npj antimicrobials and resistance最新文献

The refractoriness of persistent infections to antibiotics necessitates lengthy treatment regimens to prevent therapeutic failures and relapses. Persistence has been attributed to entry of a small fraction of bacterial cells into a slowly growing or non-growing physiological state, which is thought to protect them against antibiotics targeting growth-related processes. However, these conclusions are largely based on studies conducted with lab-adapted strains carrying mutations that confer abnormally high levels of persistence. Here, we perform single-cell studies of ampicillin-mediated killing and persistence in a clinical isolate of uropathogenic Escherichia coli (UPEC). We show that the majority of surviving cells are growing and dividing normally at the time of ampicillin exposure. Conversely, we find that the majority of non-growing cells are readily killed by ampicillin exposure. These findings challenge the widespread assumption that bacterial dormancy and persistence are inextricably linked.

Antibiotic resistance (AR) is an escalating public health threat, necessitating innovative strategies to control resistant bacterial populations. One promising approach involves engineering genetic elements that can spread within microbial communities to eliminate AR genes. Previously, we developed Pro-Active Genetics (Pro-AG), a CRISPR-based gene-drive-like system capable of reducing AR colony-forming units (CFU) by approximately five logs. Here, we advance this technology by integrating Pro-AG into a conjugative transfer system, enabling efficient dissemination of an anti-AR gene cassette between two bacterial strains. Additionally, we characterize a complementary homology-based deletion (HBD) process, a CRISPR-driven mechanism that precisely removes target DNA sequences flanked by short direct repeats. Our findings reveal that Pro-AG and HBD are differentially influenced by the bacterial RecA pathway and that HBD components can be delivered via plasmids or phages to selectively delete Pro-AG cassettes. This built-in safeguard prevents uncontrolled spread of a gene cassette and mitigates unanticipated side effects. These refinements enhance the efficiency and flexibility of Pro-AG, expanding its potential applications in microbiome engineering, environmental remediation, and clinical interventions aimed at combating antibiotic resistance. More broadly, this work establishes a proof-of-principle for microbiome engineering strategies that could be leveraged to improve health and restore ecological balance.

Food safety risks are controlled in agrifood settings by reducing the microbial burden in food ingredients and food production environments. Hygiene programmes involve an incremental implementation of chemical treatments (e.g., disinfectants) and engineering controls (e.g., elimination of susceptible harbourage sites). The strategies to disrupt the presence and transmission of microbial risks to foods are being refined by advanced microbiology and genomics that provide actionable evidence on the precise nature of local ecologies.

The prevalence and proliferation of antimicrobial-resistant bacteria is considered one of the critical issues of our time. Wastewater is a habitat for complex microbial communities where bacteria share antimicrobial-resistance genes through horizontal gene transfer. Hospital wastewater plumbing systems are an ideal reservoir for environmental and pathogenic bacteria to interface and exchange antimicrobial-resistance genes. Replacement of contaminated plumbing may be the most intuitive and widely deployed response to the detection and colonization of highly-resistant potentially pathogenic bacteria in hospital sink drains. In this study, we analyzed sink-drain biofilms from six intensive-care patient rooms using shotgun metagenomic sequencing and microbial culture. We show an evident shift in biofilm community structure toward increased abundance of Enterobacteriaceae following plumbing replacement. Higher resistome load and abundance of clinically relevant resistance and typically encountered mobile genes in the newly replaced plumbing was also observed. Taken together, these finding suggest that exchanging contaminated plumbing for new plumbing may actually have the unexpected consequence of increased abundance of Enterobacterales and antimicrobial-resistance genes in the sink drains. Disruption of preexisting complex environmental biofilms may result in an unintended microbial population shifts and a potential subsequent increase in the amount of antimicrobial-resistant Enterobacterales which are targeted for elimination.

Antimicrobial resistance (AMR) databases enable the identification of AMR determinants from pathogen sequence data and the prediction of resistance profiles, enhancing AMR surveillance and informing a range of public health interventions. This review compares freely available and regularly updated AMR databases, explores their public health value and highlights key challenges to and opportunities for fully harnessing their potential.

Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.

Biocides are used in large amounts in industrial, medical, and domestic settings. Benzalkonium chloride (BAC) is a commonly used biocide, for which previous research revealed that Escherichia coli can rapidly adapt to tolerate BAC-disinfection, with consequences for antibiotic susceptibility. However, the consequences of BAC tolerance for selection dynamics and resistance evolution to antibiotics remain unknown. Here, we investigated the effect of BAC tolerance in E. coli on its response upon challenge with different antibiotics. Competition assays showed that subinhibitory concentrations of ciprofloxacin-but not ampicillin, colistin and gentamicin-select for the BAC-tolerant strain over the BAC-sensitive ancestor at a minimal selective concentration of 0.0013-0.0022 µg∙mL^-1. In contrast, the BAC-sensitive ancestor was more likely to evolve resistance to ciprofloxacin, colistin and gentamicin than the BAC-tolerant strain when adapted to higher concentrations of antibiotics in a serial transfer laboratory evolution experiment. The observed difference in the evolvability of resistance to ciprofloxacin was partly explained by an epistatic interaction between the mutations conferring BAC tolerance and a knockout mutation in ompF encoding for the outer membrane porin F. Taken together, these findings suggest that BAC tolerance can be stabilized in environments containing low concentrations of ciprofloxacin, while it also constrains evolutionary pathways towards antibiotic resistance.

The gut microbiome regulates immunity, inflammation, and metabolism. Disruption by antibiotic and non-antibiotic drugs, termed microbiotoxicity, may impair efficacy of treatments, including cancer immunotherapy and vaccination, and contribute to antimicrobial resistance (AMR). This review explores microbiotoxicity's clinical impacts, highlighting non-antibiotic drug effects. Further research into drug-microbiome interactions in future may help inform prescribing practices and drug development as a way to improve health outcomes, reduce toxicity, and support AMR stewardship.

Rapid prediction of antimicrobial resistance (AMR) from genome sequences is essential for timely therapy, yet models based on curated marker panels or core-genome Single Nucleotide Polymorphisms (SNPs) often fail to generalize to novel bacterial lineages. We evaluate AMR prediction in Staphylococcus aureus using pan-genome features that encode homologous gene copy number (including absence) and compare them to SNP-based models across six antibiotics and 4255 isolates. Gradient-boosted decision tree ensembles (XGBoost) trained on gene copy number achieve macro-averaged F1-scores of 0.925-0.988, surpassing SNP-based models (0.838-0.935). Under lineage-held-out evaluation, which withholds entire clades to mimic previously unseen lineages, gene-content models retain markedly higher performance (F1 = 0.875 and 0.904 across two split schemes), whereas SNP-based models degrade substantially (F1 = 0.557 and 0.638). Feature ablation indicates that predictive signal is distributed across many homologous gene families rather than dominated by a few markers, a structure consistent with stronger cross-lineage generalization. Because gene-content features can be robustly obtained even from low-coverage sequencing, this approach extends genome-based AMR prediction to real-world clinical and epidemiological datasets. Together, these results show that copy-number-based pan-genome representations provide a robust alternative to SNP-only approaches, particularly when models must generalize to lineages not represented in training data.