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PubMed2022

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.

BACKGROUND: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. METHODS: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. RESULTS: A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. CONCLUSIONS: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. FUNDING: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. CLINICAL TRIAL NUMBER: NCT04405934.

Humans↗

PubMed2026

Understanding Candidozyma (Candida) auris: genomic evolution, antifungal resistance and the growing challenges in global infection control.

Candida auris (recently renamed Candidozyma auris) is an emerging multidrug-resistant fungal pathogen, first identified in Japan in 2009. C. auris exhibits remarkable persistence on human skin and inanimate surfaces, resistance to multiple antifungals, notably fluconazole, and biofilm formation, which hinders infection control and leads to hospital outbreaks with high mortality rates. Despite ongoing research, key aspects of its reservoir origin, transmission routes and the best way to combat its spread and multidrug resistance remain unclear. Improving genomic surveillance and antifungal strategies is crucial to contain its spread and mitigate the growing public health threat posed by this resilient and potentially fatal fungal pathogen.

Humans↗

PubMed2026

From Infection Control to Healthcare System Resilience: Lessons Learned from SARS-CoV-2 Research in Healthcare Workers.

The COVID-19 pandemic placed unprecedented pressure on healthcare systems and exposed healthcare workers (HCWs) to biological hazards, organizational pressures, and psychological strain. Evidence generated during the emergency shows that HCW protection cannot rely on isolated measures, but requires an integrated framework combining epidemiological surveillance, contact tracing, infection prevention and control, vaccination, occupational health, and workforce support. Contact tracing helped identify occupational exposures and clarify how duration, proximity, and inadequate use of personal protective equipment jointly shaped infection risk. Subsequent studies of reinfection showed that susceptibility reflected the interaction of viral circulation, individual immunity, and vaccination status. Vaccination reduced the clinical impact of SARS-CoV-2 and supported service continuity, although uptake depended on trust, communication, and management of adverse event concerns. The pandemic also highlighted substantial economic consequences and a high burden of psychological distress and burnout among HCWs. Building on this evidence, future preparedness should translate these lessons into permanent, adaptable infrastructure rather than temporary emergency arrangements, integrating interoperable, AI-assisted surveillance capable of combining occupational, diagnostic, vaccination, and genomic data to detect emerging risks early, while ensuring robust data governance and human oversight. Equally central is the need to address long-term workforce vulnerabilities, including Long COVID, attrition, and burnout, through early identification, rehabilitation, flexible return-to-work models, and sustained psychosocial support. Achieving this requires structured multidisciplinary collaboration among occupational medicine, infection control, epidemiology, mental health, and digital health specialists, moving from fragmented infection-control protocols to an integrated, proactive, and learning-oriented preparedness strategy. Protecting HCWs is therefore not only an occupational safety priority but a foundational prerequisite for safe, equitable, and sustainable healthcare delivery during future infectious threats.

Humans↗

PubMed2026

Identification of circulating parasite and host biomarkers in the serum proteome of Trypanosoma vivax-infected sheep under immunosuppression.

Bovine trypanosomiasis, caused by Trypanosoma vivax, presents a major threat to livestock health, primarily due to the lack of efficient field diagnostic tools. This study aimed to identify potential parasite and host-derived biomarkers through a longitudinal proteomic analysis of serum from sheep experimentally infected with a T. vivax isolate. Utilizing LC-MS/MS and bioinformatics, 154 proteins were identified, comprising 150 host (Ovis aries) and four pathogen proteins. Principal Component Analysis (PCA) demonstrated a clear separation of samples according to infection stages: Control, Infection (15 parasites/field), and Peak Infection (30-60 parasites/field) Among the parasite proteins, TvY486_0014340, TvY486_0040500, and TvY486_0042480 were identified as candidate antigens for future evaluation. In silico analysis revealed these proteins contain multiple B-cell epitopes with no cross-reactivity to related Trypanosoma species, supporting their potential for immunodiagnostic development. Additionally, three host proteins-folate receptor 3 (FOLR3) and complement components C1QA and C1QC-were significantly modulated across all infection phases. The upregulation of FOLR3 likely reflects a compensatory response to parasite-induced anemia, while the downregulation of C1Q components suggests immune evasion strategies. These findings highlight specific parasite antigens and host regulatory patterns that may serve as candidate biomarkers for the diagnosis and monitoring of T. vivax infection, facilitating the development of improved point-of-care assays.

Animals↗

PubMed2025

Controlled human infection model of Neisseria lactamica in late pregnancy investigating mother-to-infant transmission in the UK: a single-arm pilot trial.

BACKGROUND: The infant respiratory microbiome is derived largely from the mother and is associated with downstream health and disease. Manipulating maternal respiratory flora peripartum to influence the infant microbiome has not previously been investigated. Neisseria lactamica is a harmless pharyngeal commensal that correlates inversely with Neisseria meningitidis carriage and disease. Intranasal N lactamica inoculation is a safe and well characterised controlled human infection model (CHIM) in non-pregnant healthy adults. We hypothesised that N lactamica inoculation in pregnancy induces mother-to-infant N lactamica transmission postnatally. METHODS: In this single-arm trial, 21 healthy pregnant female participants aged 18 years or older were inoculated at 36-38 weeks' gestation with 105 colony-forming units of N lactamica Y92-1009 at University Hospital Southampton Clinical Research Facility, Southampton, UK. N lactamica selective culture, genome sequencing, and serological testing were performed on maternal and infant oral, nasopharyngeal, breastmilk, and serum samples over 15 weeks postpartum. Seven female participants naturally colonised with N lactamica at baseline were followed up, but not inoculated. Oral samples were obtained from 12 cohabiting siblings younger than 5 years. The primary endpoint was infant N lactamica colonisation. This study was registered with ClinicalTrials.gov, NCT04784845, and is now complete. FINDINGS: Between Oct 25, 2021, and March 7, 2022, 31 adult female participants (median age 33·5 years [range 23·1-39·9]; 26 [84%] were White, British) were screened and enrolled, of whom seven were already colonised with N lactamica. After exclusion of three participants, 21 participants were inoculated, of whom 15 (71%) became N lactamica-colonised, and no sustained N lactamica Y92-1009 transmission to their infants was observed. Conversely, non-Y92-1009 N lactamica strain sharing was observed in four (57%) of seven uninoculated mother-sibling pairs, and Moraxella catarrhalis strain sharing in nine (38%) of 24 mother-infant pairs completing the study. Anti-N lactamica serum IgG titres increased in seven (88%) of eight N lactamica Y92-1009-colonised female participants, but none of their infants (where paired sera were available). There were no serious adverse reactions to the inoculum. INTERPRETATION: As the world's first perinatal CHIM, this trial demonstrates that this model in pregnancy is feasible, and that N lactamica Y92-1009 can safely and efficiently colonise pregnant individuals. Lack of sustained mother-to-infant N lactamica transmission, despite evidence supporting mother-to-infant M catarrhalis and sibling-to-mother N lactamica transmission, challenges conventional perceptions of infants as passive recipients of maternal microbes, suggesting that respiratory commensal transmission is selective and microbe-specific. FUNDING: Medical Research Council and National Institute for Health Research Southampton Biomedical Research Centre.

Adult↗

PubMed2026

Whole cell inactivated poly-bacterial preparation MV130 effect on nasal mucosal immunity and experimental human pneumococcal carriage: double-blind randomised controlled trial with controlled human infection model.

BACKGROUND: Bacterial mucosal immunotherapy has shown protection of children and adults from both viral and bacterial respiratory infections, offering the potential to reduce antimicrobial use, and hence also control antimicrobial resistance (AMR). Pneumococcal carriage of vaccine type Streptococcus pneumoniae remains high in Malawi despite infant conjugate vaccination and AMR is increasing. We compared nasal inflammation following sublingual bacterial immunotherapy including S. pneumoniae (MV130, Inmunotek, Spain) or placebo and determined the effect in an experimental human pneumococcal carriage model. METHODS: A double-blind, randomised, placebo-controlled trial in healthy adult volunteers was conducted at Queen Elizabeth Central Hospital in Blantyre, Malawi. Participants were randomly allocated to receive MV130 or placebo sublingually once daily for 42 days. Mucosal inflammation (neutrophil to T cell ratio, NTR) was measured in nasal micro-biopsies. Post-treatment, participants were challenged with 160,000 CFU/naris S. pneumoniae 6B (Spn6b). Experimental pneumococcal carriage rates post inoculation were compared between the two arms. All participants completing the study were included in the analysis. Prospective trial registration: PACTR202403820001276. FINDINGS: 107 participants were enrolled and randomised to MV130/placebo between May and December 2024. There were no serious adverse events, complete compliance was good (72%) and all adverse events were mild. 96 participants (53 male, 43 female) completed the study with 52 participants randomised to MV130 and 44 to placebo. There was no difference in mucosal inflammation (neutrophil to T cell ratio) at day 14 of the intervention MV130 NTR median = 0.737 (IQR 0.294, 2.059) and placebo NTR = 0.831 (IQR 0.450, 2.073), p = 0.64. Secondary analyses showed a rise in mucosal neutrophils after MV130 treatment and after experimental pneumococcal inoculation. There was no difference in nasal or serum anti-pneumococcal immunoglobulin or in experimental pneumococcal carriage proportion between MV130 (12/52, 23%) and placebo (10/44, 23%) groups (unadjusted risk ratio 1.02 (CI 0.49-2.12) p = 1.0). INTERPRETATION: MV130 induced non-specific mild neutrophil inflammation of the nasal mucosa but had no protective effect against experimental human pneumococcal carriage. FUNDING: Wellcome Trust.

Humans↗

PubMed2025

Genomic detection of Panton-Valentine Leucocidins encoding genes, virulence factors and distribution of antiseptic resistance determinants among Methicillin-resistant S. aureus isolates from patients attending regional referral hospitals in Tanzania.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable public scourge causing worldwide mild to severe life-threatening infections. The ability of this strain to swiftly spread, evolve, and acquire resistance genes and virulence factors such as pvl genes has further rendered this strain difficult to treat. Of concern, is a recently recognized ability to resist antiseptic/disinfectant agents used as an essential part of treatment and infection control practices. This study aimed at detecting the presence of pvl genes and determining the distribution of antiseptic resistance genes in Methicillin-resistant Staphylococcus aureus isolates through whole genome sequencing technology. MATERIALS AND METHODS: A descriptive cross-sectional study was conducted across six regional referral hospitals-Dodoma, Songea, Kitete-Kigoma, Morogoro, and Tabora on the mainland, and Mnazi Mmoja from Zanzibar islands counterparts using the archived isolates of Staphylococcus aureus bacteria. The isolates were collected from Inpatients and Outpatients who attended these hospitals from January 2020 to Dec 2021. Bacterial analysis was carried out using classical microbiological techniques and whole genome sequencing (WGS) using the Illumina Nextseq 550 sequencer platform. Several bioinformatic tools were used, KmerFinder 3.2 was used for species identification, MLST 2.0 tool was used for Multilocus Sequence Typing and SCCmecFinder 1.2 was used for SCCmec typing. Virulence genes were detected using virulenceFinder 2.0, while resistance genes were detected by ResFinder 4.1, and phylogenetic relatedness was determined by CSI Phylogeny 1.4 tools. RESULTS: Out of the 80 MRSA isolates analyzed, 11 (14%) were found to harbor LukS-PV and LukF-PV, pvl-encoding genes in their genome; therefore pvl-positive MRSA. The majority (82%) of the MRSA isolates bearing pvl genes were also found to exhibit the antiseptic/disinfectant genes in their genome. Moreover, all (80) sequenced MRSA isolates were found to harbor SCCmec type IV subtype 2B&5. The isolates exhibited 4 different sequence types, ST8, ST88, ST789 and ST121. Notably, the predominant sequence type among the isolates was ST8 72 (90%). CONCLUSION: The notably high rate of antiseptic resistance particularly in the Methicillin-resistant S. aureus strains poses a significant challenge to infection control measures. The fact that some of these virulent strains harbor the LukS-PV and LukF-PV, the pvl encoding genes, highlight the importance of developing effective interventions to combat the spreading of these pathogenic bacterial strains. Certainly, strengthening antimicrobial resistance surveillance and stewardship will ultimately reduce the selection pressure, improve the patient's treatment outcome and public health in Tanzania.

Methicillin-Resistant Staphylococcus aureus↗

PubMed2026

FTIR typing of the emerging NDM-14-producing Klebsiella pneumoniae ST147 clone.

UNLABELLED: The emergence and rapid dissemination of NDM-14-producing Klebsiella pneumoniae ST147 represents a major challenge for infection control, requiring timely and reliable outbreak detection tools. In this study, we evaluated Fourier-transform infrared (FTIR) spectroscopy as a rapid typing method for outbreak investigation and compared its performance with whole-genome sequencing (WGS). A collection of 64 carbapenemase-producing K. pneumoniae isolates, including 30 NDM-14-producing ST147 isolates associated with a regional outbreak in the Canary Islands, was analyzed using FTIR spectroscopy and WGS. FTIR-based clustering was optimized using the polysaccharide spectral region and a customized distance cutoff. Genomic relatedness was assessed using multilocus sequence typing, core-genome single-nucleotide polymorphism (SNP) analysis at multiple thresholds, and clustering agreement indices. FTIR identified a dominant spectral cluster comprising 31 isolates, capturing all outbreak-related isolates with 100% sensitivity and 97% specificity. FTIR clustering showed concordance with genomic outbreak definitions at stringent SNP thresholds (10-18 SNPs), with accuracy exceeding 98%. Pairwise distance analysis revealed low FTIR dissimilarity among closely related isolates, whereas increased dispersion occurred at intermediate genomic distances (15-30 SNPs). Agreement indices showed improved concordance as genomic stringency increased, with the Modified Adjusted Rand Index values reaching 94.75 at the 10-SNP threshold. Importantly, FTIR identified an NDM-14-producing isolate from a distinct clonal background. Overall, FTIR spectroscopy provides a rapid and reliable first-line screening tool for identifying homogeneous outbreak clusters. However, due to lineage-dependent behavior and limited resolution at intermediate genomic distances, WGS remains essential for confirmatory analysis and precise delineation of transmission events. IMPORTANCE: The rapid spread of multidrug-resistant Klebsiella pneumoniae poses a major challenge for infection control, particularly during hospital outbreaks where timely identification of transmission is essential. In this study, we evaluate Fourier-transform infrared (FTIR) spectroscopy as a rapid typing approach and compare its performance with whole-genome sequencing in the context of an outbreak caused by NDM-14-producing K. pneumoniae ST147. Our results show that FTIR can reliably identify highly related isolates within a clonal outbreak, supporting early outbreak recognition. However, its performance is influenced by the underlying genomic structure of the population and may require dataset-specific optimization. These findings highlight the potential of FTIR as a first-line screening tool while emphasizing the need for cautious interpretation and integration with genomic methods for accurate outbreak delineation.

Klebsiella pneumoniae↗

PubMed2025

Novel, rapid, and reliable typing of vancomycin-resistant Enterococcus faecium CC17/ST80 strains using MALDI-TOF MS.

Vancomycin-resistant Enterococcus faecium (VREfm) is an important nosocomial pathogen. The recent emergence of the highly virulent clonal complex 17 (CC17) is posing a challenge for both therapeutic interventions and hospital infection control measures. Hence, prompt discrimination of CC17 VREfm from unrelated and less-virulent VREfm strains is essential for preventing its spread in hospitals and beyond. Between January 2022 and November 2024, 340 VREfm primary isolates have been identified in our lab and underwent genotyping by pulsed-field gel electrophoresis (PFGE) to survey a potential outbreak in the Tyrol region. In addition, whole-genome sequencing (WGS) was performed on a selected subset (n = 40). To curtail the lengthy time-to-result (TTR) of these methods, a novel typing protocol using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was established, validated, and optimized for rapid sample processing. PFGE and WGS showed that 61.2% of isolates (n = 208) belonged to a specific VREfm cluster identified as CC17 sequence type (ST) 80 vanA VREfm. A comprehensive MALDI-TOF MS analysis identified a distinct peak pattern specific to this lineage. This phenotypic characterization was used as a novel typing method with excellent performance (sensitivity: 1.00 [0.98-1.00], specificity: 0.89 [0.70-0.97]) and demonstrated a short TTR of 1 day after the cultural growth of VREfm. A rapid and novel MALDI-TOF MS-based typing approach for a specific CC17/ST80 vanA VREfm cluster was developed and enabled real-life application in routine diagnostics to assure accurate infection prevention and control measures. Future outbreak investigations may benefit from adopting this cost- and labor-efficient approach.IMPORTANCEThis study addresses the urgent need for faster ways to detect problematic hospital bacteria. A highly transmissible strain of Enterococcus faecium (CC17) has been spreading in healthcare settings, making infections harder to treat and control. Traditional methods to identify and track outbreaks are accurate but slow and resource-intensive, delaying critical infection control actions. By developing and validating a new method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, the researchers demonstrated that this strain can be identified quickly, reliably, and at lower cost. Importantly, the new approach delivers results within a day, compared to the lengthy turnaround times of existing methods. This rapid detection tool provides hospitals with a practical solution to respond to outbreaks more effectively, prevent further spread, and protect vulnerable patients. The findings highlight a valuable step forward in strengthening hospital infection control and improving patient safety.

Enterococcus faecium↗

PubMed2025

Mpox: current knowledge and understanding-a scoping review.

Mpox in humans is a rash illness resulting from infection with monkeypox virus (MPXV). In 2022, a public health emergency of international concern (PHEIC) was declared with 115 countries reporting cases of Mpox. Most of these countries had not previously reported cases. This global outbreak was sustained primarily by human-to-human transmission within complex sexual networks. Whilst these cases were similar to previous clade II West African MPXV isolates, they were sufficiently genomically distinct to result in WHO recognizing two subclades within clade II: clade IIa and clade IIb. In 2024, a second PHEIC was declared, resulting from a marked increase in cases of clade I MPXV. In this scoping review, we compare the major clinical, epidemiological, and genomic features of the major mpox lineages and the implications for vaccination, transmission, infection control and treatment..

Humans↗

PubMed2026

Transcriptomic analysis provides molecular insights into the innate immune defense of Mactra veneriformis against Vibrio alginolyticus infection.

Mactra veneriformis is an economically important bivalve mollusc in China, but its aquaculture is frequently threatened by Vibrio infections, particularly Vibrio alginolyticus. To investigate the molecular immune response of M. veneriformis to V. alginolyticus, we performed RNA-seq analysis of hepatopancreatic tissues collected at 48 h post-infection, the peak mortality time point, with PBS-injected individuals used as controls. Infection with V. alginolyticus caused severe histopathological damage in the hepatopancreas and resulted in a cumulative mortality of 53.3% over 14 d, compared with 3.3% in the control group. Transcriptomic analysis identified 2623 differentially expressed genes (DEGs), including 1585 significantly up-regulated genes and 1038 down-regulated genes. KEGG enrichment analysis demonstrated that DEGs were significantly enriched in immune related and metabolism pathways, including the JAK-STAT signaling pathway, RIG-I-like receptor (RLR) signaling pathway, and cytochrome P450 (CYP450) signaling pathway. Collectively, these findings revealed candidate immune related genes (tlr3, tlr5, myd88, nfkb1, il-17d, and ifi44l), a putative TLR-MyD88-NF-κB signaling axis, and KEGG signaling pathways, including JAK-STAT, RLR and CYP450, that may be involved in the innate immune response of M. veneriformis to V. alginolyticus infection. These results provide a transcriptomic basis for understanding host-pathogen interactions in this species and highlight candidate genes and pathways for future functional validation and potential application in disease-resistance breeding.

Animals↗

PubMed2026

Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.

Understanding the geographic spread of emerging respiratory viruses is critical for pandemic preparedness, yet the early spatiotemporal dynamics of the 2009 H1N1 pandemic influenza and severe acute respiratory syndrome coronavirus 2 in the United States remain unclear. While mobility and genomic data have revealed important aspects of pandemic spatial spread, several key questions remain: Did the two pandemics follow similar spatial transmission routes? How rapidly did they spread across the United States? What role did stochastic processes play in early spatial transmission? To address these questions, we integrated high-resolution disease data with a robust, data-efficient inference framework combining air travel, commuting flows, and pathogen superspreading potentials to reconstruct their spatial spread across US metropolitan areas. The two pandemics exhibited distinct transmission pathways across locations; however, both pandemics established local circulation in most metropolitan areas within weeks, driven by several shared transmission hubs. Early spatial spread was more strongly associated with air travel than with commuting, though stochastic dynamics introduced substantial uncertainty in transmission routes, creating challenges for timely detection and control. Simulations indicate that broad wastewater surveillance coverage beyond top transmission hubs coupled with effective infection control may slow initial spatial expansion. Our findings highlight the rapid, stochastic spread of pandemic respiratory pathogens and the difficulties of early outbreak containment.

Humans↗

PubMed2026

Emergence of Acinetobacter soli harboring three carbapenemase-encoding genes (blaNDM-1, blaIMP-14, and blaOXA-58) on a single plasmid in an ICU patient.

Acinetobacter soli is an environmentally adaptable species increasingly recognized as an emerging pathogen in hospital settings, particularly in intensive care units (ICUs). In this study, we report the first A. soli isolate from an ICU patient that co-harbors three carbapenemase-encoding genes (blaNDM-1, blaIMP-14, and blaOXA-58) on a single plasmid. Whole-genome sequencing revealed that multidrug resistance in this strain is mediated by a 294,790 bp plasmid, pSLAB-A, carrying 16 antimicrobial resistance genes, including all three carbapenemases. Comparative plasmid analysis showed a highly conserved backbone but identified a unique ~40 kb multidrug-resistance region containing blaNDM-1, blaIMP-14, and eight additional resistance genes. Genetic context analysis indicated that insertion sequences (ISAba125 and ISAba3) and class 1 integrons contribute to the mobilization and accumulation of carbapenemase-encoding genes. Plasmid stability assays demonstrated that pSLAB-A remained stably maintained for more than 90 generations without antibiotic selection. A global survey of the NCBI database identified 15 A. soli strains carrying carbapenemase-encoding genes, most of which were isolated from China, with clinical specimens representing the predominant source. Seven carbapenemase-encoding genes were detected, with blaNDM-1 being the most prevalent. Among eight isolates with complete genomes, all carried carbapenemase-encoding genes on plasmids. Phylogenetic analysis revealed regional dissemination of a clonal lineage across hospitals in Zhejiang Province and sustained nosocomial transmission within a hospital in Taiwan. These findings suggest that the spread of carbapenem resistance in A. soli is largely driven by multidrug-resistance plasmids, facilitating clonal expansion in hospital environments and posing a growing challenge for antimicrobial therapy and infection control in ICUs.IMPORTANCECarbapenem-resistant A. soli is an emerging clinical concern, capable of causing severe invasive infections, including bacteremia, in intensive care unit settings, and its emergence poses substantial challenges to antimicrobial therapy. In this study, we demonstrate that carbapenem resistance in A. soli is predominantly mediated by the acquisition of multidrug-resistance plasmids carrying carbapenemase-encoding genes. Owing to its strong environmental persistence, A. soli can readily undergo nosocomial clonal dissemination once carbapenem resistance is acquired. Moreover, the spread of multidrug plasmids co-harboring multiple carbapenemase-encoding genes may accelerate the evolutionary trajectory of resistance in A. soli, further exacerbating the threat to clinical management. Given its demonstrated capacity to cause hospital-associated infections and to rapidly acquire multidrug resistance, A. soli warrants heightened vigilance from both clinical and public health perspectives.

beta-Lactamases↗

PubMed2026

How AI-supported intelligent systems support infection prevention and control training in healthcare: A systematic review of educational functions and outcomes.

AIMS: Artificial intelligence (AI)-supported intelligent systems have been increasingly incorporated into infection prevention and control (IPC) education and training, primarily to support the monitoring of observable behaviors and the provision of feedback. However, existing evidence has focused largely on short-term compliance outcomes, with limited synthesis of the educational role of AI-supported intelligent systems in supporting sustained IPC competence. This systematic review examined how AI-supported intelligent systems have been designed and used to support IPC education and training, with a focus on system characteristics, educational functions, and reported outcomes. DESIGN: A systematic literature search was conducted across the PubMed/MEDLINE, Embase, Cochrane, and CINAHL databases. DATA SOURCES: A total of 18 studies met the inclusion criteria. Findings were qualitatively synthesized according to system design characteristics, educational functions, and outcome domains. REVIEW METHODS: Methodological quality was appraised using the Mixed Methods Appraisal Tool. RESULTS: Most AI-supported intelligent systems focused on hand hygiene and relied on fully automated monitoring systems to capture behaviors and provide performance feedback. Educational functions were predominantly limited to performance assessment, automated feedback, and reminders. Outcomes were mainly measured using compliance or performance metrics, whereas sustained behavioral change and decision quality were rarely assessed. CONCLUSIONS: AI-supported intelligent systems have been used primarily to reinforce short-term IPC performance and compliance. However, their current applications for supporting sustained competence over time remain limited. The findings of this review suggest that AI-supported intelligent systems may serve as maintenance-oriented educational support by extending learning beyond initial instruction through repeated practice and feedback. Future research should prioritize outcome measures that capture the durability of performance and decision-making processes to better align AI-supported intelligent systems used in IPC education and training with the educational demands of clinical practice.

Humans↗

PubMed2026

Early use of genomics to guide acquisition investigation of Salmonella Typhi.

BACKGROUND: As most Salmonella Typhi (S. Typhi) cases notified to public health units in Australia are acquired overseas, a case without recent travel raises concerns of local transmission. We describe a case of S. Typhi in a hospital inpatient without recent travel, where early use of genomic sequencing suggested remote acquisition from Chile in the 1980s, with chronic asymptomatic carriage. This facilitated the stand-down of a complex acquisition investigation. CASE: A notification of S. Typhi on stool culture was received for a female aged over 90 years living in Melbourne, Australia in October 2023. She had been hospitalised for three weeks (unrelated illness) and transferred into a residential aged care facility (RACF) six days prior to the result being known. She was asymptomatic and the sample was collected due to a recent ward gastroenteritis outbreak. INVESTIGATION: Epidemiological investigation identified the case had emigrated to Australia in 1981 from Chile. Recent typhoid-like illness, overseas travel or contact with travellers from endemic areas were excluded. Subsequent genomic sequencing identified the isolate was multilocus sequence type 2 and did not cluster with any strains isolated in Victorian or international databases, most closely clustering with historical South American strains, with potential in-host changes over time. MANAGEMENT: The case was presumed infectious throughout their hospital stay, with chronic carriage. There were 18 contacts, of whom 14 provided screening samples and were negative. Antibiotic case clearance was not recommended by the treating clinician due to patient comorbidity, treatment toxicity risks and unlikely treatment success without gallbladder removal. Enhanced infection control measures were instituted in the RACF (e.g. private bathroom, contact precautions for personal care, no food preparation). No additional cases were reported after two incubation periods (60 days). CONCLUSION: Early genomic sequencing enhanced the efficiency of the public health investigation by rapidly confirming overseas acquisition and chronic carriage, obviating the need for extensive local upstream investigation.

Humans↗

PubMed2026

Proteomic insights into Helicobacter pylori infection in stomach cells, revealing host response and host-targeted therapeutics repurposing.

BACKGROUND: Helicobacter pylori (H. pylori) is a globally prevalent gastric pathogen strongly associated with chronic gastritis, peptic ulcers, and gastric cancer. While bacterial factors have been extensively studied, host proteomic responses and their therapeutic potential remain largely underexplored. RESEARCH DESIGN AND METHODS: Current analyses employed a systematic proteomics-based data integration and harmonization approach (retrospective qualitative cohort study) to identify important differentially regulated host proteins. Proteomic datasets were curated from in vitro studies and analyzed for functional enrichment, protein-protein interaction networks, and hub protein identification. To explore therapeutic repurposing, drug repositioning was performed using the DrugBank database. RESULTS: Data summation describing protein differential regulation in human gastric cells as a result of the infection revealed 1672 perturbed host proteins. Bioinformatics analysis revealed 11 proteins including CSK, MET, RELA, MARK2, GRB2, FTO, PLCG1, CRKL, RPS5, RPS9, and RPS27A to be ideal host targets for therapeutic repurposing. Clinically approved drugs such as Dasatinib (targeting CSK) and Crizotinib (targeting MET) emerged as promising candidates due to favorable pharmacokinetics and known bioactivity. CONCLUSIONS: Host-directed therapeutics could offer alternative strategies to conventional antibiotic therapy, addressing challenges such as resistance and infection recurrence, providing a foundation for future experimental validation and development of host-targeted interventions for infection control.

Humans↗

PubMed2026

In vivo porcine multi-omics integration identifies microbiome-driven histamine elevation and lasting gut perturbations following Ascaris suum infection and fenbendazole treatment.

Ascaris roundworms impair human and swine health. While treatments using anthelmintic drugs are generally effective in eliminating worms, their effects on the gut microenvironment remain poorly understood. Here we applied integrated multi-omics to characterize infection- and treatment-associated alterations in the pig-Ascaris system. In vitro anaerobic cultures were conducted as supportive validation of selected observations. Ascaris suum infection altered microbial composition and dysregulated 182 serum and fecal metabolites, including histamine and p-cresol sulfate. Compared with time-matched uninfected controls, infected pigs treated with fenbendazole showed marked differences in gut microbial composition 13 days after confirmed worm clearance. Eleven microbial pathways were enriched in successfully treated pigs, including peptidoglycan biosynthesis and histidine metabolism, indicating that infection-associated alterations may persist after treatment. In vitro co-exposure of Lactobacillus reuteri to fenbendazole and A. suum proteins increased histamine production by approximately 79% at 48 h (p < 0.05), serving as supportive evidence of a microbiome contribution. Collectively, our in vivo findings support that host-microbiota-parasite interactions are multifaceted. Microbiota-derived metabolites were associated with regulation of host gene expression, such as TFF2 and IL8. Microbiota plasticity allows the exploitation of the niche differentiated upon infection, resulting in the proliferation of certain Lactobacillus strains in treated animals. Nevertheless, interpretations of treatment effects are made cautiously given the absence of an uninfected drug-only group and the cross-sectional design. Understanding these complex interactions will be important for the design of next-generation functional anthelmintics.

Animals↗

PubMed2026

Achromobacter species in cystic fibrosis and chronic lung disease: a review of virulence, antibiotic resistance, diagnostic challenges, and emerging therapies.

Achromobacter species (spp) is an emerging opportunistic organism more frequently isolated from immunocompromised patients' and hospital settings. This bacterium was once considered an environmental bacterium, but now it is recognized as a serious cause of respiratory infections, bloodstream infections, and urinary tract infections, particularly among patients with cystic fibrosis (CF), chronic illnesses, and medical devices. The purpose of this review is to highlight Achromobacte's clinical significance, pathogenic mechanism, and recent approaches for diagnosis and treatment. By utilizing specific keywords relevant to Achromobacter spp., a comprehensive literature search was performed in PubMed and Google Scholar. To summarize existing knowledge and highlight gaps in the literature, peer-reviewed studies on clinical relevance, pathogenicity, antimicrobial resistance, and therapeutic approaches were gathered, screened, and narratively assembled. Among the 19 identified species, Achromobacter xylosoxidans (A. xylosoxidans) is the most prevalent and clinically relevant, especially in CF settings. This review explores the organism's microbiological characteristics, virulence strategies-including robust biofilm formation, motility, and secretion systems-and its alarming intrinsic and acquired resistance to antibiotics. Misidentification due to phenotypic overlap with other non-fermenting Gram-negative bacilli complicates diagnosis, while limited MALDI-TOF MS and database representation hinders species-level identification. Genotyping methods, including multi-locus sequence analysis and housekeeping gene sequencing, offer superior resolution but remain underutilized in clinical diagnostics. With rising resistance mediated by β-lactamases, efflux pumps, and adaptive genomic traits, Achromobacter spp presents a growing challenge for treatment and infection control. This review highlights the urgent need for improved diagnostic strategies, species-level clinical and microbiological data, and tailored therapeutic approaches to manage Achromobacter spp. infections effectively.

Humans↗