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Background: Acinetobacter baumannii (Ab) disease in the United States is commonly attributed to outbreaks of 1 or 2 monophyletic carbapenem resistance (CR) Ab lineages that vary by region. However, there is limited knowledge regarding CRAb epidemiology and population structures in the U.S. Deep South, and few studies compare contemporary CR and carbapenem-susceptible (Cs) Ab, despite relative prevalence of the latter. Methods: We performed a multiyear analysis of 2462 Ab cases in a large healthcare system in Birmingham, AL, and 89 post-2021 Ab isolates were sequenced and phenotyped by antibiotic susceptibility tests. Results: Although the cumulative CR rate was 17.7% in our cohort, rates regularly increased in winter months as result of seasonal changes in case incidence of CsAb, specifically. Genotyped CRAb belonged to clonal group (CG) 1, CG2, CG108, CG250, or CG499, with local clones of CG108, CG250, and CG499 persisting over multiple months. There was no clonal expansion of any CsAb lineage. Among CRAb isolates, levels of ß-lactam antibiotic resistance and the repertoire of related genetic resistance determinants, which included the novel CR-conferring FtsI A515V polymorphism, differed according to CG. CG108 and CG499 isolates displayed specific heteroresistance to sulbactam and trimethoprim/sulfamethoxazole, respectively, which resulted in discrepant susceptibility results in microbroth versus agar-based antibiotic susceptibility tests modalities. Conclusions: We report an unusually high degree of CRAb phylogenetic diversity principally driven by emergent U.S. lineages harboring novel resistance elements that must be incorporated into diagnostic, surveillance, and preclinical research efforts.

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David Taylor-Robinson has been an inspiration to many investigators in the field of sexually transmitted infections (STIs) as, arguably, the father of modern mycoplasmology. Born in 1931, his career as a physician-scientist was initially in virology, researching chickenpox and the common cold, for both of which he made key discoveries at a time when little was known about these conditions. Soon, however, David's attention turned to bacteriology, developing a passionate interest in mycoplasmas and chlamydia. This gave rise to research collaborations all around the world in marginalized and regional communities, stretching from Tristan da Cunha and Antarctica to the South Pacific and sub-Saharan Africa. He was the discoverer of Mycoplasma genitalium, which today is a commonly diagnosed and increasingly antibiotic-resistant pathogen of the genitourinary tract and a significant cause of female infertility. His problem-solving mindset led to research on associations between mycoplasmas with rheumatological conditions and chlamydia with coronary artery plaque formation late into his working life. Throughout his distinguished career, David Taylor-Robinson, affectionately truncated to "DTR" to all who knew him professionally, has been a beloved mentor to hundreds of aspiring scientists, some of whom are now leaders in their field. His open-door policy meant that there was rarely a time when there was no visiting researcher from each of the six inhabited continents under his expert tutelage. A strong work ethic and drive for scientific excellence, allied to his unstinting kindness and jovial demeanor, has provided a source of inspiration to a wide diaspora of research colleagues over more than six decades. This is as much David's legacy to medical science as the undoubted public health impact of his own pioneering research on STIs.

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Intrapartum azithromycin prophylaxis has shown the potential to reduce maternal infections but showed no effect on neonatal sepsis and mortality. Antibiotic exposure early in life may affect gut microbiota development, leading to undesired consequences. Therefore, we here assessed the impact of 2 g oral intrapartum azithromycin on gut microbiota development from birth to the age of 3 years, by 16S-rRNA gene profiling of rectal samples from 127 healthy Gambian infants selected from a double-blind randomized placebo-controlled clinical trial (PregnAnZI-2). Microbiota trajectories showed, over the first month of life, a slower community transition and increase of Enterobacteriaceae (p = 0.001) and Enterococcaceae (p = 0.064) and a decrease of Bifidobacterium (p < 0.001) in the azithromycin compared to the placebo arm. Intrapartum azithromycin alters gut microbiota development and increases proinflammatory bacteria in the first month of life, which may have undesirable effects on the child.

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Compounds targeting host control of infectious diseases provide an attractive alternative to antimicrobials. A phenotypic screen of a kinase library identified compounds targeting glycogen synthase kinase 3 as potent inhibitors of Mycobacterium tuberculosis (Mtb) intracellular growth in the human THP-1 cell line and primary human monocytes-derived macrophages (hMDM). CRISPR knockouts and siRNA silencing showed that GSK3 isoforms are needed for the growth of Mtb and that a selected compound, P-4423632 targets GSK3ß. GSK3 inhibition was associated with macrophage apoptosis governed by the Mtb secreted protein tyrosine phosphatase A (PtpA). Phospho-proteome analysis of macrophages response to infection revealed a wide array of host signaling and apoptosis pathways controlled by GSK3 and targeted by P-4423632. P-4423632 was additionally found to be active against other intracellular pathogens. Our findings strengthen the notion that targeting host signaling to promote the infected cell's innate antimicrobial capacity is a feasible and attractive host-directed therapy approach.

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Timely adjustments of antibiotic and corticosteroid treatments are vital for patients with diffuse parenchymal lung diseases (DPLDs). In this study, 41 DPLD patients with negative metagenomic next-generation sequencing (mNGS) results who were responsive to corticosteroids were enrolled. Among these patients, about 26.8% suffered from drug-induced DPLD, while 9.8% presented autoimmune-related DPLD. Following the report of the negative mNGS results, in 34 patients with complete antibiotics administration profiles, 79.4% (27/34) patients discontinued antibiotics after receiving negative mNGS results. Moreover, 70.7% (29/41) patients began or increased the administration of corticosteroid upon receipt of negative mNGS results. In the microbiota analysis, Staphylococcus and Stenotrophomonas showed higher detection rates in patients with oxygenation index (OI) below 300, while Escherichia and Stenotrophomonas had higher abundance in patients with pleural effusion. In summary, our findings demonstrated the clinical significance of mNGS in assisting the antibiotic and corticosteroid treatment adjustments in corticosteroid-responsive DPLD. Lung microbiota may imply the severity of the disease.

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Systemic cryptococcosis is often fatal even with the current antifungal therapy and there is no vaccine available. Induction therapy with amphotericin B (AmB) is essential for its treatment, which can be either in the form of AmB deoxycholate at 1 mg/kg/day for 7 days or a single dose of liposomal AmB (AmB-LLs) at 10 mg/kg, both in combination with flucytosine. AmB is highly toxic and it is imperative to further increase its efficacy without increasing its toxicity. Previously, we developed a targeted antifungal drug delivery system (DectiSome) that uses liposomes decorated with host-pathogen receptor dectins to target AmB to fungal cells. Here, we showed that a single dose of Dectin-2 coated liposomal AmB, relative to AmB-LLs, reduced fungal burden and prolonged animal survival in the murine model of systemic cryptococcosis. Our results demonstrate that DectiSomes are a promising antifungal delivery system that could improve cryptococcosis therapy in the future.

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Medical microbiology laboratories play an essential role in patient care-appertaining to infectious diseases diagnostics and treatment, infection prevention, and antimicrobial stewardship. Collaboration between clinicians and the microbiology laboratory can promote and enhance the safety, quality, and efficiency of patient care. We review practical, evidence-informed core concepts to explicate how effective partnership between clinicians and the microbiology laboratory improves patient outcomes.

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We examined from a large exploratory study cohort of COVID-19 patients (N = 549) a validated panel of neutrophil extracellular traps (NETs) markers in different categories of disease severity. Neutrophil elastase (NE), myeloperoxidase (MPO), and circulating nuclear DNA (cir-nDNA) levels in plasma were seen to gradually and significantly (p < 0.0001) increase with the disease severity: mild (3.7, 48.9, and 15.8 ng/mL, respectively); moderate (9.8, 77.5, and 27.7 ng/mL, respectively); severe (11.7, 99.5, and 29.0 ng/mL, respectively); and critical (13.1, 110.2, and 46.0 ng/mL, respectively); and are also statistically different with healthy individuals (N = 140; p < 0.0001). All observations made in relation to the Delta variant-infected patients are in line with Omicron-infected patients. We unexpectedly observed significantly higher levels of NETs in asymptomatic individuals as compared to healthy subjects (p < 0.0001). Moreover, the balance of cir-nDNA and circulating mitochondrial DNA level was affected in COVID-19 infected patients attesting to mitochondrial dysfunction.

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Bacterial meningitis, frequently caused by Streptococcus pneumoniae (pneumococcus), represents a substantial global health threat leading to long-term neurological disorders. This study focused on the cholesterol-binding toxin pneumolysin (PLY) released by pneumococci, specifically examining clinical isolates from patients with meningitis and comparing them to the PLY-reference S. pneumoniae strain D39. Clinical isolates exhibit enhanced PLY release, likely due to a significantly higher expression of the autolysin LytA. Notably, the same single amino acid (aa) D380 substitution in the PLY D4 domain present in all clinical isolates significantly enhances cholesterol binding, pore-forming activity, and cytotoxicity toward SH-SY5Y-derived neuronal cells. Scanning electron microscopy of human neuronal cells and patch clamp electrophysiological recordings on mouse brain slices confirm the enhanced neurotoxicity of the PLY variant carrying the single aa substitution. This study highlights how a single aa modification enormously alters PLY cytotoxic potential, emphasizing the importance of PLY as a major cause of the neurological sequelae associated with pneumococcal meningitis.

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Malaria is a disease caused by infection with parasite Plasmodium spp. We studied the circadian regulation of host responses to the parasite, in a mouse model of cerebral malaria. The course of the disease was markedly affected by time of infection, with decreased parasitemia and increased inflammation upon infection in the middle of the night. At this time, there were fewer reticulocytes, which are target cells of the parasites. We next investigated the effects of desynchronization of host clocks on the infection: after 10 weeks of recurrent jet lags, mice showed decreased parasite growth and lack of parasite load rhythmicity, paralleled by a loss of glucose rhythm. Accordingly, disrupting host metabolic rhythms impacted parasite load rhythmicity. In summary, our findings of a circadian modulation of malaria parasite growth and infection shed light on aspects of the disease relevant to human malaria and could contribute to new therapeutic or prophylactic measures.

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Streptococcus suis is a zoonotic pathogen that can cause meningitis and septicaemia. The consumption of undercooked pig products is an important risk factor for zoonotic infections, suggesting an oral route of infection. In a human enteroid model, we show that the zoonotic CC1 genotype has a 40% higher translocation frequency than the non-zoonotic CC16 genotype. Translocation occurred without increasing the permeability or disrupting the adherens junctions and tight junctions of the epithelial monolayer. The translocation of zoonotic S. suis was correlated with the presence of Gb3-positive cells, a human glycolipid receptor found on Paneth cells and targeted by multiple enteric pathogens. The virulence factors Streptococcal adhesin Protein and suilysin, known to interact with Gb3, were not essential for translocation in our epithelial model. Thus, the ability to translocate across an enteroid monolayer correlates with S. suis core genome composition and the presence of Gb3-positive cells in the intestinal epithelium.

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Klebsiella pneumoniae (Kp) infection is an important healthcare concern. The ST258 classical (c)Kp strain is dominant in hospital-acquired infections in North America and Europe, while ST23 hypervirulent (hv)Kp prevails in community-acquired infections in Asia. This study aimed to develop symptomatic mucosal infection models in mice that mirror natural infections in humans to gain a deeper understanding of Kp mucosal pathogenesis. We showed that cKp replicates in the nasal cavity instead of the lungs, and this early infection event is crucial for the establishment of chronic colonization in the cecum and colon. In contrast, hvKp replicates directly in the lungs to lethal bacterial load, and early infection of esophagus supported downstream transient colonization in the ileum and cecum. Here, we have developed an in vivo model that illuminates how differences in Kp tropism are responsible for virulence and disease phenotype in cKp and hvKp, providing the basis for further mechanistic study.

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Tuberculosis (TB) afflicted 10.6 million people in 2021, and its global burden is increasing due to multidrug-resistant TB (MDR-TB) and extensively resistant TB (XDR-TB). Here, we analyze multi-domain information from 5,060 TB patients spanning 10 countries with high burden of MDR-TB from the NIAID TB Portals database to determine predictors of TB treatment outcome. Our analysis revealed significant associations between radiological, microbiological, therapeutic, and demographic data modalities. Our machine learning model, built with 203 features across modalities outperforms models built using each modality alone in predicting treatment outcomes, with an accuracy of 83% and area under the curve of 0.84. Notably, our analysis revealed that the drug regimens Bedaquiline-Clofazimine-Cycloserine-Levofloxacin-Linezolid and Bedaquiline-Clofazimine-Linezolid-Moxifloxacin were associated with treatment success and failure, respectively, for MDR non-XDR-TB. Drug combinations predicted to be synergistic by the INDIGO algorithm performed better than antagonistic combinations. Our prioritized set of features predictive of treatment outcomes can ultimately guide the personalized clinical management of TB.

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The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.

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Antimicrobial resistance (AMR) is an urgent and growing global health concern, and a clear understanding of existing capacities to address AMR, particularly in low-income and middle-income countries (LMICs), is needed to inform national priorities, investment targets and development activities. Across LMICs, there are limited data regarding existing mechanisms to address AMR, including national AMR policies, current infection prevention and antimicrobial prescribing practices, antimicrobial use in animals, and microbiological testing capacity for AMR. Despite the development of numerous individual tools designed to inform policy formulation and implementation or surveillance interventions to address AMR, there is an unmet need for easy-to-use instruments that together provide a detailed overview of AMR policy, practice and capacity. This paper describes the development of a framework comprising five assessment tools which provide a detailed assessment of country capacity to address AMR within both the human and animal health sectors. The framework is flexible to meet the needs of implementers, as tools can be used separately to assess the capacity of individual institutions or as a whole to align priority-setting and capacity-building with AMR National Action Plans (NAPs) or national policies. Development of the tools was conducted by a multidisciplinary team across three phases: (1) review of existing tools; (2) adaptation of existing tools; and (3) piloting, refinement and finalisation. The framework may be best used by projects which aim to build capacity and foster cross-sectoral collaborations towards the surveillance of AMR, and by LMICs wishing to conduct their own assessments to better understand capacity and capabilities to inform future investments or the implementation of NAPs for AMR.

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The pathogenesis of endometriosis is a complex process, and recent research has introduced novel hypotheses in this field. This review summarizes recent studies on the pathogenesis of endometriosis. We focused on several classical hypotheses, as well as their interactions with the microenvironment of hormonal dependence and immunosuppression. Furthermore, we highlighted the emergence of bacterial factors associated with endometriosis. Recent advances in next-generation sequencing (NGS) have revealed the presence and detailed distribution of these bacteria as well as the involvement of specific bacteria in pathogenesis. These factors alter the microenvironment in the early stages of endometriosis development, leading to lesion formation. Understanding the mechanisms underlying the early development of endometriosis from a new perspective would be helpful for the development of novel therapeutic agents for endometriosis.

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The recent developments in genomic sequencing have permitted the publication of many new complete genome sequences of Treponema pallidum pallidum, the bacterium responsible for syphilis, which has led to a new understanding of its phylogeny and diversity. However, few archived samples are available, because of the degradability of the bacterium and the difficulties in preservation. We present a complete genome obtained from a Formalin-Fixed Paraffin-Embedded (FFPE) organ sample from 1947, kept at the Strasbourg Faculty of Medicine. This is the preliminary, proof-of concept study of this collection/biobank of more than 1.5 million FFPE samples and the evaluation of the feasibility of genomic analyses. We demonstrate here that even degraded DNA from fragile bacteria can be recovered from 75-year-old FFPE samples and therefore propose that such collections as this one can function as sources of biological material for genetic studies of pathogens, cancer, or even the historical human population itself.

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The 2030 Global Task Force on Cholera Control Roadmap hinges on strengthening the implementation of multistranded cholera interventions, including community engagement and health system strengthening. However, a composite picture of specific facilitators and barriers for these interventions and any overlapping factors existing between the two, is lacking. Therefore, this study aims to address this shortcoming, focusing on cholera-reporting countries, which are disproportionately affected by cholera and may be cholera endemic. A scoping methodology was chosen to allow for iterative mapping, synthesis of the available research and to pinpoint research activity for global and local cholera policy-makers and shareholders. Using the Arksey and O'Malley framework for scoping reviews, we searched PubMed, Web of Science and CINAHL. Inclusion criteria included publication in English between 1990 and 2021 and cholera as the primary document focus in an epidemic or endemic setting. Data charting was completed through narrative descriptive and thematic analysis. Forty-four documents were included, with half relating to sub-Saharan African countries, 68% (30/44) to cholera endemic settings and 21% (9/44) to insecure settings. We identified four themes of facilitators and barriers to health systems strengthening: health system cooperation and agreement with external actors; maintaining functional capacity in the face of change; good governance, focused political will and sociopolitical influences on the cholera response and insecurity and targeted destruction. Community engagement had two themes: trust building in the health system and growing social cohesion. Insecurity and the community; cooperation and agreement; and sociopolitical influences on trust building were themes of factors acting at the interface between community engagement and health system. Given the decisive role of the community-health system interface for both sustained health system strengthening and community engagement, there is a need to advocate for conflict resolution, trust building and good governance for long-term cholera prevention and control in cholera reporting countries.

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Undergraduate students in the biomedical sciences are mostly unaware of how clinical microbiology laboratories handle suspected agents of bioterrorism or emerging infectious diseases. The Public Health Security Bioterrorism Preparedness and Response Act of 2002 requires the US Department of Health and Human Services (HHS) to maintain a list of microbes that pose serious biological threats to human health and safety, including Tier 1 agents with the potential for use in bioterrorism. The Laboratory Response Network (LRN), founded by the Centers for Disease Control and Prevention, the Federal Bureau of Investigation, and the Association of Public Health Laboratories, coordinates the response of sentinel, reference, and national laboratories to these biothreats. The sentinel laboratories, which comprise most hospital-based and commercial laboratories, are the first to encounter a suspicious agent. For this reason, the LRN has published a series of testing guidelines to assist the sentinel laboratories in deciding whether a microbial isolate should be considered potentially hazardous and thus sent to a reference or national laboratory for further characterization. Here, we describe a simple laboratory exercise that teaches sentinel-level testing requirements in the context of an applied setting of a potential outbreak of anthrax that would require a sentinel laboratory to recognize a potential threat, attempt to rule it out, and refer to a national laboratory for identification.

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Adherens junctions between tubular epithelial cells are disrupted in renal ischemia/reperfusion (I/R) injury. Syndecan-1 (SDC-1) is involved in maintaining cell morphology. We aimed to study the role of SDC-1 shedding induced by renal I/R in the destruction of intracellular adherens junctions. We found that SDC-1 shedding was increased while the expression of E-cadherin was decreased. This observation was accompanied by the activation of STAT3 in the kidneys. Inhibiting the shedding of SDC-1 induced by I/R could alleviate this effect. Mild renal I/R could induce more severe renal injury, lower E-cadherin expression, damaged cell junctions, and activated STAT3 in knockout mice with the tubule-specific deletion of SDC-1 mice. The results in vitro were consistent with those in vivo. Inhibiting the shedding of SDC-1 could alleviate the decreased expression of E-cadherin and damage of cell adherens junctions through inhibiting the activation of STAT3 during ischemic acute kidney injury.