patients with first CPE-BSI episodes. Periods of intervention were defined according to implementation of diagnostic bundle tests in the microbiology laboratory: pre-intervention (January 2014-December 2017) and post-intervention (January 2018-December 2021). TTR was defined as time elapsed from positivity time of the blood culture bottles to physicians' notification of CPE-BSI episodes, and was evaluated in patients who received inappropriate empirical and switched to appropriate targeted treatment (switch group). Analysis of a composite unfavourable outcome (mortality at Day 30 and/or persistent and/or recurrent bacteraemia) was performed for the total episodes and in the switch group.

RESULTS

One hundred and nine episodes were analysed: 66 pre-intervention and 43 post-intervention. Compared with pre-intervention, patients in the post-intervention period were younger (68 versus 63 years, P = 0.04), had INCREMENT score > 7 (31.8% versus 53.5%, P = 0.02) and unfavourable outcome (37.9% versus 20.9%, P = 0.04). Proportion of TTR > 30 h was more frequent pre-intervention than post-intervention (61.7% versus 35.5%, P = 0.02). In multivariate analysis of the 109 episodes, source other than urinary or biliary (OR 2.76, 95% CI 1.11-6.86) was associated with unfavourable outcome, while targeted appropriate treatment trended to being protective (OR 0.17, 95% CI 0.03-1.00). Considering the switch group (n = 78), source other than urinary or biliary (OR 14.9, 95% CI 3.25-69.05) and TTR > 30 h (OR 4.72, 95% CI 1.29-17.22) were associated with unfavourable outcome.

CONCLUSIONS

Decreased TTR in the post-intervention period was associated with the outcome in patients with CPE-BSI episodes.

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.

Symbiosis between Cretaceous dinosaurs and feather-feeding beetles

Extant terrestrial vertebrates, including birds, have a panoply of symbiotic relationships with many insects and arachnids, such as parasitism or mutualism. Yet, identifying arthropod-vertebrate symbioses in the fossil record has been based largely on indirect evidence; findings of direct association between arthropod guests and dinosaur host remains are exceedingly scarce. Here, we present direct and indirect evidence demonstrating that beetle larvae fed on feathers from an undetermined theropod host (avian or nonavian) 105 million y ago. An exceptional amber assemblage is reported of larval molts (exuviae) intimately associated with plumulaceous feather and other remains, as well as three additional amber pieces preserving isolated conspecific exuviae. Samples were found in the roughly coeval Spanish amber deposits of El Soplao, San Just, and Peñacerrada I. Integration of the morphological, systematic, and taphonomic data shows that the beetle larval exuviae, belonging to three developmental stages, are most consistent with skin/hide beetles (family Dermestidae), an ecologically important group with extant keratophagous species that commonly inhabit bird and mammal nests. These findings show that a symbiotic relationship involving keratophagy comparable to that of beetles and birds in current ecosystems existed between their Early Cretaceous relatives.

Real-world Use of Bezlotoxumab and Fecal Microbiota Transplantation for the Treatment of Clostridioides difficile Infection

Background

We aimed to describe the frequency of use and effectiveness of bezlotoxumab (BZX) and fecal microbiota transplantation (FMT) in patients with Clostridioides difficile infection (CDI) in real-world practice.

Methods

This was a retrospective study conducted in a university hospital in which adult patients treated with BZX or FMT from January 2018 to April 2021 were included. The primary objective was to evaluate the effectiveness of BZX and FMT in preventing early (within 8 weeks) and late (within 1 year) CDI recurrences (rCDI). A multivariate analysis of risk factors for early recurrence was performed.

Results

Of 1377 consecutive CDI episodes, 117 (8.5%) received BZX or FMT, with full information available for 100 of the episodes: 51 received BZX, and 49 received FMT. BZX was used mostly in immunosuppressed patients (66.7%) and in first episodes or first recurrences in 70.6% of the cases. FMT was prescribed only in CDI recurrences. Despite the different conditions of the patients, there were no significant differences between BZX and FMT in preventing early rCDI (19.6% vs 24.5%; P = .55) or late rCDI (9.8% vs 18.4%; P = .31). In the multivariate analysis, risk factors for recurrence were presence of ≥2 previous rCDI episodes (odds ratio [OR], 2.90; 95% CI, 1.03-8.63) and use of non-CDI antibiotics (OR, 3.45; 95% CI, 1.24-9.57).

Conclusions

BZX and FMT were infrequently used in real-world practice. Both treatments had similar effectiveness in preventing CDI recurrence despite their application to different populations.

Characterization of the gut microbiome of patients with Clostridioides difficile infection, patients with non-C. difficile diarrhea, and C. difficile-colonized patients

Introduction

Clostridioides difficile infection (CDI) is the main cause of nosocomial diarrhea in developed countries. A key challenge in CDI is the lack of objective methods to ensure more accurate diagnosis, especially when differentiating between true infection and colonization/diarrhea of other causes. The main objective of this study was to explore the role of the microbiome as a predictive biomarker of CDI.

Methods

Between 2018 and 2021, we prospectively included patients with CDI, recurrent CDI (R-CDI), non-CDI diarrhea (NO-CDI), colonization by C. difficile, and healthy individuals. Clinical data and fecal samples were collected. The microbiome was analyzed by sequencing the hypervariable V4 region of the 16S rRNA gene on an Illumina Miseq platform. The mothur bioinformatic pipeline was followed for pre-processing of raw data, and mothur and R were used for data analysis.

Results

During the study period, 753 samples from 657 patients were analyzed. Of these, 247 were from patients with CDI, 43 were from patients colonized with C. difficile, 63 were from healthy individuals, 324 were from NOCDI, and 76 were from R-CDI. We found significant differences across the groups in alpha and beta diversity and in taxonomic abundance. We identified various genera as the most significant biomarkers for CDI (Bacteroides, Proteus, Paraprevotella, Robinsoniella), R-CDI (Veillonella, Fusobacterium, Lactobacillus, Clostridium sensu stricto I), and colonization by C. difficile (Parabacteroides, Faecalicoccus, Flavonifractor, Clostridium XVIII).

Discussion

We observed differences in microbiome patterns between healthy individuals, colonized patients, CDI, R-CDI, and NOCDI diarrhea. We identified possible microbiome biomarkers that could prove useful in the diagnosis of true CDI infections. Further studies are warranted.

Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis

BACKGROUND

Candidaemia and invasive candidiasis are typically hospital-acquired. Genotyping isolates from patients admitted to different hospitals may be helpful in tracking clones spreading across hospitals, especially those showing antifungal resistance.

METHODS

We characterized Candida clusters by studying Candida isolates (C. albicans, n = 1041; C. parapsilosis, n = 354, and C. tropicalis, n = 125) from blood cultures (53.8%) and intra-abdominal samples (46.2%) collected as part of the CANDIMAD (Candida in Madrid) study in Madrid (2019-2021). Species-specific microsatellite markers were used to define the genotypes of Candida spp. found in a single patient (singleton) or several patients (cluster) from a single hospital (intra-hospital cluster) or different hospitals (widespread cluster).

RESULTS

We found 83 clusters, of which 20 were intra-hospital, 49 were widespread, and 14 were intra-hospital and widespread. Some intra-hospital clusters were first detected before the onset of the COVID-19 pandemic, but the number of clusters increased during the pandemic, especially for C. parapsilosis. The proportion of widespread clusters was significantly higher for genotypes found in both compartments than those exclusively found in either the blood cultures or intra-abdominal samples. Most C. albicans- and C. tropicalis-resistant genotypes were singleton and presented exclusively in either blood cultures or intra-abdominal samples. Fluconazole-resistant C. parapsilosis isolates belonged to intra-hospital clusters harboring either the Y132F or G458S ERG11p substitutions; the dominant genotype was also widespread.

CONCLUSIONS

the number of clusters-and patients involved-increased during the COVID-19 pandemic mainly due to the emergence of fluconazole-resistant C. parapsilosis genotypes.

Blood and intra-abdominal Candida spp. from a multicentre study conducted in Madrid using EUCAST: emergence of fluconazole resistance in Candida parapsilosis, low echinocandin resistance and absence of Candida auris

OBJECTIVES

We prospectively monitored the epidemiology and antifungal susceptibility of Candida spp. from blood cultures and intra-abdominal samples in patients admitted to hospitals in the Madrid area.

METHODS

Between 2019 and 2021, we prospectively collected incident isolates [one per species, patient and compartment (blood cultures versus intra-abdominal samples)] from patients admitted to any of 16 hospitals located in Madrid. We studied the antifungal susceptibilities to amphotericin B, triazoles, micafungin, anidulafungin and ibrexafungerp following the EUCAST E.Def 7.3.2 procedure.

RESULTS

A total of 2107 Candida spp. isolates (1895 patients) from blood cultures (51.7%) and intra-abdominal samples were collected. Candida albicans, the Candida glabrata complex, the Candida parapsilosis complex, Candida tropicalis and Candida krusei accounted for 96.9% of the isolates; in contrast, Candida auris was undetected. Fluconazole resistance in Candida spp. was higher in blood cultures than in intra-abdominal samples (9.1% versus 8.2%; P > 0.05), especially for the C. parapsilosis complex (16.6% versus 3.6%, P < 0.05), whereas echinocandin resistance tended to be lower in blood cultures (0.5% versus 1.0%; P > 0.05). Resistance rates have risen, particularly for fluconazole in blood culture isolates, which increased sharply in 2021. Ibrexafungerp showed in vitro activity against most isolates. Species distributions and resistance rates varied among hospitals.

CONCLUSIONS

Whereas no C. auris isolates were detected, fluconazole-resistant C. parapsilosis isolates have been spreading across the region and this has pulled up the rate of fluconazole resistance. In contrast, the rate of echinocandin resistance continues to be low.

Clostridioides difficile infection epidemiology and clinical characteristics in COVID-19 pandemic

Information on Clostridioides difficile infection (CDI) in patients with COVID-19 is scarce and points to an overall decrease of episodes during the pandemic. This situation results paradoxical, as COVID-19 patients had long periods of hospital stay and high use of antibiotics. We conducted a retrospective study from January 1st 2019 to December 31st 2020 comparing the incidence of hospital-acquired episodes of CDI (HA-CDI) among patients with and without COVID-19 admitted to our institution. During the study period, there were 47,048 patient admissions in 2019, 35,662 admissions of patients without COVID-19 in 2020 and 6,763 of COVID-19 patients. There were 68 episodes of HA-CDI in COVID-19 patients (14.75/10,000 days), 159 in 2020-non-COVID-19 patients (5.54/10,000 days) and 238 in 2019 (6.80/10,000 days). Comparison of HA-CDI in COVID-19 and non-COVID-19 patients indicates it occurs more frequently, in terms of CDI disease severity, COVID-19 does not seem to have a negative impact.

Bezlotoxumab in the treatment of Clostridioides difficile infections: a real-life experience

OBJECTIVE

Following the approval of bezlotoxumab in 2017, studies evaluating its effectiveness in prevention of Clostridioides difficile infection under "real-life" conditions are scarce.

METHODS

We conducted a retrospective study developed in a large tertiary care hospital describing the use and outcomes of patients with Clostridioides difficile infection (CDI) treated with bezlotoxumab.

RESULTS

A total of 16 patients were include, all of whom had an episode of CDI with high probability of recurrence and 14 of them had some kind of immunosuppression. Bezlotoxumab was effective in the prevention of CDI recurrence in 11 of the 14 cases in which follow up was possible, without significant side effects.

CONCLUSIONS

Bezlotoxumab was well tolerated and the incidence of recurrent CDI in a high-risk population for recurrence was only 21.4%.

High incidence of COVID-19 at nursing homes in Madrid, Spain, despite preventive measures

OBJECTIVE

To assess the impact of COVID-19 at nine nursing homes in Madrid, Spain, during the first wave of COVID-19 infection and lockdown period when preventive measures were taken to avoid transmission among residents.

METHODS

Nine hundred forty-two residents and 846 staff members from nine nursing homes participated in the study (April 18 to June 20, 2020). All participants were tested for SARS-CoV-2 in the nasopharynx by PCR and for IgG antibodies detection. Microbiological status at sampling was defined as active infection (positive PCR ± presence of antibodies), past infection (negative PCR + presence of antibodies), or naïve participants (negative PCR + absence of antibodies).

RESULTS

Laboratory results helped classify the residents as having active infection (n=224; 23.8%), past infection (n=462; 49.1%), or being naïve (n=256; 27.1%); staff members were actively infected (n=127; 15.1%), had had a past infection (n=290; 34.2%), or were naïve (n=429; 50.7%). Overall, the percentage of participants with COVID-19 was significantly higher in residents than in staff members (72.8% vs 49.2%; P=0.001). The clinical situation of residents vs staff at sampling was as follows: acute manifestations compatible with COVID-19 (7.3% vs 3.9%; P<0.01) and no manifestations of infection (92.7% vs 96.0%; P<0.01). A large proportion of both asymptomatic and symptomatic residents (69.4% vs 86.6%; P=0.015) had positive PCR results (mostly alongside positive IgG determinations).

CONCLUSIONS

COVID-19 affects 75% of the residents in nursing homes in Madrid. The high impact in these settings, despite the strict restrictions adopted during the lockdown, demonstrates the ability of SARS-CoV-2 to cause outbreaks.

The role of biofilm production in Cutibacterium acnes strains isolated from breast implants

The role of C. acnes biofilm production in the pathogenesis of breast implants infections has not been deeply assessed. We analyze biofilm production (in terms of biomass and metabolic activity) between 40 Cutibacterium acnes strains isolated from breast implants and 32 from other sites. C. acnes strains isolated from breast implants showed higher metabolic activity than those isolated from other-locations and, especially, those from patients with capsular contracture .

Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain

Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases.

Dinosaur bonebed amber from an original swamp forest soil

Dinosaur bonebeds with amber content, yet scarce, offer a superior wealth and quality of data on ancient terrestrial ecosystems. However, the preserved palaeodiversity and/or taphonomic characteristics of these exceptional localities had hitherto limited their palaeobiological potential. Here, we describe the amber from the Lower Cretaceous dinosaur bonebed of Ariño (Teruel, Spain) using a multidisciplinary approach. Amber is found in both a root layer with amber strictly in situ and a litter layer mainly composed of aerial pieces unusually rich in bioinclusions, encompassing 11 insect orders, arachnids, and a few plant and vertebrate remains, including a feather. Additional palaeontological data—charophytes, palynomorphs, ostracods— are provided. Ariño arguably represents the most prolific and palaeobiologically diverse locality in which fossiliferous amber and a dinosaur bonebed have been found in association, and the only one known where the vast majority of the palaeontological assemblage suffered no or low-grade pre-burial transport. This has unlocked unprecedentedly complete and reliable palaeoecological data out of two complementary windows of preservation—the bonebed and the amber—from the same site.

SARS-CoV-2 superinfection and reinfection with three different strains

We report a corona virus disease (COVID‐19) case with unprecedented viral complexity. In the first severe episode, two different severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains (superinfection) were identified within a week. Three months after discharge, the patient was readmitted and was infected in a nosocomial outbreak with a different strain, suffering a second milder COVID‐19 episode.

Ticagrelor and Infection Risk in Patients with Coronary Artery Disease

BACKGROUND

Ticagrelor has a bactericidal effect in vitro, and clinical studies suggest a beneficial effect in infections. Our aim was to determine the incidence of infections in patients treated with 3 different P2Y12 receptor inhibitors.

METHODS

Retrospective registry in a cardiology department. Patients with coronary artery disease discharged on ticagrelor, prasugrel, or clopidogrel from March 2017 to June 2019 were included. The risk of infection was analyzed during the period of P2Y12 inhibitor treatment (12.4 ± 6.7 months).

RESULTS

A total of 250 patients were included (ticagrelor 91 [36.4%], prasugrel 89 [35.6%], clopidogrel 70 [28.0%]). Mean age was 61.0 ± 13.1 years, and 63 (25.2%) were women. The most common reason to use these drugs was ST-segment elevation acute myocardial infarction (STEMI) (152 patients - 60.8%). STEMI was the reason to use prasugrel in 84 patients (94.4%), ticagrelor in 44 (48.4%), and clopidogrel in 24 (34.3%), p < 0.001. An infection during follow-up was seen in 87 patients (34.8%), 23 treated with ticagrelor (25.3%), 30 with prasugrel (33.7%) and 34 with clopidogrel (48.6%), p = 0.009. Ticagrelor was independently associated with a lower likelihood of infection (Hazard Ratio [HR] 0.52, 95% confidence interval [CI] 0.28-0.95; p = 0.035) compared to prasugrel (HR 0.96, 95% CI 0.54-1.73; p = 0.909) and clopidogrel (HR = 1).

CONCLUSIONS

In patients admitted with coronary artery disease patients treated with ticagrelor had a lower frequency of infections during follow-up than those treated with other P2Y12 inhibitors. Further studies are necessary to clarify the bactericidal effect of ticagrelor in this context.

Palaeoneurology of the early cretaceous iguanodont Proa valdearinnoensis and its bearing on the parallel developments of cognitive abilities in theropod and ornithopod dinosaurs

Proa valdearinnoensis is a relatively large-headed and stocky iguanodontian dinosaur from the latest Early Cretaceous of Spain. Its braincase is known from three specimens. Similar to that of other dinosaurs, it shows a mosaic ossification pattern in which most of the bones seem to have fused together indistinguishably while a few (frontoparietal, basioccipital) might have remained loosely attached. The endocasts of the three specimens are described based on CT data and digital reconstructions. They show unmistakable morphological similarities with the endocast of closely related taxa, such as Sirindhorna khoratensis (which is close in age but from Thailand). This supports a high conservatism of the endocranial cavity. The issue of volumetric correspondence between endocranial cavity and brain in dinosaurs is analyzed. Although a brain-to-endocranial cavity (BEC) index of 0.50 has been traditionally used, we employ instead 0.73. This is indeed the mid-value between the situation in adults of Alligator mississippiensis and Gallus gallus, which are members of the extant bracketing taxa of dinosaurs (Crocodilia and Aves). We thence gauge the level of encephalization of P. valdearinnoensis through the calculation of the encephalization quotient (EQ), which remains valuable as a metric for assessing the degree of cognitive function in extinct taxa, especially those with fully ossified braincases like dinosaurs and other archosaurs. The EQ obtained for P. valdearinnoensis (3.611) suggests that this species was significantly more encephalized than most if not all extant nonavian, nonmammalian amniotes. Our work adds to the growing body of data concerning theoretical cognitive capabilities in dinosaurs and supports the idea that an increasing encephalization was fostered not only in theropods but also in parallel in the shorter-lived lineage of ornithopods. P. valdearinnoensis was ill-equipped to respond to theropod dinosaurs and possibly lived in groups as a strategy to mitigate the risk of being predated upon. We hypothesize that group-living and protracted caring of juveniles in this and possibly many other iguanodontian ornithopods favored a degree of encephalization that was outstanding by reptile standards.

Epidemiological, clinical and genomic snapshot of the first 100 B.1.1.7 SARS-CoV-2 cases in Madrid

We present clinical, genomic and epidemiological data on the first 106 cases with the SARS-CoV-2 B.1.1.7 variant in Madrid. Even from the start, the increase of this variant was due to transmission events within the community, some causing extensive clusters, rather than further imports. Most cases developed non-severe disease.

Identifying Anaerobic Bacteria Using MALDI-TOF Mass Spectrometry: A Four-Year Experience

Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1μl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.

Different dynamics of mean SARS-CoV-2 RT-PCR Ct values between the first and second COVID-19 waves in the Madrid population

SARS‐CoV‐2 RT‐PCR cycle threshold values from 18,803 cases (2 March–4 October) in Madrid define three stages: (i) initial ten weeks with sustained reduction in viral load (Ct: 23.4–32.3), (ii) stability with low viral loads (Ct: 31.9–35.5) in the next nine weeks and (iii) sudden increase with progressive higher viral loads until reaching stability at high levels in the next twelve weeks, coinciding with an increased percentage of positive cases and reduced median age. These data indicate differential virological/epidemiological patterns between the first and second COVID‐19 waves in Madrid.

Origin and evolution of turiasaur dinosaurs set by means of a new ‘rosetta’ specimen from Spain

Turiasauria is a non-neosauropod eusauropod clade of dinosaurs known since 2006, when the description of Turiasaurus was published. This group, including Losillasaurus, was originally thought to have been restricted to the Late Jurassic of Spain. However, over the last decade, our knowledge of this group has improved with the discovery of new taxa such as Zby from the Portuguese Late Jurassic, Tendaguria from the Tanzanian Late Jurassic and Mierasaurus and Moabosaurus from the Early Cretaceous of the USA. Here, we describe a new specimen of Losillasaurus from Spain, which allows us to better understand the character variation in the cranial and postcranial skeleton. The review of some sauropod fauna of Madagascar, and inclusion of some specimens of Turiasauria, suggest that this clade might have arisen in the Middle Jurassic. According to our phylogenetic results, a specimen found in the early 19th century in Madagascar is shown to be the oldest and only member of Turiasauria represented in the Middle Jurassic thus far. This is named Narindasaurus thevenini gen. & sp. nov.. Turiasauria is thus known from the Middle Jurassic in Pangaea, diversified in the Late Jurassic in Gondwana and Laurasia, and dispersed during the Early Cretaceous to North America.

Cretaceous amniote integuments recorded through a taphonomic process unique to resins

Fossil records of vertebrate integuments are relatively common in both rocks, as compressions, and amber, as inclusions. The integument remains, mainly the Mesozoic ones, are of great interest due to the panoply of palaeobiological information they can provide. We describe two Spanish Cretaceous amber pieces that are of taphonomic importance, one bearing avian dinosaur feather remains and the other, mammalian hair. The preserved feather remains originated from an avian dinosaur resting in contact with a stalactite-shaped resin emission for the time it took for the fresh resin to harden. The second piece shows three hair strands recorded on a surface of desiccation, with the characteristic scale pattern exceptionally well preserved and the strands aligned together, which can be considered the record of a tuft. These assemblages were recorded through a rare biostratinomic process we call "pull off vestiture" that is different from the typical resin entrapment and embedding of organisms and biological remains, and unique to resins. The peculiarity of this process is supported by actualistic observations using sticky traps in Madagascar. Lastly, we reinterpret some exceptional records from the literature in the light of that process, thus bringing new insight to the taphonomic and palaeoecological understanding of the circumstances of their origins.

Clinical impact of a Clostridioides (Clostridium) difficile bedside infectious disease stewardship intervention

Objectives

To evaluate the clinical impact of a bedside visit to patients with a positive Clostridioides difficile test on the antimicrobial stewardship of C. difficile infection (CDI) and non-C. difficile infections.

Methods

All patients ≥18 years old with positive CDI laboratory tests hospitalized between January 2017 and August 2017 received an immediate bedside intervention that consisted mainly of checking protective measures and providing recommendations on infection control and the management of CDI and other infections.

Results

A total of 214 patients were evaluated. The infectious disease (ID) physician was the first to establish protective measures in 25.2% of the cases. In 22/29 (75.9%) cases, physicians in charge accepted ID consultant recommendations to stop CDI treatment in asymptomatic patients. Unnecessary non-CDI antibiotics were discontinued in 19.1% of the cases. ID recommendations were not accepted by physicians in charge in only 12.6% of the cases.

Conclusions

A bedside rapid intervention for patients with a CDI-positive faecal sample was effective in avoiding overdiagnosis and unnecessary antibiotic treatment, optimizing anti-CDI drugs, increasing compliance with infection control measures and providing educational advice.

Recommendations for the diagnosis and treatment of Clostridioides difficile infection: An official clinical practice guideline of the Spanish Society of Chemotherapy (SEQ), Spanish Society of Internal Medicine (SEMI) and the working group of Postoperative Infection of the Spanish Society of Anesthesia and Reanimation (SEDAR)

This document gathers the opinion of a multidisciplinary forum of experts on different aspects of the diagnosis and treatment of Clostridioides difficile infection (CDI) in Spain. It has been structured around a series of questions that the attendees considered relevant and in which a consensus opinion was reached. The main messages were as follows: CDI should be suspected in patients older than 2 years of age in the presence of diarrhea, paralytic ileus and unexplained leukocytosis, even in the absence of classical risk factors. With a few exceptions, a single stool sample is sufficient for diagnosis, which can be sent to the laboratory with or without transportation media for enteropathogenic bacteria. In the absence of diarrhoea, rectal swabs may be valid. The microbiology laboratory should include C. difficile among the pathogens routinely searched in patients with diarrhoea. Laboratory tests in different order and sequence schemes include GDH detection, presence of toxins, molecular tests and toxigenic culture. Immediate determination of sensitivity to drugs such as vancomycin, metronidazole or fidaxomycin is not required. The evolution of toxin persistence is not a suitable test for follow up. Laboratory diagnosis of CDI should be rapid and results reported and interpreted to clinicians immediately. In addition to the basic support of all diarrheic episodes, CDI treatment requires the suppression of antiperistaltic agents, proton pump inhibitors and antibiotics, where possible. Oral vancomycin and fidaxomycin are the antibacterials of choice in treatment, intravenous metronidazole being restricted for patients in whom the presence of the above drugs in the intestinal lumen cannot be assured. Fecal material transplantation is the treatment of choice for patients with multiple recurrences but uncertainties persist regarding its standardization and safety. Bezlotoxumab is a monoclonal antibody to C. difficile toxin B that should be administered to patients at high risk of recurrence. Surgery is becoming less and less necessary and prevention with vaccines is under research. Probiotics have so far not been shown to be therapeutically or preventively effective. The therapeutic strategy should be based, rather than on the number of episodes, on the severity of the episodes and on their potential to recur. Some data point to the efficacy of oral vancomycin prophylaxis in patients who reccur CDI when systemic antibiotics are required again.

Three different patterns of positive Clostridium difficile laboratory tests. A comparison of clinical behavior

Clostridium difficile (CD) diagnosis is very varied and under discussion. Different research groups disagree on the clinical significance of patients with negative direct toxin and positive polymerase chain reaction (PCR) or even more with direct toxin and glutamate dehydrogenase (GDH) both negatives, but CD detected by toxigenic culture (TC). The objective was to analyze the characteristics of patients with 3 different diagnostic criteria. We compared these 3 groups of patients: group 1: (GDH+/direct toxin+/PCR+), group 2: (GDH+/direct toxin-/PCR+) and group 3: (GDH-/direct toxin-/PCR not done/TC+). The proportion of patients with CD infection (CDI) (not colonization) for groups 1 to 3 was, respectively, 90.3%, 95.4%, and 59.1%. No differences between severity (40.8%, 38.5%, 27.3%), recurrence (20.3%, 24.1%, 7.6%), or related mortality (12.5%, 5.2%, 0%) were found within the 3 groups of patients. Laboratory clinical results should not be used as the only tool to differentiate CDI versus colonization or severity. We recommend that PCR or a second-look TC be performed on all patients.

Faecal microbiota transplantation for recurrent Clostridioides difficile infection: experience with lyophilized oral capsules

BACKGROUND

Faecal microbiota transplantation (FMT) is a highly effective approach for refractory and recurrent Clostridioides difficile infection (CDI). Despite its excellent efficacy, FMT is not yet a routine procedure in most centres. There is very little experience with FMT based on lyophilized capsules, and data from European institutions are lacking. This article describes our experience with FMT to treat recurrent CDI using lyophilized oral capsules.

METHODS

A prospectively recorded single-centre case series of patients with recurrent CDI who underwent FMT between January 2018 and May 2019 were analysed. The primary outcome was defined as resolution of CDI without recurrences over a two-month period. Overall resolution was defined as resolution of diarrhoea without recurrence of CDI within two months after a further cycle of FMT. The FMT process involved oral ingestion of four or five lyophilized capsules in a single dose. All stool donors were rigorously screened.

FINDINGS

FMT was performed in 32 patients. Primary cure was achieved in 81.3% of patients, and the overall cure rate was 87.5%. FMT via lyophilized capsules was well tolerated. No FMT procedure-related adverse events and no further complications were observed for lyophilized-capsule FMT.

CONCLUSIONS

This initial clinical experience suggests that FMT based on oral lyophilized preparations is a safe, well-tolerated, and highly effective treatment for recurrent CDI. Administration of oral lyophilized capsules seems feasible in hospital routine and will enable FMT to be more widely used.

Susceptibility of uncommon Candida species to systemic antifungals by the EUCAST methodology

The incidence of infections by uncommon Candida species has increased in recent years, however, in vitro susceptibility data are scarce. Here we assess the susceptibility of C. krusei, C. dubliniensis, C. lusitaniae, and C. guilliermondii complex isolates (n = 120) to antifungal agents by the EUCAST methodology. C. dubliniensis proved to be the most susceptible species, similar to that of C. albicans (P &lt; .05), whereas C. guilliermondii was the least susceptible. Two C. krusei isolates were echinocandin-resistant and harbored a point mutation (L701M) in the FKS1. Some isolates were either fluconazole-resistant (C. lusitaniae, n = 2) or fluconazole non-wild type (C. guilliermondii, n = 3).

A new goniopholidid crocodyliform, Hulkepholis rori sp. nov. from the Camarillas Formation (early Barremian) in Galve, Spain)

Background

The neosuchian crocodyliform genus Hulkepholis constitutes the longirostral lineage of the European Goniopholididae. It comprises two species ranging from the Valanginian of southern England to the lower Albian of the northern Teruel (Spain). A new species of Hulkepholis is described based on a partially complete skull from the lower Barremian Camarillas Formation. We investigate its phylogenetic position and the palatal patterns among members of Goniopholididae and the closely related Thalattosuchia and Tethysuchia.

Methods

Phylogenetic relationships were investigated with two matrices using a previously published dataset as the basis: the first differed only by the addition of the new species, the second had newly discovered states for 11 characters, the new species plus several additional specimens of Hulkepholis and Anteophthalmosuchus. Both matrices were processed using TNT v. 1.1, in a heuristic analysis of maximum parsimony, with tree bisection and reconnection 1,000 random addition replicates and saving the 10 most parsimonious trees per replicate, and up to 10 suboptimal trees to calculate Bremer supports. The skull geometry of nine species from Thalattosuchia, Tethysuchia and Goniopholididae was explored to test shape variation between the rostral and postrostral modules, and to visualize the differences on the secondary palate. A set of 18 landmarks was used to delimit significant anatomical features, and the skulls were isotropically scaled using Adobe Illustrator, with the longest skull (Sarcosuchus imperator) as the baseline for comparison.

Results

The European lineages of goniopholidids are two clades (Nannosuchus + Goniopholis) plus (Hulkepholis + Anteophthalmosuchus). The new species, Hulkepholis rori sp. nov, shares with the latter clade the following apormorphies: a long anterolateral postorbital process, postorbital process almost reaching the anterior jugal ramus, and basioccipital tubera with lateral edges turned posteriorly. Anteophthalmosuchus was found to be monophyletic, and Hulkepholis paraphyletic due to the poor preservation of H. willetti. Hulkepholis rori is distinguished by having vascular fossae and a mid-protuberance on the ventral surface of the basioccipital, and wide internal fossae in the quadrate. Among Goniopholididae differences on the secondary palate are the presence of a palatal cleft, the narrowness of the secondary choana, and a wide foramen of the median pharyngeal tube.

Conclusions

The new species is the earliest Hulkepholis from the Iberian Peninsula. New characters have been recognized in the organization of the palate and in the occipital region raising unexpected questions on the evolution of Goniopholididae. The set of palatal characters is discussed as part of a singular palatogenesis in Goniopholididae. The protruding occipital areas suggest that the longirostral Hulkepholis would have had an aquatic lifestyle with particular neck and skull movements.

Diversity of Staphylococcus aureus clones in wild mammals in Aragon, Spain, with detection of MRSA ST130-mecC in wild rabbits

AIMS

To determine the Staphylococcus aureus carriage rate in wild mammals in Aragon, northern Spain, to analyse their antimicrobial resistance phenotype/genotype and to characterize the recovered isolates.

METHODS AND RESULTS

Nasal and rectal swabs of 103 mammals were collected in Aragón during the period 2012-2015. Antimicrobial susceptibility, the presence of antimicrobial resistance genes and virulence factors were investigated. Molecular characterization was carried out by spa, MLST, agr and SCCmec. Staphylococcus aureus were recovered from 23 animals (22%). Four of the 23 S. aureus were methicillin-resistant S. aureus (MRSA). Three MRSA were mecC-positive and were isolated from European rabbits and were typed as t843 (ascribed to CC130). The remaining MRSA was a mecA-carrying isolate from European hedgehog, typed as ST1-t386-SCCmecIVa-agrIII and it harboured the blaZ, erm(C), ant(6)-Ia and aph(3´)-IIIa resistance genes. A high diversity of spa-types was detected among the 19 methicillin-susceptible S. aureus isolates, which showed high susceptibility to the antimicrobials tested. The tst gene and different combinations of staphylococcal enterotoxins were found.

CONCLUSIONS

Staphylococcus aureus were detected in nasal and rectal samples of wild mammals. Wild rabbits could be a reservoir of mecC-MRSA.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides information on the presence and characteristics of S. aureus from mammals in a defined geographic region in Spain.

Prediction of poor outcome in Clostridioides difficile infection: A multicentre external validation of the toxin B amplification cycle

Classification of patients according to their risk of poor outcomes in Clostridioides difficile infection (CDI) would enable implementation of costly new treatment options in a subset of patients at higher risk of poor outcome. In a previous study, we found that low toxin B amplification cycle thresholds (C_t) were independently associated with poor outcome CDI. Our objective was to perform a multicentre external validation of a PCR-toxin B C_t as a marker of poor outcome CDI. We carried out a multicentre study (14 hospitals) in which the characteristics and outcome of patients with CDI were evaluated. A subanalysis of the results of the amplification curve of real-time PCR gene toxin B (XpertTM C. difficile) was performed. A total of 223 patients were included. The median age was 73.0 years, 50.2% were female, and the median Charlson index was 3.0. The comparison of poor outcome and non-poor outcome CDI episodes revealed, respectively, the following results: median age (years), 77.0 vs 72.0 (p = 0.009); patients from nursing homes, 24.4% vs 10.8% (p = 0.039); median leukocytes (cells/μl), 10,740.0 vs 8795.0 (p = 0.026); and median PCR-toxin B C_t, 23.3 vs 25.4 (p = 0.004). Multivariate analysis showed that a PCR-toxin B C_t cut-off <23.5 was significantly and independently associated with poor outcome CDI (p = 0.002; OR, 3.371; 95%CI, 1.565-7.264). This variable correctly classified 68.5% of patients. The use of this microbiological marker could facilitate early selection of patients who are at higher risk of poor outcome and are more likely to benefit from newer and more costly therapeutic options.

Fecal microbiota transplantation for recurrent Clostridium difficile infection: Experience, protocol, and results

OBJECTIVE

Fecal microbiota transplantation (FMT) is a highly effective therapy for recurrent Clostridium difficile infection (R-CDI). Despite its excellent efficacy, it is still not a routine procedure in most European centers. FMT has not been widely used in Spain to date. We describe our experience with FMT, including a novel approach based on oral fecal capsules.

METHODS

We analyzed a prospectively recorded case series of patients with R-CDI treated with FMT at a single center (June 2014-July 2017). Primary outcome was defined as resolution of CDI without recurrence in a two-month period. FMT was administered via colonoscopy, nasojejunal tube, or oral capsules. All stool donors were rigorously screened.

RESULTS

FMT was performed in 13 patients with R-CDI. Median age was 75.0 years and 76.9% were females. Six FMT were performed via nasojejunal tube, 5 via oral capsules, and 2 by colonoscopy. There were no procedure-related adverse events, except for bacteremia in one patient. During follow-up, R- CDI was observed in one patient at one month after FMT. The primary resolution rate was 83.3% and the overall resolution rate was 91.7%. FMT by capsules achieved a 100% resolution rate, colonoscopy 100%, and nasojejunal tube 80.0%.

CONCLUSIONS

In our cohort, FMT proved to be safe and effective, even in high risk patients. Oral administration in capsules also proved to be safe, well-tolerated, and highly effective for R-CDI. In our experience, the FMT capsule formulation seems feasible in the routine of a hospital. This administration method will allow FMT to be more widely used.

Fast track SSTI management program based on a rapid molecular test (GeneXpert® MRSA/SA SSTI) and antimicrobial stewardship

PURPOSE

This study examines the impacts of a skin and soft tissue infection (SSTI) management program involving a rapid diagnostic algorithm (Gram stain plus real-time PCR, GeneXpert® MRSA/SA SSTI) performed directly on clinical samples plus antimicrobial stewardship (AMS) counseling of the responsible physician.

METHODS

Participants were 155 consecutive adult inpatients with SSTI and good quality clinical samples submitted to the microbiology laboratory from April 2016 to January 2017. Results of the rapid test and AMS recommendations were phoned through to the responsible physician. The comparison group was a historical cohort.

RESULTS

Most SSTI were surgical wound infections (41.3% vs 38.1% for the intervention and comparison groups respectively) followed by diabetic foot (14.2% and 18.1%), abscesses (13.5% both) and cellulitis (12.9% both). Isolated microorganisms were mostly Gram-negative bacilli (two-thirds), followed by Staphylococcus aureus (SA). The ratio methicillin-susceptible SA (MSSA) to methicillin-resistant SA (MRSA) was 4:1. Improvements in the intervention cohort were: DOT (22.0 vs. 24.3 days, p = 0.007), treatment duration per SSTI episode (14.1 vs. 15.0 days, p = 0.072), treatment cost (433.1 vs. 533.3 €, p = 0.039), length of stay (18.6 vs 20.7 days, p = 0.031), related mortality (1 vs. 4 patients, p = 0.022) and Clostridium difficile infection (CDI) (4 vs. 8 patients, p = 0.050). In 48 cases (31.4%) in the intervention group, advice was given to improve empiric antibiotic treatment.

CONCLUSION

This type of program could help adjust antibiotic treatment when inappropriate, reducing antibiotic use and costs, length of stay, CDI and related mortality.

Identification of Porphyromonas isolates from clinical origin using MALDI-TOF Mass Spectrometry

Despite the wide implementation of MALDI-TOF MS for the rapid and reliable identification of most microorganisms, some taxonomic groups such as the Porphyromonas genus remain largely untested. In this study we evaluated the performance of MALDI-TOF MS on this genus using a collection of 39 isolates sent for routine identification to our institution over a 16-year period. All of them were identified by DNA-sequencing analysis of the 16S rRNA gene plus the hsp60 gene when the previous one did not yield species-level assignment. MALDI-TOF MS provided correct identification at least at the genus level of 21/39 isolates (53.9%). Twelve isolates were correctly identified at the species level with a score value ≥ 2.0 and 9 more with score values < 2.0 and ≥ 1.7. The species most represented in the database (P. gingivalis and P. somerae) lay within this category. However, the species poorly represented in this database (P. asaccharolytica and P. uenonis) were mostly identified with lower scores (1.35-1.67) or remained unidentified by MALDI-TOF MS. The addition of two P. asaccharolytica reference spectra to our in-house library allowed 72.9% of genus-level identifications with 17/37 isolates (45.9%) identified with score values ≥ 2.0. Our results showed a high level of correlation between MALDI-TOF MS and DNA-based identification for Porphyromonas spp. strains at the species level, even with score values < 2.0. The reliability provided by MALDI-TOF MS increased when the database was fed with spectra from the species poorly represented in the commercial database.

Descendants of the Jurassic turiasaurs from Iberia found refuge in the Early Cretaceous of western USA

A new, largely complete eusauropod dinosaur with cranial and postcranial elements from two skeletons, Mierasaurus bobyoungi gen. nov., sp. nov. from the lower Yellow Cat Member (Early Cretaceous) of Utah (USA), is the first recognized member of Turiasauria from North America. Moreover, according to our phylogenetic results, Moabosaurus utahensis from the lower Yellow Cat Member of Utah (USA) is also a member of this clade. This group of non-neosauropod eusauropods, which now includes five genera (Losillasaurus, Turiasaurus, Mierasaurus, Moabosaurus and Zby), was previously known only from the Jurassic of Europe. These recent discoveries in Utah suggest that turiasaurs as a lineage survived the Jurassic-Cretaceous extinction boundary and expanded their known range, at least, into western North America. The revised spatiotemporal distribution of turiasaurs is consistent with the presence of a land connection between North America and Europe sometime during the late Tithonian to Valanginian (c.147-133 Ma). Mierasaurus and Moabosaurus are the only non-neosauropod eusauropods known from North America, despite being younger than the classic neosauropods of the Morrison Formation (c.150 Ma).

Rifaximin-resistant Clostridium difficile strains isolated from symptomatic patients

BACKGROUND

Rifaximin has been proposed as an alternative treatment for specific cases of Clostridium difficile infection (CDI) and intestinal decontamination. Rifaximin-resistant C. difficile has occasionally been reported. Antibiotic susceptibility testing relies on anaerobic agar dilution (reference method), which is cumbersome and not routinely used. There is no commercial test for detection of resistance to rifaximin.

OBJECTIVES

To assess resistance to rifaximin by C. difficile and to evaluate the correlation between the results of the rifampicin E-test and susceptibility to rifaximin.

METHODS

We compared the in vitro susceptibility of clinical CDI isolates to rifaximin over a 6-month period using the agar dilution method with susceptibility to rifampicin using the E-test. All isolates were characterized using PCR-ribotyping. Clinical data were recorded prospectively.

RESULTS

We recovered 276 consecutive C. difficile isolates and found that 32.2% of episodes were caused by rifaximin-resistant strains. The MICs for rifaximin ranged from <0.0009-256 mg/L, with a geometric mean (GM) of 0.256 mg/L, an MIC_50/90 of 0.015/>256 mg/L. Rifaximin and rifampicin MICs were comparable, and all strains classed as resistant by agar dilution were correctly classified as resistant by E-test. The most common ribotypes were 001 (37.2%), 078/126 (14.3%), and 014 (12.0%). Ribotype 001 exhibited the highest MICs for rifaximin.

CONCLUSIONS

Resistance to rifaximin was common; resistance rates were higher in ribotype 001 strains. Susceptibility to rifaximin determined by agar dilution correlated with susceptibility to rifampicin determined using the E-test, including rifaximin-resistant strains. Our results suggest that the rifampicin E-test is a valid method for the prediction of rifaximin-resistant C. difficile.

Direct identification of clinical pathogens from liquid culture media by MALDI-TOF MS analysis

OBJECTIVES

We propose using MALDI-TOF MS as a tool for identifying microorganisms directly from liquid cultures after enrichment of the clinical sample in the media, to obtain a rapid microbiological diagnosis and an adequate administration of the antibiotic therapy in a clinical setting.

METHODS

To evaluate this approach, a series of quality control isolates were grown in thioglycollate (TG) broth and brain heart infusion (BHI) broth and extracted under four different protocols before finally being identified by MALDI-TOF MS. After establishing the best extraction protocol, we validated the method in a total of 300 liquid cultures (150 in TG broth and 150 in BHI broth) of different types of clinical samples obtained from two tertiary Spanish hospitals.

RESULTS

The initial evaluation showed that the extraction protocol including a 5 minute sonication step yielded 100% valid identifications, with an average score value of 2.305. In the clinical validation of the procedure, 98% of the microorganisms identified from the TG broth were correctly identified relative to 97% of those identified from the BHI broth. In 24% of the samples analysed, growth by direct sowing was only successful in the liquid medium, and no growth was observed in the direct solid agar cultures.

CONCLUSIONS

Use of MALDI-TOF MS plus the sonication-based extraction method enabled direct and accurate identification of microorganisms in liquid culture media in 15 minutes, in contrast to the 24 hours of subculture required for conventional identification, allowing the administration of a targeted antimicrobial therapy.

HCV core-antigen assay as an alternative to HCV RNA quantification: A correlation study for the assessment of HCV viremia

INTRODUCTION

Detection of hepatitis C virus (HCV) RNA and the HCV core antigen assay (HCV-Ag) are reliable techniques for the diagnosis of active and chronic HCV infection. Our aim was to evaluate the HCV-Ag assay as an alternative to quantification of HVC RNA.

METHODS

A comparison was made of the sensitivity and specificity of an HCV-Ag assay (204 serum samples) with those of a PCR assay, and the correlation between the two techniques was determined.

RESULTS

The sensitivity and specificity of HCV-Ag was 76.6% and 100%, respectively. Both assays were extremely well correlated (Pearson coefficient=0.951). The formula (LogCV=1.15*LogAg+2.26) was obtained to calculate the viral load by PCR from HCV-Ag values. HCV-Ag was unable to detect viral loads below 5000IU/mL.

CONCLUSION

Although the HCV-Ag assay was less sensitive than the PCR assay, the correlation between both assays was excellent. HCV-Ag can be useful as a first step in the diagnosis of acute or chronic HCV infection and in emergency situations.