Clinical Microbiology Reviews[JOURNAL]
Sun
200 papers
Diagnostic challenges in re-emerging rickettsioses: why current tools fall short.
Mir YB, Manzoor T, Mushtaq D … +6 more , Najar AH, Kawoosa F, Bhatia D, Qadri SM, Siraj F, Ahmad SM
Clin Microbiol Rev · 2026 Jul · PMID 42390463 · Publisher ↗
SUMMARYRickettsial diseases, encompassing scrub typhus, spotted fever group rickettsioses, and typhus group rickettsioses, represent a significant and escalating public health threat worldwide, particularly in the Asia-P...
SUMMARYRickettsial diseases, encompassing scrub typhus, spotted fever group rickettsioses, and typhus group rickettsioses, represent a significant and escalating public health threat worldwide, particularly in the Asia-Pacific and sub-Saharan African regions. Despite their high morbidity and potential for fatal outcomes if left untreated, these infections remain notoriously underdiagnosed due to their nonspecific clinical presentation, which frequently overlaps with other acute undifferentiated febrile illnesses (AUFIs) such as dengue, malaria, and leptospirosis. This review evaluates the evolving diagnostic landscape, highlighting the severe limitations of conventional methods: the Weil-Felix test lacks necessary specificity, while the gold standard indirect immunofluorescence assay (IFA) is primarily retrospective due to delayed seroconversion. Molecular diagnostics, particularly multiplex polymerase chain reaction (mPCR), have emerged as a critical advancement, enabling early, species-specific identification during the acute phase of infection when doxycycline therapy is most effective. We further explore the paradigm shift toward syndromic molecular panels, such as the TaqMan Array Card (TAC), which facilitate simultaneous screening for multiple AUFI pathogens. Emerging platforms, including digital PCR (dPCR) for absolute quantification and CRISPR-Cas-based point-of-care (POC) systems (SHERLOCK and DETECTR), offer promising solutions for low-resource settings. Finally, this review underscores the necessity of integrating molecular surveillance within a One Health framework and utilizing artificial intelligence (AI) to address technical and implementation barriers. Overcoming these challenges is essential for transforming rickettsial diagnosis from a reactive to a proactive strategy, ultimately reducing the global burden of these neglected zoonoses.
Current progress in developing mRNA-lipid nanoparticle vaccines against human bacterial pathogens.
Pullinger B, Harbison-Price N, Sebina I … +3 more , Na J, Belz GT, Walker MJ
Clin Microbiol Rev · 2026 Jul · PMID 42390268 · Publisher ↗
SUMMARYThe messenger RNA (mRNA)-lipid nanoparticle (LNP) vaccine platform is the newest tool in the vaccination arsenal for combating infectious diseases, rare genetic diseases, and cancer. Since 2020, major advances in...
SUMMARYThe messenger RNA (mRNA)-lipid nanoparticle (LNP) vaccine platform is the newest tool in the vaccination arsenal for combating infectious diseases, rare genetic diseases, and cancer. Since 2020, major advances in preclinical and clinical studies have demonstrated the efficacy of mRNA-LNP vaccines against viral pathogens and in cancer. However, studies investigating the efficacy of mRNA-LNP vaccines against bacterial pathogens remain sparse due to substantial bacterial vaccine-specific challenges. Here, we highlight key challenges impeding the development of mRNA-LNP vaccines against human bacterial pathogens, the advantages that can be gained by utilizing the mRNA-LNP platform for bacterial vaccines, and progress toward the development of mRNA-LNP vaccines against bacterial infections.
The gut microbiome and colorectal cancer.
Dietz M, Subramanian S, Staley C
Clin Microbiol Rev · 2026 Jun · PMID 42370690 · Publisher ↗
Colorectal cancer (CRC) is a significant global health concern that is growing in prevalence, especially in younger populations. The gut microbiome is an increasingly recognized factor in the development and progression...
Colorectal cancer (CRC) is a significant global health concern that is growing in prevalence, especially in younger populations. The gut microbiome is an increasingly recognized factor in the development and progression of numerous diseases, including CRC. This review explores the current research on the causal relationship between the microbiome and CRC, including the strengths and limitations of the current models for studying this complex interaction. We then delve into key microbial metabolites and their effects on host signaling pathways in the context of CRC and highlight specific bacterial species with direct links to CRC development and progression. Existing microbiota-targeted therapies such as pre- and pro-biotics and fecal microbiota transplantation are described, as well as innovative microbiome-focused strategies that are currently in development, like quorum quenching. Finally, we address the major challenges in the field, such as conflicting research findings and the need for a systems-level, multi-omic approach to describe the intertwined and bidirectional host-microbe interactions.
Influence of fungi on epithelial homeostasis and role in inflammatory diseases.
Peterson LF, Wang J, Gow NAR … +2 more , LeibundGut-Landmann S, Brewer MG
Clin Microbiol Rev · 2026 Jun · PMID 42312840 · Publisher ↗
SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immuno...
SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera and . We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.
Coxsackievirus A6 on the rise: epidemiology, pathogenicity, evolutionary dynamics, and antiviral strategy.
Zhou X, He F, Lin Z … +4 more , Wen W, Yang S, Xu T, Li H
Clin Microbiol Rev · 2026 Jun · PMID 42312839 · Publisher ↗
In recent years, coxsackievirus A6 (CVA6) has become a predominant cause of hand, foot, and mouth disease (HFMD) worldwide, surpassing enterovirus A71 (EV-A71) and CVA16. The rise of CVA6 is of particular public health c...
In recent years, coxsackievirus A6 (CVA6) has become a predominant cause of hand, foot, and mouth disease (HFMD) worldwide, surpassing enterovirus A71 (EV-A71) and CVA16. The rise of CVA6 is of particular public health concern due to its association with atypical and severe clinical presentations, including extensive vesiculobullous eruptions and neurological complications. These diverse and often non-classical manifestations, which also occur in adults, complicate clinical diagnosis and highlight the need for enhanced molecular surveillance. Furthermore, the potential impact of enteroviral infection during pregnancy and on neonatal outcomes remains an important clinical consideration. While both structural and non-structural proteins of CVA6 are known to contribute to viral virulence, the underlying pathogenic mechanisms are not fully understood. Continuous evolution of CVA6 through genetic variation and frequent recombination has led to the emergence of distinct lineages and recombinants, posing substantial challenges to the development of effective antivirals and vaccines. To address these gaps, this review systematically examines the global epidemiology, pathogenic mechanisms, evolutionary dynamics, current diagnostic tools, and antiviral strategies for CVA6. By integrating these perspectives, this work aims to inform public health preparedness and guide future research toward mitigating outbreaks driven by emerging recombinants and novel enterovirus serotypes.
Intravesical therapies for catheter-associated urinary tract infections: current approaches and future directions.
Linham C, Webber M, Qi S
Clin Microbiol Rev · 2026 Jun · PMID 42307232 · Publisher ↗
SUMMARYUrinary tract infections (UTIs) are among the most common bacterial infections worldwide, with catheter-associated UTIs (CAUTIs) representing a major subset in healthcare settings. CAUTIs significantly increase pa...
SUMMARYUrinary tract infections (UTIs) are among the most common bacterial infections worldwide, with catheter-associated UTIs (CAUTIs) representing a major subset in healthcare settings. CAUTIs significantly increase patient morbidity, mortality, hospital stays, and healthcare costs, while driving antibiotic overuse and antimicrobial resistance (AMR). Systemic antibiotics often fail due to poor biofilm penetration, localized infection sites, and rising multidrug resistance, highlighting the urgent need for alternative, targeted therapies. This review discusses the role of intravesical therapies in both the treatment and prevention of CAUTIs, with a primary emphasis on therapeutic applications. The bladder is an accessible target for local treatment, as catheters can be repurposed for drug delivery. These devices are frequently colonized by biofilm-forming bacteria that contribute to persistent infection and treatment failure. This review explores intravesical therapy, the direct instillation of antimicrobial agents into the bladder, as a promising strategy to improve CAUTI management and mitigate AMR. We examine CAUTI pathogenesis, biofilm development, and current clinical approaches, including antimicrobial stewardship, catheter management, and coating technologies. Evidence for intravesical antibiotics such as gentamicin, amikacin, colistin, fosfomycin, and trimethoprim is reviewed alongside limited data from clinical trials, and applications in other urological disorders. Non-antibiotic alternatives, including sterile saline, antiseptic solutions, bacteriophages, antimicrobial peptides, natural bioactives, probiotics, and silver nanoparticles, are also discussed, particularly for their potential synergistic use with antibiotics to reduce resistance emergence. Despite encouraging results, intravesical therapy faces challenges such as limited clinical data, lack of standardized protocols, and delivery barriers. This review summarizes current evidence, identifies research gaps, and proposes directions to advance this underused strategy against CAUTIs amid escalating antibiotic resistance.
malaria in India: microbiological barriers to diagnosis, treatment, and elimination.
Kumar C, Bharti PK, Gupta H
Clin Microbiol Rev · 2026 Jun · PMID 42307231 · Publisher ↗
SUMMARY remains a major barrier to global malaria elimination due to dormant liver-stage hypnozoites that drive relapse and sustain transmission even in low-endemic settings. India accounts for nearly half of the global...
SUMMARY remains a major barrier to global malaria elimination due to dormant liver-stage hypnozoites that drive relapse and sustain transmission even in low-endemic settings. India accounts for nearly half of the global burden, placing it at the center of elimination efforts. This review synthesizes current evidence on the epidemiology, biology, and control of in India. Despite progress, early gametocytogenesis, hypnozoites, low parasitemia, and immune evasion complicate diagnosis and treatment. Recent single-cell and multi-omics studies are elucidating gene regulation, epigenetic control of hypnozoite dormancy, and quiescent liver-stage biology. Diagnostic gaps persist because microscopy and rapid diagnostic tests poorly detect asymptomatic infections, and molecular surveillance cannot map relapse without hypnozoite biomarkers. Standard radical cure with chloroquine and 14-day primaquine is limited by poor adherence and restricted glucose-6-phosphate dehydrogenase testing, while single-dose tafenoquine awaits wider implementation. Urban malaria, largely driven by and , is increasing as a consequence of rapid urbanization and vector adaptation. National initiatives such as the Integrated Health Information Platform, Tribal Malaria Action Plans, and Urban Malaria Schemes are critical but face constraints in surveillance integration, private sector reporting, and cross-border coordination. We highlight emerging experimental liver models, single-cell technologies, and systems biology frameworks as essential tools for addressing key knowledge gaps in relapse biology. Sustained investment and interdisciplinary collaboration will be required for India to lead elimination and translate national progress into global impact.
The gut microbiome in preterm infants: development, dysbiosis, and disease implications.
Tao E, Wang L, Yuan T
Clin Microbiol Rev · 2026 Jun · PMID 42294884 · Publisher ↗
SUMMARYPreterm infants face a unique trajectory of gut microbiome assembly, shaped by the convergence of physiological immaturity, necessary clinical interventions, and the neonatal intensive care unit environment. This...
SUMMARYPreterm infants face a unique trajectory of gut microbiome assembly, shaped by the convergence of physiological immaturity, necessary clinical interventions, and the neonatal intensive care unit environment. This dysbiotic ecosystem-characterized by low diversity, depletion of beneficial commensals such as , and expansion of pathobionts, including Enterobacteriaceae-is increasingly recognized as a central mediator of neonatal morbidity. This review synthesizes current evidence on preterm microbiome development, its role in necrotizing enterocolitis through mechanisms involving Toll-like receptor 4 signaling, bile acid dysmetabolism, and immune dysregulation, and its systemic impact via gut-organ axes linking the intestine to the brain, lung, eye, and systemic circulation. We critically evaluate microbiome-targeted interventions across the translational spectrum, from foundational practices such as human milk feeding and antibiotic stewardship to active modulation with probiotics and prebiotics, and emerging precision strategies, including postbiotics, phage therapy, and fecal microbiota transplantation. Methodological advances in multi-omics, machine learning, and digital twin modeling are paving the way for personalized, predictive microbiome-mediated care. We also address the hidden burden of antimicrobial resistance in the preterm gut and the challenges of translating mechanistic insights into clinical practice. Looking forward, embracing the complexity of the preterm microbiome as a dynamic, multi-kingdom ecosystem is essential for developing holistic interventions that improve both short-term survival and long-term neurodevelopmental, respiratory, and metabolic outcomes.
Marburg virus disease: a comprehensive review.
Woolsey C, Geisbert TW
Clin Microbiol Rev · 2026 Jun · PMID 42294865 · Publisher ↗
SUMMARYMarburg virus disease (MVD) is a highly fatal illness closely resembling Ebola disease, caused by either Marburg virus (MARV) or Ravn virus (RAVV). It typically begins with a sudden onset of high fever, headache,...
SUMMARYMarburg virus disease (MVD) is a highly fatal illness closely resembling Ebola disease, caused by either Marburg virus (MARV) or Ravn virus (RAVV). It typically begins with a sudden onset of high fever, headache, and malaise, followed by severe gastrointestinal symptoms, bleeding disorders, and, in the most severe cases, multi-organ failure. Case fatality rates vary widely, from 24% up to 90%. MARV and RAVV are zoonotic pathogens, with fruit bats recognized as the main reservoir. Human-to-human transmission generally occurs through direct exposure to infected bodily fluids. Historically, MVD outbreaks were primarily restricted to Central and Eastern Africa. In recent years, however, the disease has appeared in new regions: Ghana recorded its first cases in 2022, followed by concurrent outbreaks in Equatorial Guinea and Tanzania in 2023. Rwanda and Ethiopia experienced their debut outbreaks in 2024 and 2025, respectively, and another outbreak occurred in early 2025 in Tanzania. These incidents point to a troubling rise in annual MVD outbreaks and emphasize the ongoing risk of spillover from wildlife reservoirs and continued human-to-human transmission. Currently, there are no approved vaccines or antiviral treatments for MVD. Patient care focuses on supportive therapies, including aggressive fluid resuscitation, management of blood pressure and circulation, and intensive critical care. Nonetheless, promising countermeasures, such as monoclonal antibodies and antiviral drugs, are advancing through research and clinical trials. Experimental vaccines, particularly those based on viral-vector technologies, have demonstrated robust immune responses and are undergoing human testing. This review provides clinicians with the most recent knowledge of MVD, with a focus on epidemiological patterns, diagnostic procedures, clinical management, and the latest progress in developing medical countermeasures.
Gut microbiota-derived short-chain fatty acids (SCFAs): immunomodulatory effects and therapeutic potential in infections.
Yu J, Li W, Xu Y … +1 more , Tang J
Clin Microbiol Rev · 2026 Jun · PMID 42267834 · Publisher ↗
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 hos...
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., , spp.), fungi (i.e., ), and viruses (i.e., SARS-CoV-2, influenza virus, respiratory syncytial virus, rotavirus). In terms of antibacterial effects, SCFAs exhibit antibacterial activity against most gut microorganisms, but they support the colonization of a few species (i.e., ). Given the complex interactions between SCFAs and the gut microbiota, as well as their regulatory roles in infection, further investigation of the microbiota-SCFA axis is essential for developing effective strategies to prevent and treat infectious diseases. This review systematically summarizes the mechanism and clinical evidence of SCFAs in microbial infections to provide novel ideas for infectious disease management.
Bacteriophages in the treatment of cutaneous infections and skin disorders: therapeutic advances and future directions.
Hauza E, Mutai IJ, Necel A … +5 more , Kamya D, Śliwka P, Dusza I, Węgrzyn A, Skaradzińska A
Clin Microbiol Rev · 2026 Jun · PMID 42267833 · Publisher ↗
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 im...
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, viruses that specifically infect and lyse bacteria, have re-emerged as promising therapeutic agents due to their high specificity, activity against antibiotic-resistant strains, and capacity to target biofilm-associated infections. This review provides a comprehensive overview of current advances in bacteriophage-based approaches for the treatment of cutaneous infections and skin disorders. We discuss the biological principles of phage therapy, its advantages and limitations, and the regulatory and manufacturing challenges associated with clinical translation. Particular emphasis is placed on topical and biomaterial-based phage delivery platforms, including hydrogels, nanocarriers, and adhesive wound dressings, designed to enhance phage stability, local bioavailability, and therapeutic efficacy. Furthermore, we summarize experimental and clinical evidence supporting the use of bacteriophages against the most clinically relevant skin pathogens. By integrating data from studies, animal models, clinical trials, and compassionate-use cases, this review highlights both the therapeutic potential and current limitations of phage-based interventions in dermatology. Collectively, the available evidence supports the use of bacteriophages as a viable component of future precision antimicrobial therapies for skin infections, while emphasizing the need for well-designed clinical trials, standardized production protocols, and optimized delivery systems to enable broader clinical adoption.
Advances in medical and surgical management of keratitis: a comprehensive review.
Azzopardi M, Chong YJ, Smith EP … +8 more , Barahim EK, Jenyon T, Elsheikha HM, Carnt N, Lakshminarayanan R, Mehta JS, Rauz S, Ting DSJ
Clin Microbiol Rev · 2026 Jun · PMID 42262140 · Publisher ↗
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 o...
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 highly drug-resistant cysts in chronic infection further complicates treatment. Currently, prolonged combination therapy with topical biguanides and aromatic diamidines remains the mainstay of treatment. However, recent evidence supports the use of topical biguanide monotherapy (in higher concentrations) in AK with comparable outcomes to combination treatment. Adjunctive therapies, including azoles, miltefosine, and corticosteroids, may be beneficial in refractory disease. Surgical interventions, such as therapeutic keratoplasty, are often required in advanced or non-responsive cases. The choice of therapy is frequently empirical, guided by clinician experience and drug availability. Emerging therapeutic approaches, including antimicrobial peptides, synthetic polymers, bioactive natural compounds, and ultraviolet C therapy, show promise as more effective or better-tolerated alternatives. This review provides an up-to-date overview of current medical and surgical treatments, explores novel interventions in the pipeline, and highlights the need for evidence-based, individualized management strategies in AK.
Advancing One Health genomics in Africa: opportunities and challenges for outbreak and antimicrobial resistance control.
Derar DI, Hany F, Eltaher H … +5 more , Mahmoud S, Sedarous Y, Ruan Z, Alkhaldi M, Elhadidy M
Clin Microbiol Rev · 2026 Jun · PMID 42262139 · Publisher ↗
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, part...
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 identifying critical challenges in data integration, bioinformatics capacity, and sustainable financing. Special focus is placed on the lack of African-based genomic data, with our analysis showing that only 1.82% of the global total is available. Case studies illustrate the immense potential and importance of pathogen genomics, giving policymakers a tangible sense of its impact. These examples demonstrate how genomic technologies integrated with artificial intelligence (AI) are transforming outbreak response, AMR surveillance, and stewardship programs by enabling early detection of zoonotic threats, mapping transmission pathways, and guiding vaccine development. However, to fully realize this scientific intel, it is essential to embed One Health pathogen surveillance within strong policy and system frameworks to ensure the translation of technical progress into lasting institutional capacity and sustainable impact. Long-term implementation depends on coordinated investment and advocacy across four interdependent pillars: data architecture, governance and sovereignty, human capital, and technical capacity.
Ross River virus transmission, infection, and disease: two and a half decades of research progress-an updated cross-disciplinary review.
Skinner EB, Harley D, van den Hurk AF … +4 more , Michie A, Aubry M, Martin BM, Rawle DJ
Clin Microbiol Rev · 2026 Jun · PMID 42240370 · Publisher ↗
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, refl...
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 synthesizes two decades of cross-disciplinary investigations to present an integrated perspective on the biological, clinical, ecological, and environmental dimensions of RRV infection. By consolidating findings from diverse fields, the review enhances understanding of the complex factors influencing RRV transmission and disease outcomes throughout its endemic range.
Role of the penile microbiome in female sex partner risk of bacterial vaginosis and sexually transmitted infections: a narrative review.
Mehta SD
Clin Microbiol Rev · 2026 Jun · PMID 42233652 · Publisher ↗
SUMMARYThe penile microbiome (PMB) can be dominated by skin-associated bacteria (e.g., , , and ) or by anaerobic bacteria that are associated with bacterial vaginosis (BV), and is influenced by male circumcision status,...
SUMMARYThe penile microbiome (PMB) can be dominated by skin-associated bacteria (e.g., , , and ) 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 simultaneously evaluate the penile and vaginal microbiome in sex partners, specific taxa are highly correlated, with evidence for bi-directional transmissibility. BV-associated taxa in the PMB are associated with increased risk of BV and STIs in female sex partners. Emergent trials demonstrate that antimicrobial treatment in men can reduce penile anaerobic bacteria and female sex partner's risk of BV recurrence. However, data are lacking on factors influencing penile-vaginal bacterial exchangeability, the durability of bacterial exchange, and the conditions under which exchange may lead to increased risk of adverse outcomes in the index or partner. Optimal and non-optimal PMB have not been defined. Assessment of PMB composition and function across the life course is needed. Association of PMB with intrinsic host factors (genetics and endogenous hormones) is lacking; association with behavioral and lifestyle factors is limited. Addressing these gaps may lead to the development of assays to facilitate screening and monitoring after therapeutic interventions in men and female partners, or the development of therapeutics for optimizing PMB. Studies are needed to refine and develop new treatment and counseling guidelines for men and their sexual partners.
The black aspergilli ( complex) and their role in human, animal, and plant diseases.
Bongomin F, Punt M, de Jong A … +3 more , Verweij PE, van Rhijn N, Denning DW
Clin Microbiol Rev · 2026 Jun · PMID 42228082 · Publisher ↗
SUMMARYThe complex, also known as the black aspergilli or section , comprises a diverse group of filamentous fungi with wide-ranging ecological, industrial, and pathogenic significance. While traditionally associated wi...
SUMMARYThe complex, also known as the black aspergilli or section , 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 the complex. Advances in phylogenetics and whole-genome sequencing have clarified the taxonomy of section , now comprising six core species in series . Clinically, complex is implicated in various conditions, including otomycosis, keratitis, cutaneous infections, onychomycosis, chronic pulmonary aspergillosis, and, less commonly, invasive aspergillosis. In animals, black aspergilli have been isolated from respiratory, cutaneous, and systemic infections, particularly in immunocompromised or stressed hosts. Plant pathogenicity is significant, with complex contributing to pre- and post-harvest spoilage and producing mycotoxins such as ochratoxin A and oxalic acid. The common finding of elevated minimum inhibitory concentrations (MICs) to triazoles, particularly in both environmental and clinical isolates, raises concern, with underlying mechanisms differing from those characterized in . Reduced susceptibility is potentially driven by efflux pumps and environmental exposure to azole fungicides. Due to commonly higher MICs, antifungal therapy with itraconazole and isavuconazole may have reduced efficacy, and alternatives such as voriconazole or posaconazole should be considered, guided by susceptibility testing where available. This review emphasizes the need for a One Health approach to managing black aspergilli, integrating surveillance, diagnostics, and targeted interventions across human, veterinary, and agricultural sectors.
Dissemination of ESBL-producing and carriage in the community worldwide: epidemiology, transmission pathways, molecular insights, and practical aspects.
Beaumont A-L, Danjean M, Jacquier H … +5 more , Boyd A, Jaspard M, Royer G, Surgers L, Woerther P-L
Clin Microbiol Rev · 2026 May · PMID 42200659 · Publisher ↗
SUMMARYSince the worldwide dissemination of extended-spectrum β-lactamase-producing (ESBL-Ec) in the early 2000s, ESBL-Ec community carriage has followed divergent epidemiological patterns across regions. Currently, hig...
SUMMARYSince the worldwide dissemination of extended-spectrum β-lactamase-producing (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 prevalence by bridging together information from epidemiological, clinical, and bacterial genetic data. First, geographical differences in ESBL-Ec carriage in the community could be partly related to disparities in socioeconomic levels (e.g., country-level income, Human Development Index) and their associated conditions. Few risk factors associated with ESBL-Ec carriage overlap between LMICs and HICs, except for antibiotic use. Transmission across human, animal, and environmental sectors is much more common in LMICs, whereas inter-human transmission in HICs is more prominent. From the available molecular data, distinct bacterial genetic backgrounds between LMICs (predominantly A and B1 phylogroups) and HICs (predominantly B2 phylogroup) highlight the clones able to successfully disseminate in these settings. As the dissemination of ESBL-Ec is driven by a complex interplay of socioeconomic, behavioral, and bacterial genetic factors, tailored public health strategies, including antibiotic stewardship and innovative strategies discussed herein, are essential to curb further increases in their prevalence.
Revisiting the natural history of Jorge Lobo's disease: a mycological enigma spanning unresolved taxonomy, uncertain transmission, and inadequate therapy.
Teixeira MdM, Gonçalves FG, Vianna LA … +19 more , Tenório BG, Alves LGdB, Durlacher RR, Trindade MRdS, Bernardes JPRA, Jalkh AP, Frutuoso LL, Harada LO, Moreira Alves da Silva D, Mascarenhas Amaral Barroso A, Alves E, Johansen FDC, Tonini ML, Benard G, Soares Felipe MS, Rosa PS, Florian MC, Valle Martino MD, Nobrega de Almeida Júnior J
Clin Microbiol Rev · 2026 Jun · PMID 42132385 · Full text
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 underreco...
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 progressive keloid-like nodules and plaques on exposed areas. Diagnosis relies on direct microscopy and histopathology showing chains of thick-walled yeast-like cells connected by narrow-neck budding; culture is not feasible, and molecular assays are rarely available outside reference centers. We contrast JLD with key mimickers (cutaneous leishmaniasis, chromoblastomycosis, leprosy, atypical mycobacterioses, and non-infectious lesions such as keloid scars) and summarize current management options, emphasizing when surgery alone suffices and when prolonged azole therapy should be considered. From an ecoepidemiological perspective, historical settlement patterns, occupational exposures, and environmental disturbance in humid forest biomes appear to have amplified human contact with putative environmental reservoirs. New phylogenomic data position as an early-diverging lineage within , refining prior MLST-based inferences. We outline practical surveillance steps to address under-ascertainment, standardized case definitions, sentinel reporting, and laboratory quality assurance and propose research priorities spanning environmental detection, host-pathogen interactions, and therapeutic evaluation. We contextualize the disease within broader frameworks of fungal emergence, structural neglect, and environmental disruption, arguing that revisiting JLD is not merely retrospective but a necessary scientific and ethical priority.
Infection prevention and control in low- and middle-income countries: policy, practice, and implementation challenges in sub-Saharan Africa.
Okomo U, Fitzgerald F, Feasey N … +2 more , Mehtar S, Dramowski A
Clin Microbiol Rev · 2026 Jun · PMID 42132371 · Full text
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 (WA...
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 risks to healthcare workers during outbreaks. Gram-negative pathogens such as , , and predominate, alongside methicillin-resistant , with widespread resistance to third-generation cephalosporins and other key antibiotics linking HCAIs directly to the region's antimicrobial resistance crisis. National and regional IPC policy frameworks have expanded, but facility-level implementation lags, reflected in patchy surveillance, weak accountability, and unreliable supplies of alcohol-based hand rub (ABHR), personal protective equipment, environmental cleaning materials, and core WASH and ventilation infrastructure. Evidence from sub-Saharan Africa shows that pragmatic multimodal strategies, locally produced ABHR, infrastructure designed to facilitate hand hygiene, role-specific training for clinical and non-clinical staff, and inclusive approaches involving families can improve practices and outcomes when supplies and supervision are sustained. A whole-system approach is required, prioritizing fit-for-purpose surveillance, stronger WASH and waste management services, development of an IPC workforce, and support for African-led innovation, including local manufacturing and context-specific decision-support tools. Implementing these actions through community engagement, empowered leadership at all levels, and sustainable financing is critical to reducing HCAIs, slowing antimicrobial resistance, and strengthening healthcare quality and resilience in sub-Saharan Africa.
Implementation of pathogen genomics in clinical microbiology laboratories.
Gador-Whyte AP, Sherry NL, Brischetto A … +6 more , Andersson P, Bond KA, van Hal SJ, Harris PNA, Howden BP, Australian Pathogen Genomics Program partners
Clin Microbiol Rev · 2026 Jun · PMID 42041251 · Full text
SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pat...
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 health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.
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