Diagnostic performance of real-time quantitative PCR in tear samples in various subtypes of herpes simplex keratitis.

Diagnosis of herpes simplex keratitis (HSK) is mostly based on clinical findings, yet biological confirmation supports management of challenging cases. This study evaluated the place of real-time quantitative PCR (RT-qPCR) on tear samplings in the management of HSK. Clinical records of patients who underwent tear sampling tested by RT-qPCR for herpes simplex virus type 1 for an acute episode of corneal inflammation or defect between January 2013 and December 2021 were retrospectively reviewed, and results were compared to clinical diagnosis (i.e., HSK or not) based on biomicroscopic findings and medical history. Of 465 tested tear samples from 364 patients, a clinical diagnosis of active (ongoing) HSK was recorded in 240 cases, among which 76 were RT-qPCR positive (global sensitivity of 31.6%, specificity of 99.5%). Sensitivity of RT-qPCR was higher in epithelial (97.4%) and stromal keratitis with ulceration (48.7%), compared to other types of HSK (23.5% in keratouveitis, 13.6% in endotheliitis, 11.1% in postherpetic neurotrophic keratopathy, and 8.1% in stromal keratitis without ulceration). The highest viral loads were detected from epithelial and stromal keratitis with ulceration, while in HSK with no epithelial involvement, the viral load detected was 196-fold lower, on average. The proportion of clinically characterized HSK patients with negative tear samples was higher in patients receiving antiviral treatment (P < 0.0001). RT-qPCR, performed on tear samples, can help in confirming diagnosis in case of presumed HSK, including clinical forms with no obvious epithelial involvement. The sensitivity of tear sampling is much higher whenever epithelial keratitis is present.

Ocular Manifestations of Flavivirus Infections.

Flaviviruses are a group of positive-sense, single-stranded RNA viruses predominantly transmitted by arthropods (mainly mosquitoes) that cause severe endemic infections and epidemics on a global scale. They represent a major cause of systemic morbidity and death and are expanding worldwide. Among this group, dengue fever, the West Nile virus, yellow fever, Japanese Encephalitis, and, recently, the Zika virus have been linked to a spectrum of ocular manifestations. These manifestations encompass subconjunctival hemorrhages and conjunctivitis, anterior and posterior uveitis (inclusive of vitritis, chorioretinitis, and retinal vasculitis), maculopathy, retinal hemorrhages, and optic neuritis. Clinical diagnosis of these infectious diseases is primarily based on epidemiological data, history, systemic symptoms and signs, and the pattern of ocular involvement. Diagnosis confirmation relies on laboratory testing, including RT-PCR and serological testing. Ocular involvement typically follows a self-limited course but can result in irreversible visual impairment. Effective treatments of flavivirus infections are currently unavailable. Prevention remains the mainstay for arthropod vector and zoonotic disease control. Effective vaccines are available only for the yellow fever virus, dengue virus, and Japanese Encephalitis virus. This review comprehensively summarizes the current knowledge regarding the ophthalmic manifestations of the foremost flavivirus-associated human diseases.

Atovaquone exposure and Pneumocystis jirovecii cytochrome b mutations: French data and review of the literature.

Pneumocystis jirovecii is a transmissible fungus responsible for severe pneumonia (Pneumocystis pneumonia [PCP]) in immunocompromised patients. Missense mutations due to atovaquone selective pressure have been identified on cytochrome b (CYB) gene of P. jirovecii. It was recently shown that atovaquone prophylaxis can lead to the selection of specific P. jirovecii CYB mutants potentially resistant to atovaquone among organ transplant recipients. In this context, our objectives were to provide data on P. jirovecii CYB mutants and the putative selective pressure exerted by atovaquone on P. jirovecii organisms in France. A total of 123 patients (124 P. jirovecii specimens) from four metropolitan hospitals and two overseas hospitals were retrospectively enrolled. Fourteen patients had prior exposure to atovaquone, whereas 109 patients did not at the time of P. jirovecii detection. A 638 base-pair fragment of the CYB gene of P. jirovecii was amplified and sequenced. A total of 10 single nucleotide polymorphisms (SNPs) were identified. Both missense mutations C431T (Ala144Val) and C823T (Leu275Phe), located at the Qo active site of the enzyme, were significantly associated with prior atovaquone exposure, these mutations being conversely incidental in the absence of prior atovaquone exposure (P < 0.001). Considering that the aforementioned hospitals may be representative of the national territory, these findings suggest that the overall presence of P. jirovecii CYB mutants remains low in France.

The mutations C431T (Ala144Val) and C823T (Leu275Phe) at the cytochrome b (CYB) active site of Pneumocystis jirovecii are associated with patient prior exposure to atovaquone. Conversely, these mutations are incidental in the absence of exposure. Overall, the presence of P. jirovecii CYB mutants remains low in France.

Multicenter Comparative Assessment of the TIB MolBiol Toxoplasma gondii Detection Kit and Four Laboratory-Developed PCR Assays for Molecular Diagnosis of Toxoplasmosis.

Toxoplasmosis can be a life-threatening infection, particularly during pregnancy and in immunocompromised patients. The biological diagnosis of toxoplasmosis is challenging and has been revolutionized by molecular detection methods. This article summarizes the data of a multicenter study involving four centers to assess the performances of a commercial PCR assay as compared with four in-house PCR assays using Toxoplasma gondii standards, 20 external quality control specimens, and 133 clinical samples. This clinical cohort includes well-characterized clinical samples corresponding to different clinical situations: confirmed congenital toxoplasmosis (44 samples), toxoplasmosis in immunocompromised patients (25 samples), and chorioretinitis (5 samples). Furthermore, 59 samples from patients without toxoplasmosis were included as negative controls. The analytical sensitivities of the five methods tested were very similar; and the limit of Toxoplasma DNA detection was around 0.01 T. gondii genome per reaction for all the methods. The overall concordance between the commercial PCR and the four in-house PCR assays was 97.7% (130/133). The clinical sensitivity and specificity were >98% and could be increased for the commercial kit when PCR was performed in multiplicate to detect low parasitic loads. In conclusion, the commercial PCR assay shows suitable performances to diagnose the different clinical forms of toxoplasmosis.

Moraxella keratitis: epidemiology and outcomes.

We aimed to assess the prevalence, risk factors, and visual outcome of Moraxella keratitis. We retrospectively reviewed the medical charts of patients diagnosed with Moraxella spp. keratitis at the Quinze-Vingts National Ophthalmology Hospital, Paris, France, between January 2016 and December 2018. Definitive microbiological identification was performed on archival strains using matrix-assisted laser desorption ionization time of flight coupled to mass spectrometry. One hundred one culture-proven cases of Moraxella keratitis were identified. The most common isolates were Moraxella lacunata (50%) and Moraxella nonliquefasciens (38%). Systemic predisposing factors, principally diabetes mellitus (13%) were identified in 28% of patients, and 87% of patients had ocular surface conditions, including blepharitis (25%), prior ocular surgery (21%), glaucoma (17%), exposure keratopathy (16%), and trauma (16%). Severely affected inpatients were treated empirically with fortified antibiotics including vancomycin, piperacillin, and gentamicin. The presence of hypopyon and being over the age of 60 years were associated with a poorer final visual acuity (p < 0.05). Adjuvant treatment, mostly amniotic membrane transplantation, was required for 31 eyes. The prognostic factors significantly associated with the need for adjuvant treatment were a larger infiltrate and hypoesthesia. The clinical features including ulcer healing, treatment duration, and infiltrate size were not different between Moraxella species. Keratitis caused by Moraxella spp. are rare in France but may threaten sight. The early identification of patients with a poor ocular surface, particularly those with neurotrophic keratopathy and anesthetic cornea, is crucial to prevent delayed healing of ulcers and the need for adjuvant treatment.

Pneumocystis jirovecii Diversity in Réunion, an Overseas French Island in Indian Ocean.

Data on Pneumocystis jirovecii characteristics from the overseas French territories are still scarce whereas numerous data on P. jirovecii genotypes are available for metropolitan France. The main objective of the present study was to identify P. jirovecii multilocus genotypes in patients living in Réunion and to compare them with those identified using the same method in metropolitan France and in French Guiana. Archival P. jirovecii specimens from immunosuppressed patients, 16 living in Réunion (a French island of the Indian ocean), six living in French Guiana (a South-American French territory), and 24 living in Brest (Brittany, metropolitan France) were examined at the large subunit rRNA (mtLSUrRNA) genes, cytochrome b (CYB), and superoxide dismutase (SOD) genes using PCR assays and direct sequencing. A total of 23 multi-locus genotypes (MLG) were identified combining mtLSUrRNA, CYB, and SOD alleles, i.e., six in Reunionese patients, three in Guianese patients, and 15 in Brest patients. Only one MLG (mtLSU1-CYB1-SOD2) was shared by Reunionese and Guianese patients (one patient from each region) whereas none of the 22 remaining MLG were shared by the 3 patient groups. A total of eight MLG were newly identified, three in Réunion and five in Brest. These results that were obtained through a retrospective investigation of a relatively low number of P. jirovecii specimens, provides original and first data on genetic diversity of P. jirovecii in Réunion island. The results suggest that P. jirovecii organisms from Réunion present specific characteristics compared to other P. jirovecii organisms from metropolitan France and French Guiana.

Evaluation of quantitative FTD-Pneumocystis jirovecii kit for Pneumocystis infection diagnosis.

We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×108/ml vs. 1.45×105/ml, P < 0.0001). Lower and upper cut-off values of 3.9×105 copies/ml and 3.2×106 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSUrRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.

Trametes polyzona, an emerging filamentous basidiomycete in Réunion Island.

We describe two serious Trametes polyzona pulmonary infections, which occurred in Réunion Island, in critically ill patients. The identification was performed using sequencing of the internal transcribed spacer region of ribosomal DNA and D1/D2 region of 28S rDNA. In one case, the significance of T. polyzona in the pathological process was certain, proven by histopathological evidence of fungal lung infection. T. polyzona, an emerging filamentous basidiomycete, prevalent in tropical areas, has not been described so far in human infections.

Incidental pseudolymphomatous bladder inflammatory polyp revealing urinary schistosomiasis.

A 25-year-old female who had returned from a trip to Madagascar that was not reported, underwent an endoscopic bladder polyp resection. Histopathology examination revealed an intense pseudolymphomatous inflammatory polyp caused by a Schistosoma infection. Bladder polyps due to schistosomiasis represent a rare condition in developed countries and have to be ruled out in the case of any intense unexplained inflammation.

Mycobiota in gastrointestinal diseases.

New insights gained through the use of state-of-the-art technologies, including next-generation sequencing, are starting to reveal that the association between the gastrointestinal tract and the resident mycobiota (fungal community) is complex and multifaceted, in which fungi are active participants influencing health and disease. Characterizing the human mycobiome (the fungi and their genome) in healthy individuals showed that the gastrointestinal tract contains 66 fungal genera and 184 fungal species, with Candida as the dominant fungal genera. Although fungi have been associated with a number of gastrointestinal diseases, characterization of the mycobiome has mainly been focused on patients with IBD and graft-versus-host disease. In this Review, we summarize the findings from studies investigating the relationship between the gut mycobiota and gastrointestinal diseases, which indicate that fungi contribute to the aggravation of the inflammatory response, leading to increased disease severity. A model explaining the mechanisms underlying the role of the mycobiota in gastrointestinal diseases is also presented. Our understanding of the contribution of the mycobiota to health and disease is still in its infancy and leaves a number of questions to be addressed. Answering these questions might lead to novel approaches to prevent and/or manage acute as well as chronic gastrointestinal disease.

Genetic diversity among Candida albicans isolates associated with vertical transmission in preterm triplets.

We report a case of congenital candidiasis in triplets, in the context of premature labor at 25 weeks gestation, without symptomatic vaginitis or chorioamnionitis. All three infants died as a result of prematurity, aggravated by systemic candidiasis. Multi-locus sequence typing confirmed vertical transmission of Candida albicans from the mother to the triplets and revealed a slight diversity among the strains isolated from the neonates.

Gardnerella vaginalis as a rare cause of prosthetic joint infection.

We describe a septic loosening of a hip prosthesis in a 71-year-old woman caused by Gardnerella vaginalis. Infection was confirmed by culture and molecular identification of this bacterium. The patient was treated by a one-step exchange of prosthesis and antibiotic therapy combining trimethoprim-sulfamethoxazole and rifampin, with favorable evolution.

Two cases of type A infant botulism in Grenoble, France: no honey for infants.

We report two severe cases of infant botulism diagnosed at Grenoble University Hospital, France, respectively in 2006 and 2009. Both cases were characterized by a delay in diagnosis, severe neurological manifestations and extended period of hospitalization in intensive care unit, but a complete recovery. Infant botulism is a rare but life-threatening disease. It primarily affects infants, and the main risk factor is honey ingestion. Diagnosis should be systematically evoked by pediatricians in infants suffering from constipation, fatigue, muscle weakness, difficult feeding and altered cry, but before the onset of generalized flaccid paralysis, so as to administer specific treatment (BabyBIG®, a human derived botulinum antitoxin) at an early stage of the disease when it is most effective. In conclusion, parents should be aware of the role of honey as a source of spores of Clostridium botulinum and therefore infant botulism in the first year of life.