Clinical Microbiology Reviews

SUMMARYSkin and soft tissue infections represent a major clinical challenge. This is particularly true given the rise in antimicrobial resistance, the increasing prevalence of chronic wounds, and the growing number of immunocompromised patients. Conventional antibiotic therapies are frequently compromised by multidrug-resistant pathogens, biofilm formation, and disruption of the skin microbiome, underscoring the urgent need for alternative or adjunctive antibacterial strategies. Bacteriophages,...

SUMMARYThe human gut microbiotas constitute a complex microecosystem essential for host homeostasis. Among its metabolites, short-chain fatty acids (SCFAs) act as key signaling molecules linking microbial activity to host immunity and barrier function. Based on existing literature, we conducted a comprehensive analysis of the interaction between SCFAs and 11 key gut pathogens. These pathogens include bacteria (i.e., Staphylococcus aureus, Clostridioides difficile, Salmonella spp., Campylobacter...

SUMMARYAfrica's ongoing struggles with emerging epidemics and antimicrobial resistance (AMR) underscore the urgency of integrating pathogen genomics and surveillance systems into the continent's One Health strategy, particularly given the existing limitations in preparedness and technological resources. This review brings together current evidence on the growth of sequencing infrastructure, the development of regional genomic hubs, and the establishment of governance frameworks, while...

SUMMARYAcanthamoeba keratitis (AK) is a rare but sight-threatening corneal infection with rising global incidence, largely driven by increased contact lens use. Management remains challenging due to limited therapeutic options, variable clinical responses, and a lack of standardized treatment guidelines. Diagnosis is frequently delayed because of the non-specific clinical presentation, and early use of topical corticosteroids can exacerbate disease severity and worsen outcomes. The formation of...

SUMMARYRoss River virus (RRV) causes the most mosquito-borne disease notifications in Australia and a considerable burden of non-fatal, yet frequently prolonged rheumatic illness across the Australia-Pacific region, reflected in thousands of notifications each year and notable economic and quality-of-life losses. Research on RRV spans multiple disciplines, encompassing viral genomics, immunopathology, transmission ecology, epidemiology, entomology, and environmental science. This review...

SUMMARYThe penile microbiome (PMB) can be dominated by skin-associated bacteria (e.g., Corynebacterium, Staphylococcus, and Streptococcus) or by anaerobic bacteria that are associated with bacterial vaginosis (BV), and is influenced by male circumcision status, female partner vaginal microbiome (VMB), BV status, condom use, and antibiotic use. Penile bacteria that are associated with BV and genital mucosal inflammation are associated with men's risk of HIV and STIs. In the few studies that...

SUMMARYThe Aspergillus niger complex, also known as the black aspergilli or section Nigri, comprises a diverse group of filamentous fungi with wide-ranging ecological, industrial, and pathogenic significance. While traditionally associated with food spoilage and industrial fermentation, black aspergilli have emerged as opportunistic pathogens affecting humans, animals, and plants. This review provides a comprehensive synthesis of the taxonomy, ecology, pathogenicity, and antifungal resistance of...

SUMMARYSince the worldwide dissemination of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) in the early 2000s, ESBL-Ec community carriage has followed divergent epidemiological patterns across regions. Currently, high-income countries (HIC) have a lower prevalence of ESBL-Ec carriage compared to the more concerning prevalence observed in low- and middle-income countries (LMICs). The aim of this review is to summarize the factors that could explain variations in ESBL-Ec...

SUMMARYInfection prevention and control (IPC) programs are essential for safe healthcare; yet, implementation across sub-Saharan Africa remains constrained by chronic underfunding, weak water, sanitation, and hygiene (WASH) systems, limited laboratory capacity, and shortages of trained staff. Healthcare-associated infections (HCAIs) are presumed common, underreported, and often severe, with a disproportionate burden among hospitalized neonates and postpartum women, and they pose substantial...

SUMMARYJorge Lobo's disease (JLD) is a chronic cutaneous and subcutaneous mycosis endemic to the Amazon Basin and tropical rainforests of Latin America. Despite more than a century of study, the disease remains underrecognized, poses significant diagnostic challenges, and is often therapeutically refractory. Here, we synthesize historical, clinical, and ecoepidemiological evidence; provide a practical diagnostic approach; and highlight unresolved questions. Clinically, JLD presents as slowly...

SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public...

SUMMARYThe emerging fungal pathogen Candidozyma auris (syn. Candida auris; C. auris) has attracted considerable attention from the scientific, clinical, and public health communities due to its multidrug resistance, environmental persistence, and high transmissibility. Since its first description in Japan in 2009, C. auris has spread rapidly worldwide, with a marked acceleration following the coronavirus disease 2019 (COVID-19) pandemic. As of December 2025, 84,941 colonization or infection...

SUMMARYLatent tuberculosis infection (LTBI) is common and preventable among patients with chronic kidney disease (CKD), where uremia and iatrogenic immunosuppression heighten reactivation risk. This narrative review synthesizes evidence across pre-dialysis CKD, dialysis, and kidney transplantation to propose a pragmatic care pathway. In advanced CKD, the tuberculin skin test performs poorly, whereas interferon-γ release assays (IGRAs) are preferred. Screening should be risk-targeted in...

SUMMARYThe skin microbiome, consisting of bacteria, fungi, viruses, and archaea, plays a crucial role in maintaining skin health by regulating immune responses, preserving barrier function, and influencing metabolic processes. Dysbiosis in the microbiome is linked to dermatological diseases such as atopic dermatitis (AD), psoriasis, and acne, with specific microbes, such as Staphylococcus aureus and Cutibacterium acnes, either promoting or protecting against disease. This review summarizes...

SUMMARYOsteomyelitis refers to inflammation in the bone and is most often a consequence of bacterial infection. The most common cause, and the pathogen that causes the most severe form of infection, is Staphylococcus aureus. S. aureus is a common commensal of healthy humans, and this contributes to its predominance as a cause of osteomyelitis, but this does not account for the severity of S. aureus bone infections or their therapeutic recalcitrance to conventional antibiotic therapy. Clinical...