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Introduction. Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy. Case Presentation. We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus. Conclusion. We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was Trichosporon asahii by in situ hybridization using a DNA probe targeting 26S rRNA.

Clostridium septicum gas gangrene is a severe and deadly infection caused by an anaerobic, spore-forming, Gram-positive bacillus. As previously described, two entities are observed: traumatic and spontaneous (or non-traumatic) forms. In this report, we aim to describe the case of a fulminant and ultimately fatal C. septicum myonecrosis occurring in a patient who was first admitted for refractory cardiac arrest and placed on veino-arterial extracorporeal membrane oxygenation (ECMO). Building upon prior studies that have documented cases of spontaneous gas gangrene caused by C. septicum, we provide an updated compilation, focusing on microbiological characteristics of C. septicum, along with the diagnostic and therapeutic challenges associated with spontaneous gas gangrene. Additionally, the specific clinical situation of our case illustrates the seriousness of this infectious complication that combined both spontaneous and traumatic gas gangrene risk factors. We thus, discuss the antibiotic coverage prior to the initiation of ECMO procedure.

Tuberculosis (TB) is one of the most common pathogens of bacterial lung infections, especially in underdeveloped nations like Morocco, where the incidence of TB was 97 cases per 100 000 persons in 2019. Thanks to its national TB prevention and control plan, Morocco was able to achieve remarkable progress in the management of TB with an 80% reduction in the total number of patients diagnosed with TB between 1980 and 2018. The national plan also allowed us to reach and maintain a therapeutic rate above 86% since 2002. Sternal TB is a rare clinical condition accounting for 1% of all musculoskeletal TB cases. Due to its rarity and the lack of awareness of clinical presentations, the diagnosis of sternal TB can be quite complex. We describe the case of a 14-year-old Moroccan patient consulting in the Military Hospital Mohammed V-Rabat with central chest pain for 4 months which was not associated with breathing, physical exercise or eating. The patient also had a history of asthenia, fever and weight loss. A computed tomography scan of the chest showed a destructive lesion of the sternum. Afterward, a chirurgical biopsy was performed and enabled to confirm the microbiological diagnosis of TB with the realization of the real-time PCR. The antitubercular therapy was given to the patient who had complete resolution of symptoms. This condition should be included in the differential diagnosis of chronic chest pain that mimics costochondritis particularly in patients from endemic areas.

Protists are important key players in the microbial loop and influence their environment by grazing, which leads to the return of nutrients into the soil and reduces pathogen pressure on plants. Specifically, protists on and around plant roots are important for plants' development and growth. For this study, the fourth most important crop in the world, Hordeum vulgare, was selected. Seeds of H. vulgare were inoculated with Acanthamoeba castellanii alone or with additional soil bacteria at the beginning and during the experiment. The germination of the seeds and the growth of the plants in pouches were monitored over 3 weeks. No differences were found in leaf growth, root growth, root and leaf nitrogen content or ammonia content of the liquid from the pouches. In contrast, the relative increase in root and leaf dry weight showed a small difference compared to the controls. The results of this experiment demonstrated that seed inoculation with A. castellanii alone or with additional unidentified soil bacteria did not have a major effect on the growth and development of barley. Nevertheless, small changes in plant development were detected, indicating that A. castellanii should be considered for further investigation of co-inoculations with plant growth-promoting bacteria and additional nutrients.

Biosurfactants are naturally occurring compounds synthesized by micro-organisms that increasingly attract attention due to both their living area and application in various industries. In this study, we explore and characterize a novel bacterium, Enterobacter quasihormaechei strain BDIFST24001, isolated for its ability to produce rhamnolipid biosurfactants, with the aim of facilitating oil remediation processes. The isolation of this bacterium was carried out using Luria-Bertani (LB) broth media from environmental samples collected from oil-contaminated sites in Dhaka City. Screening tests, including the oil spreading method and drop collapse assay, were conducted to identify potential biosurfactant-producing strains, leading to the selection of E. quasihormaechei strain BDIFST24001 based on its favourable performance. Subsequent molecular identification revealed a high similarity of the strain's 16S rRNA gene to E. quasihormaechei, which was corroborated through phylogenetic analysis. Further analysis of the biosurfactant produced by this strain indicated its rhamnolipid nature, as confirmed by FT-IR spectroscopy. The rhamnolipids exhibited promising surface-active properties, including a significant reduction in surface tension and emulsification activity, as evidenced by surface tension measurements and emulsification index assays. Optimization studies revealed that the optimal conditions for rhamnolipid production by E. quasihormaechei strain BDIFST24001 were a temperature of 37 °C, pH 10.0 and salinity of 4 %. The rhamnolipids produced by this strain demonstrated effective oil remediation capabilities, as observed through controlled experiments using petrol oil. The rhamnolipids effectively reduced the surface tension of the oil-water interface, facilitating the dispersion and emulsification of the oil phase in water. Overall, our findings highlight the potential of E. quasihormaechei strain BDIFST24001 as a promising candidate for biosurfactant-mediated oil spill cleanup and environmental remediation efforts.

[This corrects the article DOI: 10.1099/acmi.0.000735.v4.].

Asthma is a significant public health concern, particularly in children with severe symptoms. Exacerbation of asthma (EOA) is life-threatening, and respiratory infections (RIs) play a crucial role. Though viruses play a significant role in EOA, patients are empirically treated with antibiotics, contributing to antibiotic resistance development. Although there are widely reported associations of EOA with viral or Mycoplasma pneumoniae infections, there are no published data for Sri Lanka. The present study aimed to identify the association of common respiratory viruses, typical respiratory bacterial pathogens and M. pneumoniae in children with EOA and relate them with the compatibility of antimicrobial use. A case-control study was conducted in the paediatric unit of North Colombo Teaching Hospital, Sri Lanka, involving two groups of children between 5 and 15 years of age. Group 1 is children with EOA and Group 2 is children with stable asthma (SA). Each group consisted of 100 children. Sputum/throat swabs were tested for common respiratory viruses using virus-specific fluorescein isothiocyanate-labelled monoclonal antibodies (MAbs), bacteria by routine culture, and M. pneumoniae by real-time polymerase chain reaction. Macrolide resistance in M. pneumoniae was detected using conventional PCR and sequencing specific genetic mutations in the 23S rRNA gene. M. pneumoniae was genotyped using nested multilocus sequence typing, which targeted eight housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC and adk). There was no significant difference in age, gender, demographic or geographical location between the two groups. In children with EOA, antibiotics were used in 66 % (66/100) and macrolides in 42 % (42/100). Samples comprised 78 % (78/100) sputum and 22 % (22/100) throat swabs. Adenovirus was the most common virus identified, and it was significantly higher in children with EOA compared to those with SA. Still, the two groups had no significant difference in typical bacteria findings. M. pneumoniae was detected in one patient with EOA, but none was detected in the SA group. The M. pneumoniae was macrolide-sensitive and ST14 by multilocus sequence typing. This study showed that the empiric use of antibiotics in children with asthma might be better targeted with prior pathogen screening to inform appropriate treatment to minimize antibiotic resistance.

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is a major public health problem in hospitals and in the community. The objective of this work was to describe the epidemiology of ESBL-E, to study their resistance profile and to determine the genes encoding the ESBL phenotype. This is a retrospective study conducted in the bacteriology laboratory of the Mohamed V Military Training Hospital in Rabat, and covering all isolates of Enterobacteriaceae from 1 January 2018 to 31 December 2020. The molecular study of ESBL genes involved a representative sample of all ESBL isolates. The overall prevalence of ESBLs in isolated Enterobacteriaceae (1402/10268) is 13.65 %. The urinary tract was the main site of isolation of ESBL (61 %). The bacterial species most concerned are Escherichia coli (41.9 %), Klebsiella pneumoniae (42.2 %) and Enterobacter cloacae (11.9 %). The study of antibiotic susceptibility showed a resistant profile marked mainly by 100 % resistance to first generation cephalosporins (1GC) and third generation cephalosporins (3GC), 55 % to piperacillin-tazobactam, 16 % to imipenem, and 87 % to fluoroquinolones. Molecular typing of ESBL strains showed a prevalence of CTX-M (95 %), SHV (50 %) and TEM (56 %). The CTX-M-1 and the CTX-M-9 groups were the most common (96.19 % and 7.62 % respectively), and CTX-M15 was found in 78.10 % of CTX-M-1 ESBL positive isolates. Most strains had more than two coexisting resistance genes. The prevalence rate of ESBL-E is critical, and preventive action at different levels (prescriber, biologist, hospital, patient, etc.) are necessary in order to limit their spread and to manage a better therapeutic strategy.

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from stoats (Mustela erminea), identifying two novel calicivirus species, named stoat vesivirus and stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92 %. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72 % similarity in ORF1, 61-62 % in ORF2 and 71 % in ORF3. Phylogenetic analysis robustly supported stoat vesivirus as belonging within the Vesivirus genus. The second calivicirus (stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus', however it clusters basally within the Valovirus genus, supporting leaving it included in this genus.