Reverse-transcriptase real-time PCR in the diagnostic strategy for invasive infections caused by Aspergillus fumigatus.

The aim was to develop an RT-qPCR targeting Aspergillus fumigatus and compare its performance to that of Aspergillus fumigatus qPCR for the diagnosis of invasive aspergillosis (IA). Samples from patients of the Lyon University hospitals for whom a suspicion of IA led to the realization of an Aspergillus fumigatus qPCR molecular diagnostic test over a 2-year period were included. The patients were classified according to the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC-MSGERC) criteria for suspected IA; RT-qPCR and qPCR assays were performed on all included samples. The sensitivities and specificities of RT-qPCR and qPCR were calculated and compared using the results of the EORTC-MSGERC classification as reference. The cycle threshold (Ct) results were compared according to IA classification and sample type. Among the 193 samples analyzed, 91 were classified as IA excluded, 46 as possible IA, 53 as probable IA, and 3 as proven IA. For all sample types, RT-qPCR was significantly more sensitive than qPCR for all IA classifications with an additional 17/102 samples detected (P-value < 0.01). For plasma samples, sensitivity was significantly higher and specificity significantly lower using RT-qPCR for all IA classifications (P-value < 0.001). The mean Ct obtained with RT-qPCR were significantly lower than those obtained with qPCR for all IA classifications and all sample types (P-value < 0.001 and P-value < 0.0001, respectively). RT-qPCR presents a higher sensitivity than qPCR for the diagnosis of IA due to Aspergillus fumigatus, particularly in samples with an intrinsically low fungal load.IMPORTANCEAspergillus fumigatus belongs to the critical priority group of the World Health Organization fungal priority pathogens list. Invasive aspergillosis (IA) is a life-threatening infection with poor prognosis and challenging diagnosis. PCR has been integrated into the 2020 European Organization for Research and Treatment of Cancer/Mycoses Study Group consensus definitions for IA diagnosis. However, due to frequent low fungal burdens, its sensitivity needs to be improved. This work presents an innovative method for detecting total nucleic acids, corresponding to both ribosomal RNA and DNA, that enables IA diagnosis with greater sensitivity than conventional techniques, especially in non-invasive samples such as blood, enhancing the monitoring of this infection in high-risk patients.

Epidemiology and management of tinea capitis in France: A 6-year nationwide retrospective survey.

Tinea capitis (TC) is still a frequent dermatophytosis in France, both autochthonous and imported. A nationwide retrospective survey was performed and a total of 4395 TC cases were recorded within 36 French mycology laboratories during a 6-year period. TC is a disease that occurs in childhood with 85% of the cases occurring before 10 years old and 94% before the age of 15. Anthropophilic origin was predominant with 779 cases of Trichophyton tonsurans (32.6%), 738 cases of Trichophyton soudanense/T. violaceum (31%), and 445 cases of Microsporum audouinii (19.2%). Of note, T. tonsurans represents more than 80% of the cases in the French West Indies (Martinique and Guadeloupe). By contrast, zoophilic species were less prevalent with mainly M. canis (10.3%) confirming the shift from zoophilic to anthropophilic species observed in many centers during the last decades. During this survey, diagnosis methods were also collected. Most labs had a classical process for the diagnosis: microscopic direct examination associated to cultures on Sabouraud and Sabouraud-cycloheximide media (incubated between 25 ± 5°C for at least 3 weeks) in all laboratories. Identification of the causal dermatophyte was performed by microscopic and macroscopic examination of the cultures in 100% of the labs, with various specific culture media available when fructification was insufficient (mainly malt or potato-dextrose agar, or Borelli medium). New techniques were also implemented with the introduction of MALDI-TOF mass spectrometry identification in more than two third of the labs, and molecular identification available if necessary in half of the labs.

A total of 4395 tinea capitis cases were recorded within 36 French mycology laboratories during a 6-year period. An anthropophilic origin was predominant with 33%, 31%, and 18.8% of cases due to Trichophyton tonsurans, T. soudanense/T. violaceum, and Microsporum audouinii, respectively.

Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues.

Histopathology is the gold standard for fungal infection (FI) diagnosis, but it does not provide a genus and/or species identification. The objective of the present study was to develop targeted next-generation sequencing (NGS) on formalin-fixed tissue samples (FTs) to achieve a fungal integrated histomolecular diagnosis. Nucleic acid extraction was optimized on a first group of 30 FTs with Aspergillus fumigatus or Mucorales infection by macrodissecting the microscopically identified fungal-rich area and comparing Qiagen and Promega extraction methods through DNA amplification by A. fumigatus and Mucorales primers. Targeted NGS was developed on a second group of 74 FTs using three primer pairs (ITS-3/ITS-4, MITS-2A/MITS-2B, and 28S-12-F/28S-13-R) and two databases (UNITE and RefSeq). A prior fungal identification of this group was established on fresh tissues. Targeted NGS and Sanger sequencing results on FTs were compared. To be valid, the molecular identifications had to be compatible with the histopathological analysis. In the first group, the Qiagen method yielded a better extraction efficiency than the Promega method (100% and 86.7% of positive PCRs, respectively). In the second group, targeted NGS allowed fungal identification in 82.4% (61/74) of FTs using all primer pairs, in 73% (54/74) using ITS-3/ITS-4, in 68.9% (51/74) using MITS-2A/MITS-2B, and in 23% (17/74) using 28S-12-F/28S-13-R. The sensitivity varied according to the database used (81% [60/74] using UNITE compared to 50% [37/74] using RefSeq [P = 0.000002]). The sensitivity of targeted NGS (82.4%) was higher than that of Sanger sequencing (45.9%; P < 0.00001). To conclude, fungal integrated histomolecular diagnosis using targeted NGS is suitable on FTs and improves fungal detection and identification.

Pulmonary aspergillosis in critically ill patients with Coronavirus Disease 2019 (COVID-19).

Occurrence of putative invasive pulmonary aspergillosis was screened in 153 consecutive adult intensive care unit (ICU) patients with respiratory samples addressed for mycological diagnosis during a 6-week period at the emergence of coronavirus disease 2019 (COVID-19) pandemic. Positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) was observed for 106 patients (69.3%). Nineteen of them (17.9%) with positive Aspergillus results were considered as having putative invasive pulmonary aspergillosis. These observations underline the risk of pulmonary aspergillosis in COVID-19 patients, even in patients not previously known to be immunosuppressed, advocating active search for Aspergillus infection and prompt antifungal treatment. Standardized surveillance protocols and updated definitions for ICU putative invasive pulmonary aspergillosis are needed. LAY ABSTRACT: Adult ICU patients with respiratory samples addressed for mycological diagnosis were screened during the emergence of COVID-19 pandemic. Positive SARS-CoV-2 PCR was observed for 106 patients, nineteen of them (17.9%) having aspergillosis. This underlines the risk of aspergillosis in COVID-19 patients.

Diagnostic accuracy of fluorescence flow-cytometry technology using Sysmex XN-31 for imported malaria in a non-endemic setting.

Malaria diagnosis based on microscopy is impaired by the gradual disappearance of experienced microscopists in non-endemic areas. Aside from the conventional diagnostic methods, fluorescence flow cytometry technology using Sysmex XN-31, an automated haematology analyser, has been registered to support malaria diagnosis. The aim of this prospective, monocentric, non-interventional study was to evaluate the diagnostic accuracy of the XN-31 for the initial diagnosis or follow-up of imported malaria cases compared to the reference malaria tests including microscopy, loop mediated isothermal amplification, and rapid diagnostic tests. Over a one-year period, 357 blood samples were analysed, including 248 negative and 109 positive malaria samples. Compared to microscopy, XN-31 showed sensitivity of 100% (95% CI: 97.13-100) and specificity of 98.39% (95% CI: 95.56-100) for the initial diagnosis of imported malaria cases. Moreover, it provided accurate species identification asfalciparumor non-falciparumand parasitaemia determination in a very short time compared to other methods. We also demonstrated that XN-31 was a reliable method for patient follow-up on days 3, 7, and 28. Malaria diagnosis can be improved in non-endemic areas by the use of dedicated haematology analysers coupled with standard microscopy or other methods in development, such as artificial intelligence for blood slide reading. Given that XN-31 provided an accurate diagnosis in 1 min, it may reduce the time interval before treatment and thus improve the outcome of patient who have malaria.

Title: Précision diagnostique de la technique de cytométrie de flux en fluorescence utilisant le Sysmex XN-31 pour le paludisme d'importation en zone non endémique. Abstract: Le diagnostic du paludisme basé sur la microscopie est rendu difficile par la disparition progressive des microscopistes expérimentés en zone non-endémique. À côté des méthodes conventionnelles, la technique de cytométrie de flux en fluorescence utilisant le Sysmex XN-31, un automate d'analyse hématologique, a été enregistrée pour participer au diagnostic du paludisme. L'objectif de cette étude prospective, monocentrique et non-interventionelle était d'évaluer la précision diagnostique du XN-31 pour le diagnostic initial et le suivi des cas de paludisme d'importation en comparaison des tests de référence dont la microscopie, l'amplification isothermale en boucle, et des tests de diagnostic rapide. Durant une période d'un an, 357 échantillons de sang ont été analysés, dont 248 négatifs et 109 positifs pour le paludisme. En comparaison de la microscopie, le XN-31 a montré une sensibilité de 100 % (95 % CI : 97.13-100) et une spécificité de 98.39 % (95 % CI : 95.56-100) pour le diagnostic initial des cas de paludisme d'importation. De plus, l'identification des espècesfalciparumet non-falciparumainsi que la parasitémie ont été précises dans un temps très court en comparaison des autres méthodes. Nous avons aussi démontré que le XN-31 était une méthode fiable pour le suivi des patients à J3, J7 et J28. Le diagnostic du paludisme peut être amélioré en zone non-endémique par l'utilisation d'automates d'hématologie spécialisés, associés à la microscopie standard ou d'autres méthodes en développement telle que l'intelligence artificielle appliquée à la lecture des lames de sang. Dans la mesure où le XN-31 produit un diagnostic précis en une minute, cela peut réduire le délai avant le traitement et donc améliorer l'issue pour les patients souffrant de paludisme.

Fatal invasive infection with fungemia due to Microascus cirrosus after heart and lung transplantation in a patient with cystic fibrosis.

Scopulariopsis species are rarely but increasingly recognized as opportunistic pathogens in immunocompromised patients. We report on a patient suffering from cystic fibrosis who developed disseminated fungal infection due to a rare Scopulariopsis species, Microascus cirrosus, after heart and lung transplantation. Despite antifungal combination therapy with voriconazole and caspofungin, the patient died 4 weeks after transplantation. Diagnostic difficulties and optimal management of disseminated Scopulariopsis/Microascus infections are discussed.

Azole Resistance in Clinical and Environmental Aspergillus Isolates from the French West Indies (Martinique).

The emergence of azole resistant Aspergillus spp., especially Aspergillus fumigatus, has been described in several countries around the world with varying prevalence depending on the country. To our knowledge, azole resistance in Aspergillus spp. has not been reported in the West Indies yet. In this study, we investigated the antifungal susceptibility of clinical and environmental isolates of Aspergillus spp. from Martinique, and the potential resistance mechanisms associated with mutations in cyp51A gene. Overall, 208 Aspergillus isolates were recovered from clinical samples (n = 45) and environmental soil samples (n = 163). They were screened for resistance to azole drugs using selective culture media. The Minimum Inhibitory Concentrations (MIC) towards voriconazole, itraconazole, posaconazole and isavuconazole, as shown by the resistant isolates, were determined using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) microdilution broth method. Eight isolates (A. fumigatus, n = 6 and A. terreus, n = 2) had high MIC for at least one azole drug. The sequencing of cyp51A gene revealed the mutations G54R and TR34/L98H in two A. fumigatus clinical isolates. Our study showed for the first time the presence of azole resistance in A. fumigatus and A. terreus isolates in the French West Indies.

First cases of Angiostrongylus cantonensis infection reported in Martinique, 2002-2017.

Neuroangiostrongyliasis is a parasitic disease caused by the accidental ingestion of the nematode Angiostrongylus cantonensis in its larval form. Human infection can lead to eosinophilic meningitis, sometimes complicated by life-threatening radiculomyelitis or encephalitis. Although some cases have been reported from other Caribbean Islands, no cases have been diagnosed in Martinique so far. Here, we report the first eight laboratory-confirmed cases of neuroangiostrongyliasis on the island of Martinique, French West Indies, between 1 January 2002 and 31 December 2017. One case was fatal and five resulted in neurological sequelae. The medical community should consider the risk of A. cantonensis infection in patients living in or returning from Martinique.

TITLE: Premiers cas d'angiostrongylose à Angiostrongylus cantonensis à la Martinique, de 2002 à 2017. ABSTRACT: L'angiostrongylose neuroméningée est une maladie parasitaire causée par l'ingestion accidentelle du nématode Angiostrongylus cantonensis sous sa forme larvaire. L'infection humaine peut conduire à une méningite à éosinophiles, pouvant évoluer en radiculomyélite ou encéphalite menaçant le pronostic vital. Bien que des cas aient été rapportés dans d'autres îles des Caraïbes, aucun cas n'avait été diagnostiqué à la Martinique jusqu'à présent. Dans cet article, nous caractérisons les huit premiers cas d'angiostrongylose neuroméningée biologiquement diagnostiqués à la Martinique, Antilles françaises, entre le 1er janvier 2002 et le 31 décembre 2017. Un cas s'est révélé mortel et cinq ont engendré des séquelles neurologiques. La communauté médicale doit désormais considérer le risque d'infection à A. cantonensis chez les patients vivant ou revenant d'un voyage à la Martinique.

Angiostrongylus costaricensis infection in Martinique, Lesser Antilles, from 2000 to 2017.

Human abdominal angiostrongyliasis (HAA) is a parasitic disease caused by the accidental ingestion of the nematode Angiostrongylus costaricensis in its larval form. Human infection can lead to severe ischemic and inflammatory intestinal lesions, sometimes complicated by life-threatening ileal perforations. Only one case had been reported in Martinique, an Island in the French Antilles, in 1988. We retrospectively reviewed the medical charts of patients diagnosed with abdominal angiostrongyliasis at the University Hospital of Martinique between 2000 and 2017. The objectives of this study were to evaluate the incidence and perform a descriptive analysis of the clinical, biological, radiological, and histopathological features of HAA in Martinique. Two confirmed cases and two probable cases were identified in patients aged from 1 to 21 years during the 18-year period, with an estimated incidence of 0.2 cases per year (0.003 case/year/100.000 inhabitants (IC95% = 0.00-0.05)). All patients presented with abdominal pain associated with high blood eosinophilia (median: 7.24 G/L [min 4.25; max 52.28 G/L]). Two developed ileal perforation and were managed by surgery, with diagnostic confirmation based on histopathological findings on surgical specimens. The other two cases were probable, with serum specimens reactive to Angiostrongylus sp. antigen in the absence of surgery. All cases improved without sequelae. The description of this case series highlights the need to increase awareness of this life-threatening disease in the medical community and to facilitate access to specific diagnostic tools in Martinique. Environmental and epidemiological studies are needed to broaden our knowledge of the burden of this disease.

TITLE: Infections par Angiostrongylus costaricensis à la Martinique, Antilles, de 2000 à 2017. ABSTRACT: L'angiostrongylose abdominale humaine (AAH) est une maladie parasitaire causée par l'ingestion accidentelle du nématode Angiostrongylus costaricensis sous sa forme larvaire. L'infection humaine peut conduire à des lésions intestinales ischémiques et inflammatoires sévères, parfois compliquées par des perforations iléales menaçant le pronostic vital. Un seul cas avait été signalé en Martinique, une île des Antilles françaises, en 1988. Nous avons revu rétrospectivement les dossiers médicaux des patients ayant reçu un diagnostic d'angiostrongylose abdominale au CHU de la Martinique entre 2000 et 2017. Les objectifs de cette étude étaient d'évaluer l'incidence et effectuer une analyse descriptive des caractéristiques cliniques, biologiques, radiologiques et histopathologiques de l'AAH en Martinique. Deux cas confirmés et deux cas probables ont été identifiés chez des patients âgés de 1 à 21 ans au cours de la période de 18 ans, avec une incidence estimée à 0,2 cas par an (0,003 cas / an / 100 000 habitants (IC95% = 0,00 − 0,05)). Tous les patients présentaient une douleur abdominale associée à une éosinophilie sanguine élevée (médiane: 7,24 G/L [min 4,25; max 52,28 G / L]). Deux ont développé une perforation iléale et ont été traités par chirurgie, avec une confirmation diagnostique basée sur les résultats histopathologiques sur des échantillons chirurgicaux. Les deux autres cas étaient probables, avec des échantillons sériques réagissant aux antigènes d'Angiostrongylus sp. en l'absence de chirurgie. Tous les cas se sont améliorés sans séquelles. La description de cette série de cas souligne la nécessité de sensibiliser davantage la communauté médicale à cette maladie potentiellement mortelle et de faciliter l'accès à des outils diagnostiques spécifiques en Martinique. Des études environnementales et épidémiologiques sont nécessaires pour élargir nos connaissances sur cette parasitose.

Reaching the WHO target of testing persons in jails in prisons will need diverse efforts and resources.

BACKGROUND: The Caribbean is the second most affected region in the world by human immunodeficiency virus (HIV), and HIV prevalence is significantly higher among persons in jails and prisons than in the free population. The aim of our study was to assess the screening rates of HIV, hepatitis B and C, syphilis and human T cell leukaemia virus type 1 among newly-arrived persons in 2014, at Ducos facility in Martinique and the testing process performance. METHODS: This is an observational monocentric study conducted within the prison's health unit. The study population consisted of all individuals incarcerated between 01/01/14 and 31/12/14. At the initial medical visit, HIV and STI testing were proposed to every newcomer. The rate of acceptance was calculated, as well as the screening process performance. RESULTS: In 2014 778 new persons were incarcerated, among those, 461 (59.3%) were tested. The main reasons for missing the testing opportunity were due to organization of the judiciary system (persons on electronic monitoring or day parole, transferred or quickly released before completion of the process) or to individual refusal. Finally, 75 persons did not get their results (all of them negative), 41 of them due to the medical staff work overload. CONCLUSIONS: HIV and STI testing rates among newcomers at Ducos have notable room for improvement. The future availability of combined (HIV, HBV, HCV and syphilis) rapid tests may be very useful in case of short term incarceration, if their cost is not prohibitive. Reaching higher levels of testing will also require more resources.

New Surge of Syphilis among Patients Living with Human Immunodeficiency Virus in Martinique in 2015.

A syphilis outbreak began in Martinique, French Antilles, in 2004, initially among men who had sex with men (MSM) and who were living with human immunodeficiency virus (HIV). The outbreak subsequently affected all groups at risk, leading to a first epidemic peak in 2008. After an initial decrease, the outbreak started growing again in 2014 among patients living with HIV with unprecedented incidence among MSM. Herein, we describe the change in medical and social parameters of the outbreak since 2005.

First case of visceral leishmaniasis caused by Leishmania martiniquensis.

We report the first case of visceral leishmaniasis (VL) caused by Leishmania martiniquensis in the Caribbean, which until now, was known only to cause cutaneous leishmaniasis. The disease presented with fatigue, anemia, and hepatosplenomegaly in a 61-year-old man with human immunodeficiency virus (HIV) infection who was receiving antiretroviral therapy. Diagnosis was made by bone marrow biopsy. VL is life-threatening, and its emergence in the Caribbean is of concern.

Ovarian reserve in young women of reproductive age with Crohn's disease.

BACKGROUND: Crohn's disease (CD) mainly affects young adults of reproductive age. Whereas a large amount of data is available concerning pregnancy in young CD women, no study has been conducted on their ovarian reserve status. This study aimed to investigate the potential effect of CD on ovarian reserve in young women in remission, as reflected by serum anti-Müllerian hormone (AMH). METHODS: This retrospective case-control study was conducted in the University Hospital of Nantes, France. Serum levels of AMH were retrospectively measured in 50 women with CD in remission and in 163 control women with normal ovarian reserve, matched by age. RESULTS: No statistical difference was found between mean serum AMH levels in CD and control women. Serum AMH levels remained comparable between CD and control women <30 years, but they were significantly lower in CD women ≥ 30 years compared to the control group. Furthermore, the negative correlation between age and AMH level tended to be more pronounced in CD than control women. Multivariate analysis of CD patients' clinical and demographic characteristics showed that serum AMH level was influenced by disease location, with a colonic location of the disease being independently associated with a high risk of altered ovarian reserve. CONCLUSIONS: Women with CD do not have severe ovarian reserve alterations compared to a control population. However, age ≥ 30 years and a colonic location of the disease could be associated with an accelerated loss of follicles. These data could encourage gastroenterologists to inform CD women of the risk of delaying childbirth.