Microorganisms

ObjectivesCandida viswanathii has been sporadically reported in Asia and South America but never in Europe. This study reports the first European outbreak of C. viswanathii in a paediatric hospital, outlining diagnostic challenges and containment measures. MethodsFifteen C. viswanathii isolates were recovered from blood cultures of consecutive paediatric patients admitted to intensive care units between April and August 2025. Identification was performed using MALDI-TOF MS, chromogenic media, F...

Mucormycosis, a rare but fatal invasive fungal infection, affects immunocompromised patients. Despite recent advancements in diagnostic tools and treatments, mortality rates remain high, reaching 79% at ninety days in disseminated forms. Quantitative Polymerase Chain Reaction (qPCR) based methods are now widely available, and help to discern colonisation and infection, although this remains a real challenge. This study aims to describe the epidemiological and clinical characteristics of a French...

BackgroundExtensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterisation of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. MethodsIsolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby-Bauer ...

Candida auris, initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris, with some strains displaying resistance to all primary antifungal drug classes. In this study, we presented the first WGS analysis of C. auris from Bangladesh, describing its origins, transmission dynamics, and antifungal suscepti...

IntroductionSARS-CoV-2 infections caused a global pandemic between 2019 and 2023. Omicron variants continued to emerge but morbidity and mortality were reduced likely due to vaccinations and increasing host immunity. COVID-19 case numbers reported from Pakistan as was genomic epidemiology of SARS-CoV-2. We studied SARS-CoV-2 variants reported between 2023 and 2024 and compare these with variants in other countries. MethodologyWe studied SARS-CoV-2 genomes submitted from Pakistan available in pu...

BackgroundCOVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. MethodsWe studied 276,525 COVID-19 cases and 1,041 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. ResultsThe highest case numbers and deaths were recorded in Sindh and Pu...

AbstractO_ST_ABSBackgroundC_ST_ABSScopulariopsis/Microascus is a rare but devastating pathogen due to its intrinsic resistance to nearly all available antifungal agents. Microascus gracilis, an ascomycetous mould in the order Microascales, family Microascaceae, has recently emerged as a significant invasive pathogen causing opportunistic infections. Objectives and MethodsWe present a case of pleural infection caused by M. gracilis with pulmonary aspergillosis in an immunocompromised man after C...

BackgroundDespite decades of vaccination whooping cough has not been eliminated and epidemics are known to occur every 3 to 5 years. As a consequence of the COVID-19 pandemic and associated non-pharmaceutical interventions, pertussis has been absent in 2020-2022. Many European countries have since seen large pertussis epidemics in 2023 and 2024. AimTo type Dutch pertussis isolates from 2023-2024 and compare these to pertussis isolates from 2015-2020. MethodsPertussis isolates received by the r...

We report a 19-fold increase in 2024 of qPCR diagnoses of Chlamydia pneumoniae infections in Marseille, Southern France, with 37 cases versus 10 between 2018-2023. These mostly affected children, and young adults. We obtained four C. pneumoniae genomes, all of serotype ST16, suggesting an epidemic circulation in our geographical area.

BackgroundCandida auris is an emerging fungal pathogen that is often multidrug-resistant. It can persist on skin and in hospital environments, leading to outbreaks and severe infections for patients at risk. Several countries and institutions are working on establishing guidelines and recommendations for prevention. This review aims to assess the evidence on factors associated with C. auris colonisation or infection, the duration of such colonisation, possible colonisation sites, and the risk of...

BackgroundMonitoring the presence of commensal and pathogenic microorganisms in the human oral, nasal and hand niches as determinants for respiratory tract infections is of critical global relevance as was evident during the COVID-19 pandemic. However, community-based surveillance is difficult because current sampling methods are not optimal for a wide age range of participants, particularly young children. We designed a platform of minimally invasive self-sampling at home and assessed its use f...

Neonatal infections due to Paenibacillus species have increasingly been reported over the last few years. We performed a structured literature review of human Paenibacillus infections in infants and adults to compare the epidemiology of infections between these distinct patient populations. Thirty-nine reports describing 176 infections met our inclusion criteria and were included. There were 37 Paenibacillus infections occurring in adults caused by 23 species. The clinical presentations of infec...

The current gold standard for clinical pathogen identification relies on a combination of culture-based methods, target-specific molecular techniques, and antigen-detection assays1. Known limitations of the first method include the requirement for viable and culturable microorganisms, while the second approach is constrained to a limited number of predefined targets. These constraints reduce their diagnostic success, as not all pathogens are culturable, easily isolated from commensal microbiota,...

In children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillances on pneumococcal colonisation and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular...

IntroductionImmune thrombocytopenic purpura (ITP) is characterized by a decrease in platelet counts and can be triggered by various factors, such as viral infections and vaccinations. Concerns have emerged regarding potential links between the vaccines for COVID-19 and the worsening of ITP. This systematic review aims to comprehensively assess the impact of COVID-19 vaccines on patients with ITP, including associated risks and outcomes. Methods and AnalysisA thorough search will be conducted ac...

The Omicron variant of SARS-CoV-2 has rapidly replace previous variants of SARS CoV2 around the globe and is now a major variant of concern. The genomic surveillance of Omicron variant also reveals spread of its subvariant BA.2 which has differing transmissibility in comparison to its other subvariant BA.1. BA.1 and BA.2 harbors different mutational profile. One of the important change in both the subvariants is the presence of 69-70 deletion in BA.1 and absence of this deletion in BA.2. This de...

Blastomycosis due to Blastomyces dermatitidis and B. gilchristii is a notable cause of respiratory mycoses in North America with recurrent outbreaks. We developed a highly sensitive, specific, and reproducible Taqman duplex real-time PCR assay for the differentiation of B. dermatitidis and B. gilchristii. The new assay permitted retrospective analysis of Blastomyces cultures (2005 to 2019), and primary clinical specimens (2013-2019) from NY patients. Blastomyces dermatitidis was the causal agent...

ObjectiveThe purpose is to clarify the overall situation of clinical related to primary immune thrombocytopenia (ITP), to evaluate the difference between published clinical trials and unpublished trials, and to evaluate the relevant information of trial publication. MethodsSearch the ClinicalTrials.gov database on March 20, 2022 to identify ITP clinical trials and obtain relevant data. Publications in PubMed were searched using standardized methods to identify the publication of completed clini...

India is currently facing the devastating second wave of COVID-19 pandemic resulting in approximately 4000 deaths per day. To control this pandemic continuous mutational surveillance and genomic epidemiology of circulating strains is very important. In this study, we performed mutational analysis of the protein coding genes of SARS-CoV-2 strains (n=2000) collected during January 2021 to March 2021. Our data revealed the emergence of a new variant in West Bengal, India, which is characterized by ...

India had witnessed unprecedented surge in SARS-CoV-2 infections and the dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. Here in, we have applied various statistical methods like correlation, hierarchical clustering to know the pattern of pathogenesis of the circulating VoCs. B.1.617.1 (Kappa) was the predominant VoC during the early phase of second wave. Delta (B.1.617.2) or Delta-lik...