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[This corrects the article DOI: 10.1371/journal.pone.0301972.].

Livestock excrement is composted and applied to agricultural soils. If composts contain antimicrobial-resistant bacteria (ARB), they may spread to the soil and contaminate cultivated crops. Therefore, we investigated the degree of transmission of ARB and related antimicrobial resistance genes (ARGs) and, as well as clonal transmission of ARB from livestock to soil and crops through composting. This study was conducted at Rakuno Gakuen University farm in Hokkaido, Japan. Samples of cattle feces, solid and liquid composts, agricultural soil, and crops were collected. The abundance of Escherichia coli , coliforms, β -lactam-resistant E . coli , and β -lactam-resistant coliforms, as well as the copy numbers of ARG (specifically the bla gene related to β -lactam-resistant bacteria), were assessed using qPCR through colony counts on CHROMagar ECC with or without ampicillin, respectively, 160 days after compost application. After the application of the compost to the soil, there was an initial increase in E . coli and coliform numbers, followed by a subsequent decrease over time. This trend was also observed in the copy numbers of the bla gene. In the soil, 5.0 CFU g -1 E . coli was detected on day 0 (the day post-compost application), and then, E . coli was not quantified on 60 days post-application. Through phylogenetic analysis involving single nucleotide polymorphisms (SNPs) and using whole-genome sequencing, it was discovered that clonal bla CTX-M -positive E . coli and bla TEM -positive Escherichia fergusonii were present in cattle feces, liquid compost, and soil on day 0 as well as 7 days post-application. This showed that livestock-derived ARB were transmitted from compost to soil and persisted for at least 7 days in soil. These findings indicate a potential low-level transmission of livestock-associated bacteria to agricultural soil through composts was observed at low frequency, dissemination was detected. Therefore, decreasing ARB abundance during composting is important for public health.

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs; 0–43.8% and 12.5–56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria. Here, the authors profile the oral phageome of 4 healthy individuals via longread shotgun metagenomics using PromethION, a recently developed highthroughput nanopore sequencer, and uncover potential new candidate phages with enhanced scaffolding and their interaction with host bacteria.

We propose and demonstrate a novel vortex Airy beam which is a superposition of an Airy beam and its laterally sheared beam with a π /2 phase shift. This new-type of vortex Airy beam exhibits stable propagation dynamics, wherein its singular point closely follows its main lobe, unlike conventional vortex Airy beams. Notably, the orbital angular mode purity of this new vortex Airy beam is up to 10% better than that of a conventional vortex Airy beam. We anticipate that this new type of vortex Airy beam, which combines the characteristics of an optical vortex and a diffraction-free Airy beam, will facilitate new directions in applications such as microscopy, material processing and nonlinear optics.

The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes. CRISPR technology is emerging as a potential antimicrobial against antimicrobial-resistant bacteria. Here the authors develop a bacteriophage delivered Cas13a system for killing target bacteria and detecting bacterial genes.

A Nonomuraea sp. strain MM565M-173N2 was isolated from deep-sea sediment off the Sanriku coast, and new antibiotics were evaluated against carbapenem-resistant Enterobacteriaceae (CRE), which is a problematic group of bacteria because of their antimicrobial resistance. From 220 l of fermented broth from strain MM565M-173N2, we isolated four new antibiotics by gel filtration and HPLC, designated as sealutomicins A (1.8 mg), B (1.5 mg), C (0.8 mg), and D (0.8 mg). Their structures were determined from MS, NMR, and CD spectra. Sealutomicin A was found to be a new enediyne antibiotic, while sealutomicins B–D were aromatized products from sealutomicin A. Sealutomicin A showed strong antibacterial activity (MIC 0.05–0.2 μg ml−1) against CRE.

Antimicrobial resistance is a global health concern; Enterobacterales resistant to third-generation cephalosporins (3GCs) and carbapenems are of the highest priority. Here, we conducted genome sequencing and standardized quantitative antimicrobial susceptibility testing of 4,195 isolates of Escherichia coli and Klebsiella pneumoniae resistant to 3GCs and Enterobacterales with reduced meropenem susceptibility collected across Japan. Our analyses provided a complete classification of 3GC resistance mechanisms. Analyses with complete reference plasmids revealed that among the bla CTX-M extended-spectrum β-lactamase genes, bla CTX-M-8 was typically encoded in highly similar plasmids. The two major AmpC β-lactamase genes were bla CMY-2 and bla DHA-1 . Long-read sequencing of representative plasmids revealed that approximately 60% and 40% of bla CMY-2 and bla DHA-1 were encoded by such plasmids, respectively. Our analyses identified strains positive for carbapenemase genes but phenotypically susceptible to carbapenems and undetectable by standard antimicrobial susceptibility testing. Systematic long-read sequencing enabled reconstruction of 183 complete plasmid sequences encoding three major carbapenemase genes and elucidation of their geographical distribution stratified by replicon types and species carrying the plasmids and potential plasmid transfer events. Overall, we provide a blueprint for a national genomic surveillance study that integrates standardized quantitative antimicrobial susceptibility testing and characterizes resistance determinants. Kayama et al . present a blueprint for a national genomic surveillance study that conducts genome sequencing of thousands of strains, integrates standardized quantitative antimicrobial susceptibility testing, and characterizes antimicrobial resistance determinants.

To evaluate non-H. pylori Helicobacter (NHPH) infections in Japan, we enrolled 673 consecutive patients who underwent gastric endoscopy during annual medical checkups at 4 hospitals during April 2022-February 2023. We collected intragastric fluid and serum samples to detect NHPH infection by PCR and serologic tests. The prevalence of NHPH was 3% (20/673); 70% (14/20) of patients were infected with H. suis and 30% (6/20) with non-H. suis NHPH species. All 14 H. suis-infected patients were men and had a history of pork offal ingestion. Among non-H. suis NHPH-infected patients, 50% (3/6) owned pet cats, whereas only 22% (145/667) of other patients owned cats. Endoscopic evaluation revealed marbled crack-like gastritis was present in 93% (13/14) of H. suis-infected patients, a significantly higher prevalence than for H. pylori-infected (28.6%) and H. pylori eradication therapy (27.6%) groups. Pork offal ingestion and having pet cats increase risk for Helicobacter spp. infections.

Significance Shigella modulates macrophage cell death by activating nucleotide-binding oligomerization domain–like receptor (NLR) inflammasome to secure its own dissemination. Here we report that Shigella invasion plasmid antigen H7.8 (IpaH7.8) plays a central role in inducing macrophage cell death via activation of NLR family pyrin domain-containing 3 and NLR family CARD domain-containing 4 inflammasomes in an IpaH7.8 enzyme 3 (E3) ligase-dependent manner. Importantly, an IpaH7.8-deficient mutant was unable to egress from macrophages efficiently, resulting in delayed bacterial multiplication. We identified glomulin—a member of the S-phase kinase-associated protein 1–F-box–like complex that originally was identified as a protein required for normal vascular development—as a target for IpaH7.8 E3 ligase-mediated polyubiquitination, which leads to NLR inflammasome activation. In vitro and in vivo studies confirmed that IpaH7.8-mediated glomulin degradation during Shigella infection activated NLR inflammasomes and promoted cell death. When nucleotide-binding oligomerization domain–like receptors (NLRs) sense cytosolic-invading bacteria, they induce the formation of inflammasomes and initiate an innate immune response. In quiescent cells, inflammasome activity is tightly regulated to prevent excess inflammation and cell death. Many bacterial pathogens provoke inflammasome activity and induce inflammatory responses, including cell death, by delivering type III secreted effectors, the rod component flagellin, and toxins. Recent studies indicated that Shigella deploy multiple mechanisms to stimulate NLR inflammasomes through type III secretion during infection. Here, we show that Shigella induces rapid macrophage cell death by delivering the invasion plasmid antigen H7.8 (IpaH7.8) enzyme 3 (E3) ubiquitin ligase effector via the type III secretion system, thereby activating the NLR family pyrin domain-containing 3 (NLRP3) and NLR family CARD domain-containing 4 (NLRC4) inflammasomes and caspase-1 and leading to macrophage cell death in an IpaH7.8 E3 ligase-dependent manner. Mice infected with Shigella possessing IpaH7.8, but not with Shigella possessing an IpaH7.8 E3 ligase-null mutant, exhibited enhanced bacterial multiplication. We defined glomulin/flagellar-associated protein 68 (GLMN) as an IpaH7.8 target involved in IpaH7.8 E3 ligase-dependent inflammasome activation. This protein originally was identified through its association with glomuvenous malformations and more recently was described as a member of a Cullin ring ligase inhibitor. Modifying GLMN levels through overexpression or knockdown led to reduced or augmented inflammasome activation, respectively. Macrophages stimulated with lipopolysaccharide/ATP induced GLMN puncta that localized with the active form of caspase-1. Macrophages from GLMN ⁺/⁻ mice were more responsive to inflammasome activation than those from GLMN ⁺/⁺ mice. Together, these results highlight a unique bacterial adaptation that hijacks inflammasome activation via interactions between IpaH7.8 and GLMN.

We report the isolation of Helicobacter ailurogastricus, a Helicobacter species that infects cats and dogs, from a person with multiple refractory gastric ulcers. In addition to H. suis, which infects pigs, Helicobacter species that infect cats and dogs should be considered as potential gastric pathogens in humans.