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We describe 7 cases of extensive tinea corporis since 2018 in a hospital in Paris, France, after failure to cure with terbinafine. Molecular analysis indicated Trichophyton mentagrophytes internal transcribed spacer type VIII (T. indotineae). This strain, which has mutations in the squalene epoxidase gene, is spreading on the Indian subcontinent.

Pneumocystis jirovecii pneumonia (PCP) is an important cause of morbidity in immunocompromised patients, with a higher mortality in non-HIV than in HIV patients. P. jirovecii is one of the rare transmissible pathogenic fungi and the only one that depends fully on the host to survive and proliferate. Transmissibility among humans is one of the main specificities of P. jirovecii . Hence, the description of multiple outbreaks raises questions regarding preventive care management of the disease, especially in the non-HIV population. Indeed, chemoprophylaxis is well codified in HIV patients but there is a trend for modifications of the recommendations in the non-HIV population. In this review, we aim to discuss the mode of transmission of P. jirovecii , identify published outbreaks of PCP and describe molecular tools available to study these outbreaks. Finally, we discuss public health and infection control implications of PCP outbreaks in hospital setting for in- and outpatients.

Background. Invasive wound mucormycosis (IWM) is associated with an extremely poor outcome among critically ill burn patients. We describe the detection of circulating Mucorales DNA (cmDNA) for the early diagnosis of IWM in those patients and report the potential value of detecting cmDNA for treatment guidance. Methods. Severely ill burn patients admitted to our tertiary referral center between October 2013 and February 2016 were included. Retrospective plasma samples were tested for the presence of cmDNA by quantitative real-time polymerase chain reaction (qPCR). Patients were then prospectively screened twice a week, and liposomal amphotericin-B therapy initiated based on a positive qPCR. The primary endpoint was the time between cmDNA detection and standard diagnosis. Secondary endpoints were the time from cmDNA detection and treatment initiation and mortality. Results. Seventy-seven patients (418 samples) were included. The average age was 46 (28–60) years, abbreviated burn severity index was 8 (7–10), and simplified acute physiology score was 33 (23–46). The total body surface area was 33% (22%–52%). cmDNA was detected 11 (4.5–15) days before standard diagnosis. The in-hospital mortality was 62% for patients with IWM and 24% for those without (P = .03). The mortality due to IWM was 80% during period A and 33% during period B (P = .46). Conclusions. This study suggests that the detection of cmDNA allows earlier diagnosis of IWM in severely ill burn patients and earlier initiation of treatment. Further studies are needed to confirm the impact of earlier treatment initiation on patient outcome.

Klebsiella pneumoniae carbapenemase (KPC) is a frequent and widespread carbapenemase, with over 260 variants identified. While KPC often evolves resistance to ceftazidime-avibactam, cefiderocol remains a key treatment option. Some variants, such as KPC-33 (D179Y), reduce cefiderocol susceptibility, but typically with only modest MIC increases. However, KPC’s genetic adaptability raises concern that further mutations could lead to high-level resistance, compromising cefiderocol’s efficacy. To anticipate this risk, we explored the mutational potential of bla KPC-2 , bla KPC-3 , and bla KPC-33 using random mutagenesis followed by 10-day selection under increasing cefiderocol pressure and whole genome sequencing. Libraries of 10 5 , 10 4 , and 10 5 mutants, respectively, yielded isolates with significantly elevated MICs, some exceeding 32 mg/L. All resistant clones shared a phenotype marked by cross-resistance to cefiderocol, ceftazidime, ceftazidime-avibactam, cefixime, and piperacillin, but restored susceptibility to carbapenems and most other β-lactams. Our findings highlight that no single mutation enables KPC to efficiently hydrolyze cefiderocol. Instead, high-level resistance requires a combination of enzymatic mutations and chromosomal alterations—such as disruptions in cirA and ybiX —suggesting a multifactorial and stepwise evolutionary pathway. Notably, ybiX has not previously been associated with cefiderocol resistance. These results underscore the importance of ongoing surveillance to detect emerging cefiderocol resistance in KPC-producing Enterobacterales .

Invasive aspergillosis (IA) caused by Aspergillus flavus remains poorly described. We retrospectively analyzed 54 cases of IA caused by A. flavus reported in France during 2012-2018. Among cases, underlying IA risk factors were malignancy, solid organ transplantation, and diabetes. Most (87%, 47/54) infections were localized, of which 33 were pleuropulmonary and 13 were ear-nose-throat (ENT) infection sites. Malignancy (70% [23/33]) and solid organ transplantation (21% [7/33]) were the main risk factors in localized pulmonary infections, and diabetes mellitus was associated with localized ENT involvement (61.5%, [8/13]). Fungal co-infections were frequent in pulmonary (36%, 12/33) but not ENT IA (0 cases). Antifungal monotherapy was prescribed in 45/50 (90%) cases, mainly voriconazole (67%, 30/45). All-cause 30-day case-fatality rates were 39.2% and 90-day rates were 47.1%, and rates varied according to risk factor, IA site, and fungal co-infections. Clinicians should remain vigilant for A. flavus and consider it in the differential diagnosis for IA.

Enterobacter hormaechei, a prominent species within the Enterobacter cloacae complex, is a significant cause of nosocomial infections and is frequently associated with multidrug resistance. Rapid genomic comparison helps guide timely infection control measures. This study aimed to develop a simple and rapid multiple-locus variable-number tandem-repeat analysis (MLVA) protocol for epidemiological surveillance of E. hormaechei. Eight variable-number tandem-repeat (VNTR) regions were selected for amplification using multiplex PCR, followed by gel electrophoresis. The method's discriminatory power was evaluated on 46 unrelated strains from 22 French hospitals. Then, suspected related strains from three potential outbreaks, including ESBL- and/or NDM-producing isolates were compared. An independent collection of 22 VIM-producing strains was also analyzed. Whole-genome sequencing (WGS) was used as the gold standard. Among 46 unrelated E. hormaechei strains, representing the five subspecies, MLVA and MLST showed similar discriminatory power (36 MLVA profiles vs. 33 STs, Hunter and Gaston diversity indices 0.9833 vs. 0.9824, respectively). Isolates with different ST typically had distinct MLVA profiles, except for three instances where different STs shared similar profiles. In STs represented by multiple strains, MLVA sometimes distinguished strains sharing the same ST. Among the three potential outbreak, epidemic strains exhibited unique MLVA profiles, with genetic distances of 0-11 SNPs using WGS, while unrelated isolates had different MLVA profiles, indicating this technique's potential as an effective screening tool for clonal groups. Similar results were observed for VIM-producing E. hormaechei, with consistent MLVA profiles within the same STs. The MLVA protocol developed is a rapid, cost-effective method for E. hormaechei epidemiological investigations that can quickly rule out unrelated strains. However, highly discriminatory techniques like WGS remain necessary when profiles are similar.

Nine new human invasive infections caused by the keratinophilic fungi Nannizziopsis obscura have been reported in France since 2004. The patients had variable clinical manifestations, had frequent dissemination, were mainly T-cell immunocompromised, and all originated from sub-Saharan West Africa. Before collection of the isolates, the etiologies of these infections were often misidentified, underscoring the extent of microscopic and cultural polymorphisms. All isolates but 1 had low MICs for the 8 antifungal drugs tested. When treated, patients received mainly azole therapy. Two of 7 patients with a known outcome died. We performed multilocus sequence analysis of N. obscura clinical strains and several strains of Nannizziopsis spp. isolated from reptiles. The human strains were clearly differentiated from the animal strains. N. obscura might be endemic to West Africa and responsible for undetected infections, which might become reactivated when immunosuppression occurs. N. obscura infection is probably underestimated because only sequencing enables proper identification.

Background Leishmaniases are regularly seen in non-endemic areas due to the increase of international travels. They include cutaneous leishmaniases (CL) and mucocutaneous (MC) caused by different Leishmania species, and visceral leishmaniases (VL) which present with non-specific symptoms. Methods We reviewed all consecutive leishmaniasis cases seen between September 2012 and May 2020. The diagnostic strategy included microscopy after May-Grünwald-Giemsa staining, a diagnostic quantitative PCR (qPCR) assay, and species identification based on sequencing of the cytochrome b gene. Results Eighty-nine patients had a definitive leishmaniasis diagnosis. Nine patients had VL with Leishmania infantum . Eighty patients had CL. Twelve patients acquired CL after trips in Latin America (7 Leishmania guyanensis , 2 Leishmania braziliensis , 2 Leishmania mexicana , and 1 Leishmania panamensis ). Species could be identified in 63 of the 68 CLs mainly after travel in North Africa (59%) with Leishmania major (65%), Leishmania tropica/killicki (24%), and L. infantum (11%), or in West Sub-Saharan Africa (32%), all due to L. major . The median day between appearance of the lesions and diagnosis was 90 [range 60–127]. Conclusions Our diagnostic strategy allows both positive diagnoses and species identifications. Travelers in West Sub-Saharan Africa and North Africa should be better aware of the risk of contracting leishmananiasis. Highlights Imported leishmaniases are regularly seen in non-endemic areas. Cutaneous forms are due to different species that need to be correctly identified for adapting treatment and epidemiologic purposes. The index of suspicion for the visceral form is often low because of the non-specificity of the clinical symptoms and the notion of travel in endemic areas often remote. The strategy, based on diagnostic quantitative PCR followed by sequencing for species identification, allows for rapid and safe diagnoses in a routine laboratory.

Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR)-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker) and multiple (more than one allele per marker) genotypes were observed in 34 (32%) and 72 (68%) samples, respectively. A genotype could be assigned to 55 samples (54 patients) and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21) in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.

Diagnosis of Pneumocystis jirovecii pneumonia relies on nucleic acid quantification in respiratory samples. Lack of standardization among molecular assays results in significant differences among assays/centers. To further promote standardization, we compared four thermocyclers and six master mixes for the detection of P. jirovecii. Whole nucleic acid (WNA) was extracted from broncho-alveolar lavages. Positive and negative sample extracts were pooled to get enough homogeneous materials. Three master mixes were tested to detect DNA by qPCR (D1, D2, and D3), and three to detect WNA by reverse transcriptase qPCR (W1, W2, and W3) manufactured by Roche, Eurogentec, Applied Biosystem, Invitrogen and Thermofischer Scientific. Experiments were performed on four thermocyclers (Roche LightCycler 480, Qiagen Rotor-Gene Q, Applied Biosystem ABI7500, and QuantStudio). Comparison of quantitative cycle (Cq) values between the methods targeting WNA versus DNA showed lower Cq values for WNA, independently of thermocycler and master mix. For high and low fungal loads, ∆Cq values between DNA and WNA amplification were 6.97 (±2.95) and 5.81 (±3.30), respectively (p < 0.0001). Regarding DNA detection, lower Cqs were obtained with D1 compared to D2 and D3, with median ∆Cq values of 2.6 (p = 0.015) and 2.9 (p = 0.039) respectively. Regarding WNA detection, no mix was superior to the others. PCR efficiency was not significantly different according to the qPCR platform (p = 0.14). This study confirmed the superiority of WNA over DNA detection. A calibration method (e.g., an international standard) for accurate comparative assessment of fungal load seems necessary.