Molecular Identification of Candida Species in the Oral Microbiota of Individuals with Down Syndrome: A Case–Control Study

Mycopathologia - Candida species are common in the human oral microbiota and may cause oral candidiasis (OC) when the microbiota equilibrium is disturbed. Immunosuppressed individuals are...     

Outbreak of Hepatitis B Virus Infections Associated with Assisted Monitoring of Blood Glucose in an Assisted Living Facility–Virginia, 2010

Introduction

In January 2010, the Virginia Department of Health received reports of 2 hepatitis B virus (HBV) infections (1 acute, 1 chronic) among residents of a single assisted living facility (ALF). Both infected residents had diabetes and received assisted monitoring of blood glucose (AMBG) at the facility. An investigation was initiated in response.

Objective

To determine the extent and mechanism of HBV transmission among ALF residents.

Design

Retrospective cohort study.

Setting

An ALF that primarily housed residents with neuropsychiatric disorders in 2 adjacent buildings in Virginia.

Participants

Residents of the facility as of March 2010.

Measurements

HBV serologic testing, relevant medical history, and HBV genome sequences. Risk ratios (RR) and 95% confidence intervals (CIs) were used to identify risk factors for HBV infection.

Results

HBV serologic status was determined for 126 (91%) of 139 residents. Among 88 susceptible residents, 14 became acutely infected (attack rate, 16%), and 74 remained uninfected. Acute HBV infection developed among 12 (92%) of 13 residents who received AMBG, compared with 2 (3%) of 75 residents who did not (RR  = 35; 95% CI, 8.7, 137). Identified infection control breaches during AMBG included shared use of fingerstick devices for multiple residents. HBV genome sequencing demonstrated 2 building-specific phylogenetic infection clusters, each having 99.8–100% sequence identity.

Limitations

Transfer of residents out of the facility prior to our investigation might have contributed to an underestimate of cases. Resident interviews provided insufficient information to fully assess behavioral risk factors for HBV infection.

Conclusions

Failure to adhere to safe practices during AMBG resulted in a large HBV outbreak. Protection of a growing and vulnerable ALF population requires improved training of staff and routine facility licensing inspections that scrutinize infection control practices.     

Isolation of Candida auris in large hospitals in the Autonomous Community of Valencia; population-based study (2013–2017)

BackgroundCandida auris is an emerging multidrug-resistant and highly virulent yeast that spreads easily among patients.AimsTo describe the characteristics of candidemia caused by C. auris in the southeast of Spain (Autonomous Community of Valencia – ACV) through a 5-year population-based study.MethodsAn analysis of all the episodes of candidemia diagnosed in the ACV, with approximately 4,500,000 inhabitants, during 2013–2017, was done. Data were obtained from the Epidemiological Surveillance Valencian Network, a network that collects all the microbiological data from the hospitals in the study region.ResultsBased on the records, 1.9% of the isolates recovered from the positive blood cultures (corresponding to 1789 patients) were yeasts. This implies an annual rate of 7.09 cases/100,000 inhabitants. Of the 23 yeast species isolated, Candida albicans was the most frequent (37.3%), showing a higher frequency than Candida parapsilosis (28.4%) and Candida glabrata (15.6%) (p < 0.0001). It is remarkable the emergence of C. auris during 2016 and 2017, as this species became the fourth more prevalent in 2016 (9.2%), and the third in 2017 (15.7%). Fungemia was more common in hospitals with >500 beds (63.3% versus 36.7% in small hospitals) (p < 0.0001), and C. auris was mostly isolated in large hospitals (8.5% versus 0.3%); its incidence was higher in autumn and among the age group of 65–84 years.ConclusionsThe information about the local epidemiology of candidemia is essential in order to decide the best empirical treatment approach. This study reports the novel presence of C. auris in large hospitals. This pathogen has usually resistance to several antifungals and causes severe fungemia, so the results of this work reveal the need to monitor the presence of this species systematically.     

Molecular Identification and Echinocandin Susceptibility of Candida parapsilosis Complex Bloodstream Isolates in Italy, 2007–2014

The Candida parapsilosis group encompasses three species: C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Here, we describe the incidence and echinocandin susceptibility profile of bloodstream isolates of these three species collected from patients admitted to an Italian university hospital from 2007 to 2014. Molecular identification of cryptic species of the C. parapsilosis complex was performed using polymerase chain reaction amplification of the gene encoding secondary alcohol dehydrogenase, followed by digestion with the restriction enzyme BanI. Minimum inhibitory concentrations were determined using the broth microdilution method according to European Committee for Antimicrobial Susceptibility Testing (EUCAST EDef 7.2) and Clinical Laboratory Standards Institute (CLSI M27-A3) guidelines, and the results were compared with those obtained using the E-test and Sensititre methods. Of the 163 C. parapsilosis complex isolates, 136 (83.4%) were identified as C. parapsilosis, and 27 (16.6%) as C. orthopsilosis. The species-specific incidences were 2.9/10,000 admissions for C. parapsilosis and 0.6/10,000 admissions for C. orthopsilosis. No resistance to echinocandins was detected with any of the methods. The percent essential agreement (EA) between the EUCAST and E-test/Sensititre methods for anidulafungin, caspofungin, and micafungin susceptibility was, respectively, as follows: C. parapsilosis, 95.6/97.8, 98.5/88.2, and 93.4/96.3; C. orthopsilosis, 92.6/92.6, 96.3/77.8, and 63.0/66.7. The EA between the CLSI and E-test/Sensititre methods was, respectively, as follows: C. parapsilosis, 99.3/100, 98.5/89.0, and 96.3/98.5; C. orthopsilosis, 96.3/92.6, 100/81.5, and 92.6/88.9. Only minor discrepancies, ranging from 16.9% (C. parapsilosis) to 11.1% (C. orthopsilosis), were observed between the CLSI and E-test/Sensititre methods. In conclusion, this epidemiologic study shows a typical C. parapsilosis complex species distribution, no echinocandin resistance, and it reinforces the relevance of using commercially available microbiological methods to assess antifungal susceptibility. These data improve our knowledge of the national distribution of species of the psilosis group, as there are very few studies of these species in Italy.     

Retrospective Study of the Epidemiology and Clinical Manifestations of Cryptococcus gattii Infections in Colombia from 1997–2011

Background

Cryptococcosis due to Cryptococcus gattii is endemic in various parts of the world, affecting mostly immunocompetent patients. A national surveillance study of cryptococcosis, including demographical, clinical and microbiological data, has been ongoing since 1997 in Colombia, to provide insights into the epidemiology of this mycosis.

Methodology/Principal Findings

From 1,209 surveys analyzed between 1997–2011, 45 cases caused by C. gattii were reported (prevalence 3.7%; annual incidence 0.07 cases/million inhabitants/year). Norte de Santander had the highest incidence (0.81 cases/million/year), representing 33.3% of all cases. The male: female ratio was 3.3∶1. Mean age at diagnosis was 41±16 years. No specific risk factors were identified in 91.1% of patients. HIV infection was reported in 6.7% of patients, autoimmune disease and steroids use in 2.2%. Clinical features included headache (80.5%), nausea/vomiting (56.1%) and neurological derangements (48.8%). Chest radiographs were taken in 21 (46.7%) cases, with abnormal findings in 7 (33.3%). Cranial CT scans were obtained in 15 (33.3%) cases, with abnormalities detected in 10 (66.7%). Treatment was well documented in 30 cases, with most receiving amphotericin B. Direct sample examination was positive in 97.7% cases. Antigen detection was positive for all CSF specimens and for 75% of serum samples. C. gattii was recovered from CSF (93.3%) and respiratory specimens (6.6%). Serotype was determined in 42 isolates; 36 isolates were serotype B (85.7%), while 6 were C (14.3%). The breakdowns of molecular types were VGII (55.6%), VGIII (31.1%) and VGI (13.3%). Among 44 strains, 16 MLST sequence types (ST) were identified, 11 of them newly reported.

Conclusions/Significance

The results of this passive surveillance study demonstrate that cryptococcosis caused by C. gattii has a low prevalence in Colombia, with the exception of Norte de Santander. The predominance of molecular type VGII is of concern considering its association with high virulence and the potential to evolve into outbreaks.     

The Spread of Dengue in an Endemic Urban Milieu–The Case of Delhi,India

Background

Dengue is a major international public health concern, one of the most important arthropod-borne diseases. More than 3.5 billion people are at risk of dengue infection and there are an estimated 390 million dengue infections annually. This prolific increase has been connected to societal changes such as population growth and increasing urbanization generating intense agglomeration leading to proliferation of synanthropic mosquito species. Quantifying the spatio-temporal epidemiology of dengue in large cities within the context of a Geographic Information System is a first step in the identification of socio-economic risk factors.

Methodology/Principal Findings

This Project has been approved by the ethical committee of Institut Pasteur. Data has been anonymized and de-identified prior to geolocalisation and analysis. A GIS was developed for Delhi, enabling typological characterization of the urban environment. Dengue cases identified in the Delhi surveillance system from 2008 to 2010 were collated, localised and embedded within this GIS. The spatio-temporal distribution of dengue cases and extent of clustering were analyzed. Increasing distance from the forest in Delhi reduced the risk of occurrence of a dengue case. Proximity to a hospital did not increase risk of a notified dengue case. Overall, there was high heterogeneity in incidence rate within areas with the same socio-economical profiles and substantial inter-annual variability. Dengue affected the poorest areas with high density of humans, but rich areas were also found to be infected, potentially because of their central location with respect to the daily mobility network of Delhi. Dengue cases were highly clustered in space and there was a strong relationship between the time of introduction of the virus and subsequent cluster size. At a larger scale, earlier introduction predicted the total number of cases.

Conclusions/Significance

DENV epidemiology within Delhi has a forest fire signature. The stochastic nature of this invasion process likely smothers any detectable socio-economic risk factors. However, the significant finding that the size of the dengue case cluster depends on the timing of its emergence emphasizes the need for early case detection and implementation of effective mosquito control. A better understanding of the role of population mobility in contributing to dengue risk could also help focus control on areas at particular risk of dengue virus importation.     

Systemic Candida infection in University Hospital 1997–1999: the distribution of Candida biotypes and antifungal susceptibility patterns

A total of 102 Candida species were isolated from blood cultures from January 1997 to October 1999. Using assimilation of carbohydrate test, 52 (51.0%) of the Candida sp. were identified as C. parapsilosis, 25.5% (26) were C. tropicalis. C. albicans made up 11.8% (12), 6.9% (7) were C. rugosa, 3.8% (4) C. glabrata and 1% (1) C. guilliermondii. No C. dubliniensis was found in the study. In vitro antifungal susceptibility tests showed that all Candida species were sensitive to nystatin, amphotericin B and ketoconazole. Although all isolates remained sensitive to fluconazole, intermediate susceptibility was found in 3 C. rugosa isolates. Antifungal agents with high frequency of resistance were econazole, clotrimazole, miconazole and 5-fluorocytosine. Candida species found to have resistance to these antifungal agents were non-C. albicans. This revised version was published online in June 2006 with corrections to the Cover Date.     

Species–area relationship and a tentative interpretation of the function coefficients in an ecosystem simulation

In this paper, we identified the best species–area relationship (SAR) models from amongst 28 different models gathered from the literature, using an artificial predator–prey simulation (EcoSim), along with investigating how sampling approaches and sampling scales affect SARs. Further, we attempted to determine a plausible interpretation of SAR model coefficients for the best performing SAR models. This is the most extensive quantitatively based investigation of the species–area relationship so far undertaken in the literature.We gathered 28 different models from the literature and fitted them to sampling data from EcoSim using non-linear regression and ΔAICc as the goodness-of-fit criterion. Afterwards, we proposed a machine-learning approach to find plausible relationships between the models’ coefficients and the spatial information that likely affect SARs, as a basis for extracting rules that provide an interpretation of SAR coefficients.We found the power function family to be a reasonable choice and in particular the Plotkin function based on ΔAICc ranking. The Plotkin function was consistently in the top three in terms of the best ranked SAR functions. Furthermore, the simple power function was the best-ranked model in nested sampling amongst models with two coefficients. We found that the Plotkin, quadratic power, Morgan–Mercer–Floid and the generalized cumulative Weibull functions are the best ranked models for small, intermediate, large, and very large scales, respectively, in nested sampling, while Plotkin (in small to intermediate scales) and Chapman–Richards (in large to very large scales) are the best ranked functions in random sampling. Finally, based on rule extractions using machine-learning techniques we were able to find interpretations of the coefficients for the simple and extended power functions. For instance, function coefficients corresponded to sampling scale size, patch number, fractal dimension, average patch size, and spatial complexity.Our main conclusions are that SAR models are highly dependent on sampling scale and sampling approach and that the shape of the best ranked SAR model is convex without an asymptote for smaller scales (small, intermediate) and it is sigmoid for larger scales (large and very large). For some of the SAR model coefficients, there are clear correlations with spatial information, thereby providing an interpretation of these coefficients. In addition, the slope z measuring the rate of species increase for SAR models in the power function family was found to be directly proportional to beta diversity, which confirms the view that beta diversity and SAR models are to some extent both measures of species richness.     

How Reliable is the Untrained Eye in the Identification of an Invasive Species? The Case of Alien Bee-Hawking Yellow-Legged Hornet in Iberian Peninsula

Biological invasions cause great damage to native ecosystems, therefore, it is extremely important to take measures to contain the progress of existing invasions and prevent new ones. Here, we used the Species Distribution Models approach to compare two independent datasets for the invasive alien species the Yellow-legged hornet in the Iberian Peninsula. One dataset compiles occurrence records gathered by expert people (e.g. environmental services’ technical staff and researchers); and the other compiles occurrence records gathered by non-expert people (e.g. amateur entomologists, beekeepers). The main aim is to assess the effectiveness and reliability of the dataset managed by non-experts when comparing it to the dataset managed by experts. Our results showed a high degree of concordance and similarity between models. Thus, both datasets would have the same reliability to be used in management strategies for this species.     

Declining Incidence of Candidemia and the Shifting Epidemiology of Candida Resistance in Two US Metropolitan Areas, 2008–2013: Results from Population-Based Surveillance

Background

Recent reports have demonstrated a decline in bacterial bloodstream infections (BSIs) following adherence to central line insertion practices; however, declines have been less evident for BSIs due to Candida species.

Methods

We conducted active, population-based laboratory surveillance for candidemia in metropolitan Atlanta, GA and Baltimore, MD over a 5-year period. We calculated annual candidemia incidence and antifungal drug resistance rates.

Results

We identified 3,848 candidemia cases from 2008–2013. Compared with 2008, candidemia incidence per 100,000 person-years decreased significantly by 2013 in both locations (GA: 14.1 to 9.5, p<0.001; MD: 30.9 to 14.4, p<0.001). A total of 3,255 cases (85%) had a central venous catheter (CVC) in place within 2 days before the BSI culture date. In both locations, the number of CVC-associated cases declined (GA: 473 to 294; MD: 384 to 151). Candida albicans (CA, 36%) and Candida glabrata (CG, 27%) were the most common species recovered. In both locations, the proportion of cases with fluconazole resistance decreased (GA: 8.0% to 7.1%, −10%; MD: 6.6% to 4.9%, −25%), while the proportion of cases with an isolate resistant to an echinocandin increased (GA: 1.2% to 2.9%, +147%; MD: 2.0% to 3.5%, +77%). Most (74%) echinocandin-resistant isolates were CG; 17 (<1%) isolates were resistant to both drug categories (multidrug resistant [MDR], 16/17 were CG). The proportion of CG cases with MDR Candida increased from 1.8% to 2.6%.

Conclusions

We observed a significant decline in the incidence of candidemia over a five-year period, and increases in echinocandin-resistant and MDR Candida. Efforts to strengthen infection control practices may be preventing candidemia among high-risk patients. Further surveillance for resistant Candida is warranted.     

The Curious Case of “Case Report” of Infections Caused by Human and Animal Fungal Pathogens: An Educational Tool,an Online Archive,or a Format in Need of Retooling

Case reports describe the unusual occurrence and complications of diseases, diagnostic challenges, and notable therapeutic successes. Some journals have discontinued the case reports, while new case report journals have appeared in recent years. During the eightieth anniversary of Mycopathologia, it is fitting to examine the relevance of the case report since the journal continues to traverse the boundaries of basic and clinical sciences. A random sample of recent case reports and other articles were selected from Mycopathologia. Springer Nature individual article download statistics, and Google Scholar and Scopus citations numbers were compared to assess the reader access and bibliometric impact of case reports. Our analysis indicated that the case report format continues to be a vital element of publication in a cross-disciplinary journal such as Mycopathologia. Medical and veterinary case reports covering fungal pathogens are widely read as evident from their download numbers. The download numbers have a positive correlation with the completeness of the report, the topics and geographic origin of reports have a neutral influence, and the recency leads to lower downloads. There is no discernible trend between the download numbers and the citations of case reports as measured by Google Scholar and Scopus. A specially designed checklist for Mycopathologia case reports and new format MycopathologiaIMAGES are being introduced to improve the quality and relevance of case reports further.     

Investigation of an on-line two-dimensional chromatographic approach for peptide analysis in plasma by LC–MS–MS

Reversed phase and hydrophilic interaction chromatography (HILIC) were successfully coupled for the on-line extraction and quantitative analysis of peptides by ESI–LC–MS/MS. A total of 11 peptides were utilized to determine the conditions for proper focusing and separation on both dimensions. Minor modifications to the initial organic composition of the first reversed-phase dimension provided options between a comprehensive (generic) or more selective approach for peptide transfer to the second HILIC dimension. Ion-pairing with trifluoroacetic acid (TFA) provided adequate chromatographic retention and peak symmetry for the selected peptides on both C₁₈ and HILIC. The resulting signal suppression from TFA was partially recovered by a post-column “TFA fix” using acetic acid yielding improvements in sensitivity. Minimal sample preparation aligned with standard on-line extraction procedures provided highly reproducible and robust results for over 300 sequential matrix injections. Final optimized conditions were successfully employed for the quantitation of peptide PTHrP (1–36) in rat K₃EDTA plasma from 25.0 to 10,000 ng/mL using PTHrP (1–34) as the analog internal standard. This highly orthogonal two-dimensional configuration was found to provide the unique selectivity required to overcome issues with interfering endogenous components and minimize electrospray ionization effects in biological samples.     

Sharing of Diverse Mycorrhizal and Root-Endophytic Fungi among Plant Species in an Oak-Dominated Cool–Temperate Forest

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through belowground plant–fungal interactions, dominant plants can benefit by interacting with host-specific mutualistic fungi and proliferate in a community based on positive plant–mutualistic fungal feedback. On the other hand, subordinate plant species may persist in the community by sharing other sets (functional groups) of fungal symbionts with each other. Therefore, revealing how diverse clades of root-associated fungi are differentially hosted by dominant and subordinate plant species is essential for understanding plant community structure and dynamics. Based on 454-pyrosequencing, we determined the community composition of root-associated fungi on 36 co-occurring plant species in an oak-dominated forest in northern Japan and statistically evaluated the host preference phenotypes of diverse mycorrhizal and root-endophytic fungi. An analysis of 278 fungal taxa indicated that an ectomycorrhizal basidiomycete fungus in the genus Lactarius and a possibly endophytic ascomycete fungus in the order Helotiales significantly favored the dominant oak (Quercus) species. In contrast, arbuscular mycorrhizal fungi were generally shared among subordinate plant species. Although fungi with host preferences contributed to the compartmentalization of belowground plant–fungal associations, diverse clades of ectomycorrhizal fungi and possible root endophytes were associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant-ectomycorrhizal and subordinate plant species can host different subsets of root-associated fungi, and diverse clades of generalist fungi can counterbalance the compartmentalization of plant–fungal associations. Such insights into the overall structure of belowground plant–fungal associations will help us understand the mechanisms that facilitate the coexistence of plant species in natural communities.     

Investigation of the First Case of Dengue Virus Infection Acquired in Western Australia in Seven Decades: Evidence of Importation of Infected Mosquitoes?

In October 2013, a locally-acquired case of dengue virus (DENV) infection was reported in Western Australia (WA) where local dengue transmission has not occurred for over 70 years. Laboratory testing confirmed recent DENV infection and the case demonstrated a clinically compatible illness. The infection was most likely acquired in the Pilbara region in the northwest of WA. Follow up investigations did not detect any other locally-acquired dengue cases or any known dengue vector species in the local region, despite intensive adult and larval mosquito surveillance, both immediately after the case was notified in October 2013 and after the start of the wet season in January 2014. The mechanism of infection with DENV in this case cannot be confirmed. However, it most likely followed a bite from a single infected mosquito vector that was transiently introduced into the Pilbara region but failed to establish a local breeding population. This case highlights the public health importance of maintaining surveillance efforts to ensure that any incursions of dengue vectors into WA are promptly identified and do not become established, particularly given the large numbers of viraemic dengue fever cases imported into WA by travellers returning from dengue-endemic regions.     

Spatial and Temporal Distribution of Culicoides Species in Mainland Portugal (2005–2010). Results of the Portuguese Entomological Surveillance Programme

Bluetongue virus (BTV) is transmitted by Culicoides biting midges and causes an infectious, non-contagious disease of ruminants. It has been rapidly emerging in southern Europe since 1998. In mainland Portugal, strains of BTV belonging to three serotypes have been detected: BTV-10 (1956-1960), BTV-4 (2004-2006 and 2013) and BTV-1 (2007-2012). This paper describes the design, implementation and results of the Entomological Surveillance Programme covering mainland Portugal, between 2005 and 2010, including 5,650 caches. Culicoides imicola Kieffer was mostly found in central and southern regions of Portugal, although it was sporadically detected in northern latitudes. Its peak activity occurred in the autumn and it was active during the winter months in limited areas of the country. Obsoletus group was present at the highest densities in the north although they were found throughout the country in substantial numbers. Culicoides activity occurred all year round but peaked in the spring. A generalized linear mixed model was developed for the analysis of the environmental factors associated with activity of the species of Culicoides suspected vectors of BTV in the country. For C. imicola Kieffer, the most important variables were month, diurnal temperature range (DTR), the number of frost days (FRS) and median monthly temperature (TMP). For the Obsoletus group, the most important factors were month, diurnal temperature range (DTR), and linear and quadratic terms for median monthly temperature (TMP). The results reported can improve our understanding of climatic factors in Culicoides activity influencing their distribution and seasonal pattern.     

Determination of Flower Structure in Elaeis guineensis: Do Palms use the Same Homeotic Genes as Other Species?

AIMS: In this article a review is made of data recently obtained on the structural diversity and possible functions of MADS box genes in the determination of flower structure in the African oil palm (Elaeis guineensis). MADS box genes play a dominant role in the ABC model established to explain how floral organ identity is determined in model dicotyledon species such as Arabidopsis thaliana and Antirrhinum majus. In the monocotyledons, although there appears to be a broad general conservation of ABC gene functions, the model itself needs to be adapted in some cases, notably for certain species which produce flowers with sepals and petals of similar appearance. For the moment, ABC genes remain unstudied in a number of key monocot clades, so only a partial picture is available for the Liliopsida as a whole. The aim of this article is to summarize data recently obtained for the African oil palm Elaeis guineensis, a member of the family Arecaceae (Arecales), and to discuss their significance with respect to knowledge gained from other Angiosperm groups, particularly within the monocotyledons. SCOPE: The essential details of reproductive development in oil palm are discussed and an overview is provided of the structural and functional characterization of MADS box genes likely to play a homeotic role in flower development in this species. CONCLUSIONS: The structural and functional data provide evidence for a general conservation of the generic 'ABC' model in oil palm, rather than the 'modified ABC model' proposed for some other monocot species which produce homochlamydeous flowers (i.e. with morphologically similar organs in both perianth whorls), such as members of the Liliales. Our oil palm data therefore follow a similar pattern to those obtained for other Commelinid species in the orders Commelinales and Poales. The significance of these findings is discussed.