Design combinations of evolved phage and antibiotic for antibacterial guided by analyzing the phage resistance of poorly antimicrobial phage

Although antibiotics are the primary method against bacterial infections, the rapid emergence of antibiotic resistance has forced interest in alternative antimicrobial strategies. Phage has been considered a new biological antimicrobial agent due to its high effectiveness in treating bacterial infections. However, the applications of phage therapy have been limited by the quick development of phage-resistant bacteria. Therefore, more effective phage treatment strategies need to be explored guided by characterizing phage-resistant mutants. In this study, Pseudomonas plecoglossicida phage vB_PpS_SYP was isolated from the sewage but exhibited weak antibacterial activity caused by phage-resistant bacteria. Phage-resistant mutants were isolated and their whole genomes were analyzed for differences. The results showed that mutations in glycosyltransferase family 1 (GT-1) and hypothetical outer membrane protein (homP) led to bacterial phage resistance. The GT-1 mutants had lower biofilm biomass and higher antibiotic sensitivity than wild-type strain. Phage SYP evolved a broader host range and improved antimicrobial efficacy to infect homP mutants. Therefore, we designed a strategy for combined antibiotic and evolved phage inhibition driven by the two phage-resistant mutants. The results showed that the combination was more effective against bacteria than either antibiotics or phage alone. Our findings presented a novel approach to utilizing poorly antimicrobial phages by characterizing their phage-resistant mutants, with the potential to be expanded to include phage therapy for a variety of pathogens. IMPORTANCE The rapid emergence of antibiotic resistance renews interest in phage therapy. However, the lack of efficient phages against bacteria and the emergence of phage resistance impaired the efficiency of phage therapy. In this study, the isolated Pseudomonas plecoglossicida phage exhibited poor antibacterial capacity and was not available for phage therapy. Analysis of phage-resistant mutants guided the design of antibacterial strategies for the combination of antibiotics with evolved phages. The combination has a good antibacterial effect compared to the original phage. Our findings facilitate ideas for the development of antimicrobial-incapable phage, which have the potential to be applied to the phage treatment of other pathogens.

Analysis of complete mitogenomes and phylogenetic relationships of Frontopsylla spadix and Neopsylla specialis

Fleas represent a group of paramount medical significance, subsisting on blood and acting as vectors for an array of naturally occurring diseases. These pathogens constitute essential elements within the plague biome, exerting deleterious effects on both human and livestock health. In this study, we successfully assembled and sequenced the whole mitochondrial genome of Frontopsylla spadix and Neopsylla specialis using long-range PCR and next-generation sequencing technologies. The mitogenomes of F. spadix and N. specialis both have 37 genes with full lengths of 15,085 bp and 16,820 bp, respectively. The topology of the phylogenetic tree elucidates that species F. spadix is clustered in a branch alongside other members of the family Leptopsyllidae, whereas species N. specialis is a sister taxon to Dorcadia ioffi and Hystrichopsylla weida qinlingensis. It also suggests that Pulicidae form a monophyletic clade, Ctenopthalmidae, Hystrichopsyllidae, Vermipsyllidae form a sister group to Ceratophyllidae/Leptopsyllidae group. The mitochondrial genomes of F. spadix and N. specialis were sequenced for the first time, which will contribute to a more comprehensive phylogenetic analysis of the Siphonaptera order. The foundation for subsequent systematic studies, and molecular biology of fleas was established.

The outstanding diversity of rhizobia microsymbionts of common bean (Phaseolus vulgaris L.) in Mato Grosso do Sul, central-western Brazil, revealing new Rhizobium species

Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization. The phylogenetic tree of the 16S rRNA gene split the 13 strains into two large clades, seven in the R. etli and six in the R. tropici clade. The MLSA with four housekeeping genes (glnII, gyrB, recA, and rpoA) confirmed the phylogenetic allocation. Genomic comparisons indicated eight strains in five putative new species and the remaining five as R. phaseoli. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparing the putative new species and the closest neighbors ranged from 81.84 to 92.50% and 24.0 to 50.7%, respectively. Other phenotypic, genotypic, and symbiotic features were evaluated. Interestingly, some strains of both R. etli and R. tropici clades lost their nodulation capacity. The data support the description of the new species Rhizobium cerradonense sp. nov. (CNPSo 3464T), Rhizobium atlanticum sp. nov. (CNPSo 3490T), Rhizobium aureum sp. nov. (CNPSo 3968T), Rhizobium pantanalense sp. nov. (CNPSo 4039T), and Rhizobium centroccidentale sp. nov. (CNPSo 4062T).

The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis

Wellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.

Outbreaks of Campylobacteriosis Caused by Drinking Raw Milk in Japan: Evidence of Relationship Between Milk and Patients by Using Whole Genome Sequencing

Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, there were three outbreaks of campylobacteriosis, presumably caused by the consumption of unpasteurized raw milk, derived from the same farm; thus, these three outbreaks seemed to be associated with a single contaminant at the farm. Therefore, we analyzed Campylobacter jejuni isolates obtained at the three locations using several genetic methods. The sequence type of each isolate, revealed by multilocus sequence typing, was ST-61, and the profile determined using pulsed-field gel electrophoresis was the same; however, neither method could distinguish these from previously obtained strains. Subsequently, we performed WGS and single nucleotide variant (SNV) analysis that provided evidence of clonality, indicating that C. jejuni contamination was attributed to the farm. As in this study, evidence suggests that SNV analysis provides molecular biological support in cases with sufficient epidemiological information. Hence, similar analytical methods may be used in other sporadic cases to elucidate the relevance of the cases.

Chimeric deletion mutation of rpoC2 underlies the leaf-patterning of Clivia miniata var. variegata

KEY MESSAGE

The deletion mutated rpoC2 leads to yellow stripes of Clivia miniata var. variegata by down regulating the transcription of 28 chloroplast genes and disturbing chloroplast biogenesis and thylakoid membrane development. Clivia miniata var. variegata (Cmvv) is a common mutant of Clivia miniata but its genetic basis is unclear. Here, we found that a 425 bp deletion mutation of chloroplast rpoC2 underlies the yellow stripes (YSs) of Cmvv. Both RNA polymerase PEP and NEP coexist in seed-plant chloroplasts and the β″ subunit of PEP is encoded by rpoC2. The rpoC2 mutation changed the discontinuous cleft domain required to form the PEP central cleft for DNA binding from 1103 to 59 aa. RNA-Seq revealed that 28 chloroplast genes (cpDEGs) were all down-regulated in YSs, of which, four involved in chloroplast protein translation and 21 of photosynthesis system (PS)I, PSII, cytochrome b6/f complex and ATP synthase are crucial for chloroplast biogenesis/development. The accuracy and reliability of RNA-Seq was verified by qRT-PCR. Moreover, the chlorophyll (Chl) a/b content, ratio of Chla/Chlb and photosynthetic rate (Pn) of YS decreased significantly. Meanwhile, chloroplasts of the YS mesophyll cells were smaller, irregular in shape, contain almost no thylakoid membrane, and even proplastid was found in YS. These findings indicate that the rpoC2 mutation down-regulated expression of the 28 cpDEGs, which disturb chloroplast biogenesis and its thylakoid membrane development. Thus, there are not enough PSI and II components to bind Chl, so that the corresponding areas of the leaf are yellow and show a low Pn. In this study, the molecular mechanism of three phenotypes of F1 (Cmvv ♀ × C. miniata ♂) was revealed, which lays a foundation for the breeding of variegated plants.

Complete mitochondrial genome sequence and phylogenetic analysis of the Taiwan tai Argyrops bleekeri (Spariformes: Sparidae)

In this study, the complete mitochondrial genome of the Taiwan tai Argyrops bleekeri was determined for the first time by next-generation sequencing. The circular mtDNA molecule was 16,646 bp in size and the overall base composition was A (27.77%), C (28.95%), G (16.60%), and T (26.68%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis based on the 13 PCGs of the Sparidae family revealed that Argyrops appears to be most closely related to Pagrus and Parargyrops, but further research is needed.

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.

Isolation and characterization of novel bacteriophage vB_KpP_HS106 for Klebsiella pneumonia K2 and applications in foods

The detection rate of Klebsiella pneumoniae in food is increasing, and it has emerged as a food pathogen. Global health is threatened due to the emergence of multidrug-resistant (MDR) and hypervirulent (hv) K. pneumoniae. Phages have a promising application as antibacterial agents and have the ability to lyse MDR strains. Hence, phage vB_KpP_HS106 against MDR-hv K. pneumoniae strains was isolated from sewage collected from a hospital. It can maintain stable activity at a pH range of 4-12 and a temperature range of 4°C to 50°C. The maximum adsorption rate of phage HS106 was found to be approximately 84.2% at 6 min. One-step growth curve analysis showed that the latent period of HS106 was 10 min and the burst size was approximately 183 PFU/cell. Furthermore, whole genome analysis indicated that the genome of phage HS106 was a double-stranded linear 76,430-bp long DNA molecule with 44% GC content. A total of 95 open reading frames were annotated in the HS106 genome, which did not contain any virulence genes or antibiotic resistance genes. Phage HS106 reduced MDR K. pneumoniae in milk by approximately 1.6 log10 CFU/mL at 25°C and in chicken by approximately 2 log10 CFU/cm3 at 25°C. Therefore, vB_KpP_HS106 is a promising alternative to antibiotics for biocontrol against multidrug-resistant K. pneumoniae in foods.

Isolation and characterization of three novel Acinetobacter baumannii phages from Beninese hospital wastewater

Acinetobacter baumannii is an opportunistic pathogen that is mostly associated with hospital-acquired infections. The rapid emergence of multi- and pan-drug-resistant Acinetobacter strains poses an increasing challenge in hospitals. Phage therapy offers one treatment option for infections caused by A. baumannii. We isolated three phages from Beninese hospital wastewater - fBenAci001, fBenAci002, and fBenAci003 - that infected clinical A. baumannii strains from Finnish patients. Phylogenetic analysis showed that these phages resemble phages of the genus Friunavirus, family Autographiviridae. The isolated phages meet the requirements set for phages used for phage therapy. However, they were found to have a narrow host range, which may limit their therapeutic use.

The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns

Introduction

Many members of the Ophiostomatales are of economic importance as they are bark-beetle associates and causative agents for blue stain on timber and in some instances contribute towards tree mortality. The taxonomy of these fungi has been challenging due to the convergent evolution of many traits associated with insect dispersal and a limited number of morphological characters that happen to be highly pleomorphic. This study examines the mitochondrial genomes for three members of Leptographium sensu lato [Leptographium aureum (also known as Grosmannia aurea), Grosmannia fruticeta (also known as Leptographium fruticetum), and Leptographium sp. WIN(M)1376)].

Methods

Illumina sequencing combined with gene and intron annotations and phylogenetic analysis were performed.

Results

Sequence analysis showed that gene content and gene synteny are conserved but mitochondrial genome sizes were variable: G. fruticeta at 63,821 bp, Leptographium sp. WIN(M)1376 at 81,823 bp and L. aureum at 104,547 bp. The variation in size is due to the number of introns and intron-associated open reading frames. Phylogenetic analysis of currently available mitochondrial genomes for members of the Ophiostomatales supports currently accepted generic arrangements within this order and specifically supports the separation of members with Leptographium-like conidiophores into two genera, with L. aureum grouping with Leptographium and G. fruticeta aligning with Grosmannia.

Discussion

Mitochondrial genomes are promising sequences for resolving evolutionary relationships within the Ophiostomatales.

Complete genome sequence of a novel bacteriophage vB_Pci_PCMW57 infecting phytobacteria pseudomonas cichorii

BACKGROUND

A novel virulent bacteriophage infecting phytobacteria Pseudomonas cichorii (P. cichorii) was isolated from leafy vegetables in Brazil. P. cichorii is a Gram-negative soil phytobacterium, the causal agent of a number of economically important plant diseases worldwide.

METHODS AND RESULTS

In this study, a new phage specific for P. cichorii was isolated from solid samples (lettuce, chicory and cabbage), designated vB_Pci_PCMW57. Electron microscopy revealed a small virion (~ 50-nm-diameter icosahedral capsid) with a short, non-contractile tail. The genome of vB_Pci_PCMW57 is 40,117 bp in size, with a GC content of 57.6% and encodes 49 open reading frames. The phage is genetically similar to P. syringae phages Pst_GM1 and Pst_GIL1, and the P. fluorescens phages WRT and KNP. According to electron microscopy and whole-genome sequence analysis, vB_Pci_PCMW57 should be classified as a Caudoviticetes, family Autographiviridae, subfamily Studiervirinae.

CONCLUSIONS

The complete phage genome was annotated, and the sequence identity of the virus with other Pseudomonas viruses was higher than 95%. To our knowledge, this is the first report of a bacteriophage infecting Pseudomonas cichorii.

The Progression in Developing Genomic Resources for Crop Improvement

Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques.

The first rare case of Candida palmioleophila infection reported in China and its genomic evolution in a human host environment

Introduction

Candida palmioleophila is a rare human pathogenic fungus, which has been poorly characterized at the genome level. In this study, we reported the first fatal case of C. palmioleophila infection in China and investigate the microevolution of C. palmioleophila in the human host environment.

Methods

A series of C. palmioleophila stains were collected from the patient at different time points for routine microbial and drug sensitivity testing. The first C. palmioleophila isolate 07202534 was identified by de novo whole genome sequencing. The in vitro and in vivo genetic evolutionary characteristics of C. palmioleophila were discussed based on the analysis of bioinformatics data.

Results

The six C. palmioleophila isolates displayed dose-dependent sensitivity to fluconazole. The C. palmioleophila genome contained homologous genes such as CDR1 and MDR1, which were recognized to be related to azole resistance. In addition, amino acid variation was detected at F105L and other important sites of ERG11. In addition, the mean divergence time between C. palmioleophila and Scheffersomyces stipites CBS 6054 was 406.04 million years, indicating that C. palmioleophila originated earlier than its closest relative. In addition, the six strains of C. palmioleophila isolated form the patient had higher homology and fewer mutation sites, which indicated the stability in C. palmioleophila genome. We also found that C. palmioleophila had a wide natural niche and may evolve slowly.

Discussion

We believe that this study will contribute to improve our understanding of the genetic evolution, pathogenicity, and drug resistance of C. palmioleophila and will aid in the prevention and control of its spread.

Identification and phylogenetic analysis in Pterorhinuschinensis (Aves, Passeriformes, Leiothrichidae) based on complete mitogenome

The Black-throated Laughingthrush (Pterorhinuschinensis) is a bird belonging to the order Passeriformes and the family Leiothrichidae, and is found in Cambodia, China, Laos, Myanmar, Thailand and Vietnam. Pterorhinuschinensis was once classified as belonging to the genus Garrulax. However, recent research has reclassified it in the genus Pterorhinus. In this study, we sequenced and characterized the complete mitogenome of P.chinensis. The complete mitochondrial genome of P.chinensis is 17,827 bp in length. It consists of 13 PCGs, 22 tRNAs, two rRNAs, and two control regions. All genes are coded on the H-strand, except for one PCG (nad6) and eight tRNAs. All PCGs are initiated with ATG and stopped by five types of stop codons. Our comparative analyses show irregular gene rearrangement between trnT and trnP genes with another similar control region emerging between trnE and trnF genes compared with the ancestral mitochondrial gene order, called "duplicate CR gene order". The phylogenetic position of P.chinensis and phylogenetic relationships among members of Leiothrichidae are assessed based on complete mitogenomes. Phylogenetic relationships based on Bayesian inference and maximum likelihood methods showed that Garrulax and (Pterorhinus + Ianthocincla) formed a clade. Leiothrix and Liocichla also formed a clade. Our study provides support for the transfer of P.chinensis from Garrulax to Pterorhinus. Our results provide mitochondrial genome data to further understand the mitochondrial genome characteristics and taxonomic status of Leiothrichidae.

Cooperative microbial interactions drive spatial segregation in porous environments

The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.

Isolation and characterization of phosphate-solubilizing bacterium Pantoea rhizosphaerae sp. nov. from Acer truncatum rhizosphere soil and its effect on Acer truncatum growth

The Acer truncatum Bunge, widely distributed in North China, shows excellent tolerance to low-P soils. However, little information is available on potential phosphate-solubilizing bacterial (PSB) strains from the A. truncatum rhizosphere. The objectives of this work were to isolate and characterize PSB from A. truncatum rhizosphere soil and to evaluate the effect of inoculation with the selected strain on A. truncatum seedlings. The strains were characterized on the basis of phenotypic characteristics, carbon source utilization pattern, fatty acid methyl esters analysis, 16S rRNA gene and the whole-genome sequence. A Gram-negative and rod-shaped bacterium, designated MQR6^T, showed a high capacity to solubilize phosphate and produce indole-3-acetic acid (IAA) and siderophores. The strain can solubilize tricalcium phosphate (TCP) and rock phosphate (RP), and the solubilization of TCP was about 60% more effective than RP. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain MQR6^T formed a distinct phyletic lineage as a new species within the genus Pantoea. The digital DNA-DNA hybridization value between strain MQR6^T and the closely related strains was 19.5-23.3%. The major cellular fatty acids were summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), summed feature 8 (C_18:1ω6c and/or C_18:1ω7c), C_14:0, C_16:0, and C_17:0 cyclo. Several genes related to IAA production, phosphonate transport, phosphate solubilization and siderophore biogenesis were found in the MQR6^T genome. Furthermore, inoculation with the strain MQR6^T significantly improved plant height, trunk diameter, dry weight and P accumulation in roots and shoot of A. truncatum seedlings compared to non-inoculated control. These plant parameters were improved even further in the treatment with both inoculation and P fertilization. Our results suggested that MQR6^T represented a new species we named Pantoea rhizosphaerae, as a plant growth-promoting rhizobacterium that can solubilize inorganic P and improve growth of A. truncatum seedlings, emerging as a potential strategy to improve A. truncatum cultivation.

Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry

Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.

Complete mitochondrial genome of Hydrolagus mitsukurii (Jordan & Snyder, 1904)

Holocephali has foreseeable value to help our understanding of vertebrate genome evolution due to its phylogenetic position. In this study, we reported a complete mitochondrial genome of Hydrolagus mitsukurii, a species of holocephalans. The mitochondrial genome is 20,486 bp in length and comprised 13 PCGs, 2 rRNA, 22 tRNA, and 1 control region (D-loop), as well as a long noncoding insertion between tRNAThr and tRNAPro. A phylogenetic tree based on 13 PCGs showed that Hydrolagus mitsukurii was grouped with the members of the family Chimaeridae. Furthermore, the phylogenetic tree further supported the paraphyletic clades of Hydrolagus and Chimera.

Vitamin B12 produced by Cetobacterium somerae improves host resistance against pathogen infection through strengthening the interactions within gut microbiota

BACKGROUND

Pathogen infections seriously affect host health, and the use of antibiotics increases the risk of the emergence of drug-resistant bacteria and also increases environmental and health safety risks. Probiotics have received much attention for their excellent ability to prevent pathogen infections. Particularly, explaining mechanism of action of probiotics against pathogen infections is important for more efficient and rational use of probiotics and the maintenance of host health.

RESULTS

Here, we describe the impacts of probiotic on host resistance to pathogen infections. Our findings revealed that (I) the protective effect of oral supplementation with B. velezensis against Aeromonas hydrophila infection was dependent on gut microbiota, specially the anaerobic indigenous gut microbe Cetobacterium; (II) Cetobacterium was a sensor of health, especially for fish infected with pathogenic bacteria; (III) the genome resolved the ability of Cetobacterium somerae CS2105-BJ to synthesize vitamin B12 de novo, while in vivo and in vitro metabolism assays also showed the ability of Cetobacterium somerae CS2105-BJ to produce vitamin B12; (IV) the addition of vitamin B12 significantly altered the gut redox status and the gut microbiome structure and function, and then improved the stability of the gut microbial ecological network, and enhanced the gut barrier tight junctions to prevent the pathogen infection.

CONCLUSION

Collectively, this study found that the effect of probiotics in enhancing host resistance to pathogen infections depended on function of B12 produced by an anaerobic indigenous gut microbe, Cetobacterium. Furthermore, as a gut microbial regulator, B12 exhibited the ability to strengthen the interactions within gut microbiota and gut barrier tight junctions, thereby improving host resistance against pathogen infection. Video Abstract.

The first chloroplast sequence of Rosa davurica Pall. var. Davurica

Rosa davurica Pall. var. davurica is a member of the plant family Rosaceae. Although R. davurica has high application value, its chloroplast genome sequence has not been reported. This study aims to reveal the genetic characteristics of the chloroplast genome of Rosa roxburghii. The length of its total chloroplast DNA is 156,971 bp, with 37.22% G/C content. Its chloroplast genome has two inverted repeat (IRa and IRb) regions totaling 26,051 bp which are separated by a large single copy (LSC) region of 86,032 bp and a small single copy (SSC) region of 18,837 bp. The genome contains 131 independent genes (86 protein-coding, 37 tRNA, and 8 rRNA), and there are 18 repeated genes within the IR region. Among these genes, 17 genes contained one or two introns. The phylogenetic analysis showed that R. davurica was relatively close to other Rosa species, such as the Rosa hybrid.

The complete chloroplast genome sequence of Phyllostachys incarnata Wen, 1982

Phyllostachys incarnata Wen, 1982 is one of the important material and edible bamboo specie of high quality in China. We reported the complete chloroplast(cp) genome of P. incarnata in this study. The cp genome of P. incarnata (GenBank accession number: OL457160) was a typical tetrad structure with a full length of 139,689 bp, comprising a pair of inverted repeated (IR) regions (21,798 bp) separated by a large single-copy (LSC) region (83,221 bp) and a small single-copy (SSC) region (12,872 bp). And the cp genome contained 136 genes, including 90 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 19 cp genomes suggested that P. incarnata was relatively close to P. glauca among the species analyzed.

Emergence of livestock-associated Mammaliicoccus sciuri ST71 co-harbouring mecA and mecC genes in Brazil

The discovery and tracking of antimicrobial resistance genes are essential for understanding the evolution of bacterial resistance and restraining its dispersion. Mammaliicoccus sciuri (formerly Staphylococcus sciuri) is the most probable evolutionary repository of the mecA gene, that later disseminated to S. aureus. In this study, we describe the first double mecA/mecC homologue-positive non-aureus staphylococci and mammaliicocci (NASM) from the American continent, also representing the first report of mecC-positive NASM in Brazil. Two clonally related methicillin-resistant M. sciuri strains co-carrying mecA and mecC genes were isolated from the teat skin swab and milk sample collected from an ewe's left udder half. Both M. sciuri strains belonged to the sequence type (ST) 71. Besides mecA and mecC genes, the M. sciuri strains carried broad resistomes for clinically important antimicrobial agents, including β-lactams, tetracyclines, lincosamide, streptogramin, streptomycin, and aminoglycosides. Virulome analysis showed the presence of the clumping factor B (clfB), ATP-dependent protease ClpP (ClpP) and serine-aspartate repeat proteins (sdrC and sdrE) virulence-associated genes. Phylogenomic analysis revealed that these M. sciuri strains are part of a globally disseminated branch, associated with farm and companion animals and even with food. Our findings suggest that M. sciuri is likely to emerge as a pathogen of global interest, carrying a broad repertoire of antimicrobial resistance genes with a remarkable co-presence of mecA and mecC genes. Finally, we strongly encourage to monitor M. sciuri under the One Health umbrella since this bacterial species is spreading at the human-animal-environment interface.

Survey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China

Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the "One Health" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.

Presumptive First Record of Myotis aurascens (Chiroptera, Vespertilionidae) from China with a Phylogenetic Analysis

Bat groups have a high degree of species diversity, and the taxonomic status and phylogenetic relationships among bat species have always been research hotspots. Due to the fact that morphological characteristics do not always reflect the evolutionary relationships among species, mitochondrial DNA has been widely used in the study of species relationships due to its maternal inheritance pattern. Myotis aurascens has been suggested as a possible synonym for M. davidii. However, the status of this classification has been controversial. In this study, the morphological and molecular characteristics of a M. aurascens captured from Inner Mongolia, China, were analyzed to determine its taxonomic status. In terms of morphological features, the body weight was 6.33 g, the head and body length were 45.10 mm, the forearm length was 35.87 mm, and the tragus length was 7.51 mm. These values all fell within the species signature data range. Nucleotide skew analysis of the protein-coding genes (PCGs) suggested that only five PCGs (ND1, ND2, COX2, ATP8, and ND4) showed AT-skew value within the mitogenome of M. aurascens. Except for ND6, the GC-skew values of the other PCGs were negative, reflecting the preference for C and T bases compared to G and A bases. Molecular phylogenetic analyses based on mitochondrial PCGs indicated that M. aurascens was a distinct species from M. davidii and phylogenetically closer to M. ikonnikovi, M. alcathoe, and M. mystacinus. Genetic distance analysis also showed that M. aurascens and M. davidii were distantly related. Therefore, the integrated analysis demonstrated that M. aurascens should be considered a distinct species rather than a synonym of M. davidii. Our study could provide a reference for enriching species diversity and research on conservation in China.

Whole-genome sequencing of Listeria innocua recovered from retail milk and dairy products in Egypt

The similarity of the Listeria innocua genome with Listeria monocytogenes and their presence in the same niche may facilitate gene transfer between them. A better understanding of the mechanisms responsible for bacterial virulence requires an in-depth knowledge of the genetic characteristics of these bacteria. In this context, draft whole genome sequences were completed on five L. innocua isolated from milk and dairy products in Egypt. The assembled sequences were screened for antimicrobial resistance and virulence genes, plasmid replicons and multilocus sequence types (MLST); phylogenetic analysis of the sequenced isolates was also performed. The sequencing results revealed the presence of only one antimicrobial resistance gene, fosX, in the L. innocua isolates. However, the five isolates carried 13 virulence genes involved in adhesion, invasion, surface protein anchoring, peptidoglycan degradation, intracellular survival, and heat stress; all five lacked the Listeria Pathogenicity Island 1 (LIPI-1) genes. MLST assigned these five isolates into the same sequence type (ST), ST-1085; however, single nucleotide polymorphism (SNP)-based phylogenetic analysis revealed 422-1,091 SNP differences between our isolates and global lineages of L. innocua. The five isolates possessed an ATP-dependent protease (clpL) gene, which mediates heat resistance, on a rep25 type plasmids. Blast analysis of clpL-carrying plasmid contigs showed approximately 99% sequence similarity to the corresponding parts of plasmids of L. monocytogenes strains 2015TE24968 and N1-011A previously isolated from Italy and the United States, respectively. Although this plasmid has been linked to L. monocytogenes that was responsible for a serious outbreak, this is the first report of L. innocua containing clpL-carrying plasmids. Various genetic mechanisms of virulence transfer among Listeria species and other genera could raise the possibility of the evolution of virulent strains of L. innocua. Such strains could challenge processing and preservation protocols and pose health risks from dairy products. Ongoing genomic research is necessary to identify these alarming genetic changes and develop preventive and control measures.

Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes

Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.

Phenotypic and genotypic characterization of antibiotic resistance of Salmonella Heidelberg in the south of Brazil

Salmonella is the main human pathogen present in the poultry chain. Salmonella Heidelberg is one of the most important serovars for public health since it has been frequently isolated in broiler chickens from different countries and may present multidrug resistance (MDR). This study was carried out with 130 S. Heidelberg isolates collected from pre-slaughter broiler farms in 2019 and 2020 in 18 cities from three Brazilian states to study relevant aspects regarding their genotypic and phenotypic resistance. The isolates were tested and identified using somatic and flagellar antiserum (0:4, H:2, and H:r), and an antimicrobial susceptibility test (AST) was performed against 11 antibiotics for veterinary use. The strains were typed by Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR, and representatives of the main clusters of the identified profiles were sequenced by Whole Genome Sequencing (WGS). AST results showed that all isolates were resistant to sulfonamide, 54 % (70/130) were resistant to amoxicillin, and only one was sensitive to tetracycline. Twelve isolates (15.4 %) were MDR. The dendrogram obtained from the ERIC-PCR showed that the strains were grouped into 27 clusters with similarity above 90 %, with some isolates showing 100 % similarity but with different phenotypic profiles of antimicrobial resistance. Identical strains collected on the same farm on other dates were identified, indicating that they were residents. WGS identified 66 antibiotic-resistance genes. The sul2 (present in all sequenced samples) and tet(A) genes were highlighted and validated in the experimental analysis. The fosA7 gene was also identified in all sequenced samples, but resistance was not observed in the phenotypic test, possibly due to the heteroresistance of the S. Heidelberg strains evaluated. Considering that chicken meat is one of the most consumed meats in the world, the data obtained in the present study can corroborate the mapping of the origin and trends of antimicrobial resistance.

Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives

Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium, Aquitalea, Iodobacter, Duganella, Massilia and Janthinobacterium. In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.

Design of Phage-Cocktail-Containing Hydrogel for the Treatment of Pseudomonas aeruginosa-Infected Wounds

Recently, the treatment of infected wounds has become a global problem due to increased antibiotic resistance in bacteria. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa is often present in chronic skin infections, and it has become a threat to public health as it is increasingly multidrug resistant. Due to this, new measures to enable treatment of infections are necessary. Treatment of bacterial infections with bacteriophages, known as phage therapy, has been in use for a century, and has potential with its antimicrobial effect. The main purpose of this study was to create a phage-containing wound dressing with the ability to prevent bacterial infection and rapid wound healing without side effects. Several phages against P. aeruginosa were isolated from wastewater, and two polyvalent phages were used to prepare a phage cocktail. The phage cocktail was loaded in a hydrogel composed of polymers of sodium alginate (SA) and carboxymethyl cellulose (CMC). To compare the antimicrobial effects, hydrogels containing phages, ciprofloxacin, or phages plus ciprofloxacin were produced, and hydrogels without either. The antimicrobial effect of these hydrogels was investigated in vitro and in vivo using an experimental mouse wound infection model. The wound-healing process in different mouse groups showed that phage-containing hydrogels and antibiotic-containing hydrogels have almost the same antimicrobial effect. However, in terms of wound healing and pathological process, the phage-containing hydrogels performed better than the antibiotic alone. The best performance was achieved with the phage-antibiotic hydrogel, indicating a synergistic effect between the phage cocktail and the antibiotic. In conclusion, phage-containing hydrogels eliminate efficiently P. aeruginosa in wounds and may be a proper option for treating infectious wounds.

Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae)

Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.

The mobile gene cassette carrying tetracycline resistance genes in Aeromonas veronii strain Ah5S-24 isolated from catfish pond sediments shows similarity with a cassette found in other environmental and foodborne bacteria

Aeromonas veronii is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen that causes diarrhea in humans and hemorrhagic septicemia in fish. In the present study, we used whole-genome sequencing (WGS) to evaluate the presence of antimicrobial resistance (AMR) and virulence genes found in A. veronii Ah5S-24 isolated from catfish pond sediments in South-East, United States. We found cphA4, dfrA3, mcr-7.1, valF, blaFOX-7, and blaOXA-12 resistance genes encoded in the chromosome of A. veronii Ah5S-24. We also found the tetracycline tet(E) and tetR genes placed next to the IS5/IS1182 transposase, integrase, and hypothetical proteins that formed as a genetic structure or transposon designated as IS5/IS1182/hp/tet(E)/tetR/hp. BLAST analysis showed that a similar mobile gene cassette (MGC) existed in chromosomes of other bacteria species such as Vibrio parahaemolyticus isolated from retail fish at markets, Aeromonas caviae from human stool and Aeromonas media from a sewage bioreactor. In addition, the IS5/IS1182/hp/tet(E)/tetR/hp cassette was also found in the plasmid of Vibrio alginolyticus isolated from shrimp. As for virulence genes, we found the tap type IV pili (tapA and tapY), polar flagellae (flgA and flgN), lateral flagellae (ifgA and IfgL), and fimbriae (pefC and pefD) genes responsible for motility and adherence. We also found the hemolysin genes (hylII, hylA, and TSH), aerA toxin, biofilm formation, and quorum sensing (LuxS, mshA, and mshQ) genes. However, there were no MGCs encoding virulence genes found in A. veronii AhS5-24. Thus, our findings show that MGCs could play a vital role in the spread of AMR genes between chromosomes and plasmids among bacteria in aquatic environments. Overall, our findings are suggesting that MGCs encoding AMR genes could play a vital role in the spread of resistance acquired from high usage of antimicrobials in aquaculture to animals and humans.

Association between Intestinal Colonization and Extraintestinal Infection with Carbapenem-Resistant Klebsiella pneumoniae in Children

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a critical public health threat. However, the association between intestinal colonization and parenteral infection among pediatric patients has not been elucidated. We collected 8 fecal CRKP strains and 10 corresponding CRKP strains responsible for extraintestinal infection from eight patients who did not manifest infection upon admission to the hospital. Paired isolates showed identical resistance to antimicrobials and identical virulence in vitro and in vivo. wzi capsule typing, multilocus sequence typing, and whole-genome sequencing (WGS) indicated high similarity between paired colonizing and infecting isolates. Mutations between colonizing and infecting isolate pairs found by WGS had a distinctive molecular signature of a high proportion of complex structural variants. The mutated genes were involved in pathways associated with infection-related physiological and pathogenic functions, including antibiotic resistance, virulence, and response to the extracellular environment. The latter is important for bacterial infection of environmental niches. Various mutations related to antibiotic resistance, virulence, and colonization that were not associated with any particular mutational hot spot correlated with an increased risk of extraintestinal infection. Notably, novel subclone carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) KL19-ST15 exhibited hypervirulence in experimental assays that reflected the severe clinical symptoms of two patients infected with the clonal strains. Taken together, our findings indicate the association between CRKP intestinal colonization and extraintestinal infection, suggesting that active screening for colonization on admission could decrease infection risk in children. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes an increasing number of nosocomial infections, which can be life-threatening, as carbapenems are last-resort antibiotics. K. pneumoniae is part of the healthy human microbiome, and this provides a potential advantage for infection. This study demonstrated that CRKP intestinal colonization is strongly linked to extraintestinal infection, based on the evidence given by whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence. Apart from these findings, our in-depth analysis of point mutations and chromosome structural variants in patient-specific infecting isolates compared with colonizing isolates may contribute insights into bacterial adaptation underlying CRKP infection. In addition, a novel subclone of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) was observed in the study. This finding highlights the importance of CRKP active surveillance among children, targeting in particular the novel high-risk CR-hvKP clone.

The complete mitochondrial genome of a fouling mussel, Xenostrobus atratus (Mollusca: Mytilidae), and its phylogenetic implication

In this study, we report the female-lineage mitochondrial genome of Xenostrobus atratus for the first time. The circular mitochondrial genome is 14,806 bp in length and contains 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. All genes are encoded on the heavy strand. The genome composition is A + T biased (66.6%), with 25.2% A, 41.4% T, 21.7% G and 11.7% C. A Bayesian inference (BI) phylogenetic tree was constructed based on the mitochondrial genomes of X. atratus and 46 other Mytilidae species. Our results demonstrate that X. atratus and Limnoperna fortunei have distinct lineages, opposing synonymizing Xenostrobus within Limnoperna. According to this study, the validity of the subfamily Limnoperninae and genus Xenostrobus is strongly supported. However, there is still an urgent need for more mitochondrial data to decide to which subfamily X. atratus belongs.

The first complete mitochondrial genome sequences for Ulidiidae and phylogenetic analysis of Diptera

BACKGROUND

Tetanops sintenisi is a pest that mainly damages the root of quinoa (Chenopodium quinoa) and it is first discovered in China in 2018.

METHODS AND RESULTS

Here, the complete mitochondrial genome (mitogenome) of T. sintenisi was sequenced and compared with the mitogenomes of other Diptera species. The results revealed that the mitogenome of T. sintenisi is 15,763 bp in length (GenBank accession number: MT795181) and is comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region (959 bp). The highly conserved gene arrangement of the mitogenome of T. sintenisi was identical to that of other Diptera insects. Twelve PCGs contained the typical insect start codon ATN, while cox1 had CGA as the start codon. The genes cox2, nad4, and nad1 contained an incomplete termination codon T; nad3, nad5, and cob contained the complete termination codon TAG; and the remaining seven PCGs contained the termination codon TAA. All tRNA genes were predicted to fold into the typical cloverleaf secondary structure. Phylogenetic analysis of 48 species based on the mitogenome sequence revealed that T. sintenisi clustered with the Tephritidae family, indicating that T. sintenisi and Tephritidae have a close phylogenetic relationship.

CONCLUSIONS

The phylogenetic relationship of T. sintenisi based on the mitogenome is consistent with the traditional morphological taxonomy, according to which T. sintenisi belongs to the family Otitidae, which is closely related to the family Muscidae.

Clinical outcomes of COVID-19 caused by the Alpha variant compared with one by wild type in Kobe, Japan. A multi-center nested case-control study

OBJECTIVES

The emergence of the Alpha variant of novel coronavirus 2019 (SARS-CoV-2) is a concerning issue but their clinical implications have not been investigated fully.

METHODS

We conducted a nested case-control study to compare severity and mortality caused by the Alpha variant (B.1.1.7) with the one caused by the wild type as a control from December 2020 to March 2021, using whole-genome sequencing. 28-day mortality and other clinically important outcomes were evaluated.

RESULTS

Infections caused by the Alpha variant were associated with an increase in the use of oxygen (43.4% vs 26.3%. p = 0.017), high flow nasal cannula (21.2% vs 4.0%, p = 0.0007), mechanical ventilation (16.2% vs 6.1%, p = 0.049), ICU care (30.3% vs 14.1%, p = 0.01) and the length of hospital stay (17 vs 10 days, p = 0.031). More patients with the Alpha variant received medications such as dexamethasone. However, the duration of each modality did not differ between the 2 groups. Likewise, there was no difference in 28-day mortality between the 2 groups (12% vs 8%, p = 0.48), even after multiple sensitivity analyses, including propensity score analysis.

CONCLUSION

The Alpha variant was associated with a severe form of COVID-19, compared with the non-Alpha wild type, but might not be associated with higher mortality.

Complete mitochondrial genome of the longicorn Anoplophora horsfieldi Hope (Coleoptera: Cerambycidae)

The chinaberry yellow-banded longhorn beetle, Anoplophora horsfieldi Hope 1842 (Coleoptera: Cerambycidae) is an important pest on many economic tree species. In this study, the complete mitochondrial genome of A. horsfieldi was determined, which was 15,837 bp in length and contained 37 genes, including 13 protein-coding genes (PCGs), two rRNA, 22 tRNA genes, and a non-coding A + T-rich region. The phylogenetic analysis based on mitochondrial genomes showed that A. horsfieldi is sister to a clade formed by A. chinensis and A. glabripennis.

Characterization of Phage vB_SalM_SPJ41 and the Reduction of Risk of Antibiotic-Resistant Salmonella enterica Contamination in Two Ready-to-Eat Foods

Salmonella enterica is a major cause of foodborne illness, and the emergence of antibiotic-resistant bacteria has led to huge pressures on public health. Phage is a promising strategy for controlling foodborne pathogens. In this study, a novel Salmonella phage vB_SalM_SPJ41 was isolated from poultry farms in Shanghai, China. Phage vB_SalM_SPJ41 was able to lyse multiple serotypes of antibiotic-resistant S. enterica, including S. Enteritidis, S. Typhimurium, S. Shubra, S. Derby, and S. Nchanga. It had a short incubation period and was still active at a temperature <80 °C and in the pH range of 3~11. The phage can effectively inhibit the growth of S. enterica in liquid culture and has a significant inhibitory and destructive effect on the biofilm produced by antibiotic-resistant S. enterica. Moreover, the phage was able to reduce S. Enteritidis and MDR S. Derby in lettuce to below the detection limit at 4 °C. Furthermore, the phage could reduce S. Enteritidis and S. Derby in salmon below the limit of detection at 4 °C, and by 3.9 log₁₀ CFU/g and· 2.1 log₁₀ CFU/g at 15 °C, respectively. In addition, the genomic analysis revealed that the phages did not carry any virulence factor genes or antibiotic resistance genes. Therefore, it was found that vB_SalM_SPJ41 is a promising candidate phage for biocontrol against antibiotic-resistant Salmonella in ready-to-eat foods.

The Complete Mitochondrial Genome of Torix tukubana (Annelida: Hirudinea: Glossiphoniidae)

Torix tukubana is a poorly understood proboscidate leech species, generally an ectoparasite on amphibian species. In this study, the complete mitochondrial genome (mitogenome) of T. tukubana was sequenced using next-generation sequencing (NGS), and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the T. tukubana mitogenome was 14,814 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (CR). The mitogenome composition presented a strong A + T bias (73.6%). All tRNAs had the typical clover structure except the trnS1 (TCT), whose dihydrouridine (DHU) arm was short, having only one complementary base pair. Additionally, 8 gene order patterns were identified among 25 known Hirudinea species, and T. tukubana was identical to the Hirudinea ground pattern. A phylogenetic analysis based on 13 PCGs indicated that all the studied species clustered into three main clades. The relationships among Hirudinea species were basically consistent with their gene arrangement results, but different from their morphological taxonomy. T. tukubana was in the monophyletic group of Glossiphoniidae, a finding consistent with previous research. Our results provided the essential characteristics of the T. tukubana mitogenome. As the first complete mitogenome of Torix, it could offer valuable information for a systematic understanding of the Hirudinea species.

Host Dependent-Transposon for a Plasmid Found in Aeromonas salmonicida subsp. salmonicida That Bears a catB3 Gene for Chloramphenicol Resistance

Plasmids that carry antibiotic resistance genes occur frequently in Aeromonas salmonicida subsp. salmonicida, an aquatic pathogen with severe consequences in salmonid farming. Here, we describe a 67 kb plasmid found in the A. salmonicida subsp. salmonicida Strain SHY15-2939 from Quebec, Canada. This new plasmid, named pAsa-2939 and identified by high throughput sequencing, displays features never found before in this bacterial species. It contains a transposon related to the Tn21 family, but with an unusual organization. This transposon bears a catB3 gene (chloramphenicol resistance) that has not been detected yet in A. salmonicida subsp. salmonicida. The plasmid is transferable by conjugation into Aeromonas hydrophila, but not into Escherichia coli. Based on PCR analysis and genomic sequencing (Illumina and PacBio), we determined that the transposon is unstable in A. salmonicida subsp. salmonicida Strain SHY15-2939, but it is stable in A. hydrophila trans-conjugants, which explains the chloramphenicol resistance variability observed in SHY15-2939. These results suggest that this bacterium is likely not the most appropriate host for this plasmid. The presence of pAsa-2939 in A. salmonicida subsp. salmonicida also strengthens the reservoir role of this bacterium for antibiotic resistance genes, even those that resist antibiotics not used in aquaculture in Québec, such as chloramphenicol.

Transcriptome profiling reveals the underlying mechanism of grape post-harvest pathogen Penicillium olsonii against the metabolites of Bacillus velezensis

Introduction

Pathogen infection influences the post-harvest shelf life of grape berries. In a preliminary study, metabolites produced by Bacillus velezensis significantly inhibited the growth of the grape postharvest pathogen Penicillium olsonii.

Methods

To investigate the mechanism of interaction between B. velezensis and P. olsonii, a draft genome was generated for P. olsonii WHG5 using the Illumina NovaSeq platform, and the transcriptomic changes in WHG5 were analyzed in response to the exposure to B. velezensis metabolites (10% v/v).

Results

The expression levels of genes associated with sporulation, including GCY1, brlA, and abaA, were down-regulated compared with those of the control. In addition, spore deformation and abnormal swelling of the conidiophore were observed. The expression of crucial enzymes, including fructose 2,6-bisphosphate and mannitol-2-dehydrogenase, was down-regulated, indicating that the glycolytic pathway of WHG5 was adversely affected by B. velezensis metabolites. The KEGG pathway enrichment analysis revealed that glutathione metabolism and the antioxidant enzyme system were involved in the response to B. velezensis metabolites. The down-regulation of the pathogenesis-related genes, PG1 and POT1, suggested that B. velezensis metabolites decreased the pathogenicity of P. olsonii. B. velezensis metabolites disrupted the homeostasis of reactive oxygen species in P. olsonii by affecting glucose metabolism, resulting in spore deformation and disruption of growth. In addition, the expression of key pathogenesis-related genes was down-regulated, thereby reducing the pathogenicity of P. olsonii.

Disscusion

This study provides insights into the responses of P. olsonii to B. velezensis metabolites and identifies potential target genes that may be useful in biocontrol strategies for the suppression of post-harvest spoilage in grapes.

Co-factor independent oxidases ncnN and actVA-3 are involved in the dimerization of benzoisochromanequinone antibiotics in naphthocyclinone and actinorhodin biosynthesis

Streptomyces produce complex bioactive secondary metabolites with remarkable chemical diversity. Benzoisochromanequinone polyketides actinorhodin and naphthocyclinone are formed through dimerization of half-molecules via single or double carbon-carbon bonds, respectively. Here we sequenced the genome of S. arenae DSM40737 to identify the naphthocyclinone gene cluster and established heterologous production in S. albus J1074 by utilizing direct cluster capture techniques. Comparative sequence analysis uncovered ncnN and ncnM gene products as putative enzymes responsible for dimerization. Inactivation of ncnN that is homologous to atypical co-factor independent oxidases resulted in the accumulation of fogacin, which is likely a reduced shunt product of the true substrate for naphthocyclinone dimerization. In agreement, inactivation of the homologous actVA-3 in S. coelicolor M145 also led to significantly reduced production of actinorhodin. Previous work has identified the NAD(P)H-dependent reductase ActVA-4 as the key enzyme in actinorhodin dimerization, but surprisingly inactivation of the homologous ncnM did not abolish naphthocyclinone formation and the mutation may have been complemented by an endogenous gene product. Our data suggests that dimerization of benzoisochromanequinone polyketides require two-component reductase-oxidase systems.

Cytotoxicity and Antimicrobial Resistance of Salmonella enterica Subspecies Isolated from Raised Reptiles in Beijing, China

BACKGROUND

Reptiles are asymptomatic carriers of Salmonella spp. Reptile-associated Salmonella infections have been noticed as a significant contributor to overall human salmonellosis. However, it remains unclear regarding the prevalence of reptile-associated Salmonella in China.

METHODS

Fecal and gastrointestinal mucosal samples were taken from 104 snakes, 21 lizards, and 52 chelonians and cultured on selective medium. The positive clones were validated and annotated by biochemical screening and multiplex PCR verification. In addition, the antibiotic resistance of identified Salmonella isolates was detected and followed by cytotoxic activity detection on human colon cells via co-culturation.

RESULTS

The overall prevalence of Salmonella in reptiles was 25.99%, with rates of 30.77%, 47.62%, and 7.69% in snakes, lizards, and chelonians, respectively. Further, all isolates showed variable drug-resistant activity to 18 antibiotics, of which 14 strains (30.43%) were resistant to more than eight kinds of antibiotics. More than half of isolated Salmonella strains were more toxic to host cells than the standard strain, SL1344. Whole genome sequencing (WGS) results showed that all lizard-associated strains belong to 4 serovar types, and 7 of them fall into the highly pathogenic serovars "Carmel" and "Pomona."

CONCLUSIONS

Our results highlight the potential threat of zoonotic salmonellosis from captive reptiles in the Beijing area of China.

Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer

BACKGROUND

Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.

RESULTS

Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria.

CONCLUSION

In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.

Comparative analysis of Penicillium genomes reveals the absence of a specific genetic basis for biocontrol in Penicillium rubens strain 212

Penicillium rubens strain 212 (PO212) is a filamentous fungus belonging to the division Ascomycete. PO212 acts as an effective biocontrol agent against several pathogens in a variety of horticultural crops including Fusarium oxysporum f.sp. lycopersici, causing vascular wilt disease in tomato plants. We assembled draft genomes of two P. rubens strains, the biocontrol agent PO212 and the soil isolate S27, which lacks biocontrol activity. We also performed comparative analyses of the genomic sequence of PO212 with that of the other P. rubens and P. chrysogenum strains. This is the first Penicillium strain with biocontrol activity whose genome has been sequenced and compared. PO212 genome size is 2,982 Mb, which is currently organized into 65 scaffolds and a total of 10,164 predicted Open Reading Frames (ORFs). Sequencing confirmed that PO212 belongs to P. rubens clade. The comparative analysis of the PO212 genome with the genomes of other P. rubens and Penicillium chrysogenum strains available in databases showed strong conservation among genomes, but a correlation was not found between these genomic data and the biocontrol phenotype displayed by PO212. Finally, the comparative analysis between PO212 and S27 genomes showed high sequence conservation and a low number of variations mainly located in ORF regions. These differences found in coding regions between PO212 and S27 genomes can explain neither the biocontrol activity of PO212 nor the absence of such activity in S27, opening a possible avenue toward transcriptomic and epigenetic studies that may shed light on this mechanism for fighting plant diseases caused by fungal pathogens. The genome sequences described in this study provide a useful novel resource for future research into the biology, ecology, and evolution of biological control agents.

Cytopathic and Genomic Characteristics of a Human-Originated Pseudorabies Virus

Pseudorabies virus (PRV) generally infects pigs and threatens the pig industry. However, recently we have isolated a PRV strain designated hSD-1/2019 from infected humans. In this study, we compared the complete genome sequence of hSD-1/2019 with those of pig-originated PRV strains. Sequence alignments revealed that the genome sequence of hSD-1/2019 was highly homologous to those of the porcine PRV strains. Phylogenetic analyses found that hSD-1/2019 was the closest related to porcine PRV endemic strains in China, particularly the variant strains circulating recently. We also showed that the glycoproteins important for the multiplication and pathogenesis of hSD-1/2019 were highly similar to those of the pig endemic strains. Diversifying selection analyses revealed that hSD-1/2019 and pig variant strains are under diversifying selection. Recombination analysis indicated that hSD-1/2019 was a recombinant of several PRV variant strains and an earlier PRV classic strain. Finally, we found that both human and pig-originated PRV strains could induce cytopathic effects in cells from humans, pigs, and mice, but only the human PRV and pig-variant PRV formed large syncytia in human cell lines. The data presented in this study contribute to our understanding of the molecular basis for the pathogenesis of human PRV from a genomic aspect.

Characterisation and sequencing of the novel phage Abp95, which is effective against multi-genotypes of carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii has become one of the most challenging conditional pathogens in health facilities. It causes various infectious diseases in humans, such as wound or urinary tract infections and pneumonia. Phage therapy has been used as an alternative strategy for antibiotic-resistant A. baumannii infections and has been approved by several governments. Previously, we have reported two potential phage therapy candidates, Abp1 and Abp9, both of which are narrow-host-range phages. In the present study, we screened and isolated 22 A. baumannii bacteriophages from hospital sewage water and determined that Abp95 has a wide host range (29%; 58/200). The biological and genomic characteristics and anti-infection potential of Abp95 were also investigated. Abp95 belongs to the Myoviridae family, with a G+C content of 37.85% and a genome size of 43,176 bp. Its genome encodes 77 putative genes, none of which are virulence, lysogeny, or antibiotic resistance genes. Abp95 was found to accelerate wound healing in a diabetic mouse wound infection model by clearing local infections of multidrug-resistant A. baumannii. In conclusion, the lytic phage Abp95, which has a wide host range, demonstrates potential as a candidate for phage therapy against multiple sequence types of carbapenem-resistant A. baumannii.

Reproductive microbiome and cytokine profiles associated with fertility outcomes of postpartum beef cows

Shifts from commensal bacteria (for example, Lactobacillus in the phylum Firmicutes) within the reproductive tract have been associated with changes in local reproductive immune responses and decreased fertility in humans. The objective of this study was to characterize the microbiome and cytokine concentrations before artificial insemination (AI) in vaginal and uterine flushes from postpartum beef cows. Twenty Bos indicus-influenced beef cows (approximately 60 d postpartum and free of reproductive, health, or physical issues) were enrolled. The B. indicus prostaglandin (PG) 5-d + controlled intervaginal drug-releasing estrus synchronization protocol was initiated on day -8 of the study with timed AI on d0. Blood samples were collected on days -3, -1, and 28 via coccygeal venipuncture. Vaginal and uterine flushes were collected on days -3 and -1. Based on days 28 pregnancy status determined by transrectal ultrasonography, cows were identified as either Open (n = 13) or Pregnant (n = 7). Bacterial community analyses were conducted targeting the V4 hypervariable region of the 16S rRNA gene. Cytokine analyses were performed using the RayBiotech Quantibody Bovine Cytokine Array Q1 and MyBioSource ELISA kits per the manufacturer's instructions. Statistical analyses for bacteria relative abundance were conducted using PROC NPAR1WAY and for cytokine concentrations using PROC GLM in SAS 9.4. Uterine concentrations of interferon γ, interleukin (IL)1α, and IL21 were greater in Open than in Pregnant cows (P < 0.05). Regardless of pregnancy status, uterine IL13 increased from days -3 to -1 (9.76 vs. 39.48 ± 9.28 pg/mL, respectively; P < 0.05). Uterine relative abundance of the phylum Firmicutes decreased from days -3 to -1 in Open cows (60.4% ± 0.9% vs. 48.5% ± 3.2%; P = 0.004). In Open cows, the genus Blautia decreased in relative abundance within the uterus from days -3 to -1 (2.1% ± 0.2% vs. 0.9% ± 0.1%; P = 0.002). Uterine relative abundance of the phylum Tenericutes increased from days -3 to -1 in Pregnant cows (1.0% ± 0.1% vs. 7.6% ± 4.1%; P = 0.002). In Pregnant cows, the genus Ureaplasma tended to increase within the uterus from days -3 to -1 (0.08% ± 0.06% vs. 7.3% ± 4.1%; P = 0.054). These findings suggest a distinct difference in the reproductive microbiome and cytokine profiles before AI for resulting Open vs. Pregnant cows.

Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides

Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.

Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia

The rise of antibiotic resistance in bacterial strains has led to vigorous exploration for alternative treatments. To this end, phage therapy has been revisited, and it is gaining increasing attention, as it may represent an efficient alternative for treating multiresistant pathogenic bacteria. Phage therapy is considered safe, and phages do not infect eukaryotic cells. There have been many studies investigating phage-host bacteria interactions and the ability of phages to target specific hosts. Escherichia coli is the causative agent of a multitude of infections, ranging from urinary tract infections to sepsis, with growing antibiotic resistance. In this study, we characterized the Escherichia phage fBC-Eco01, which was isolated from a water sample collected at Oued, Tunis. Electron microscopy showed that fBC-Eco01 phage particles have siphovirus morphology, with an icosahedral head of 61 ± 3 nm in diameter and a non-contractile tail of 94 ± 2 nm in length and 12 ± 0.9 nm in width. The genome of fBC-Eco01 is a linear double-stranded DNA of 43.466 bp with a GC content of 50.4%. Comparison to databases allowed annotation of the functions to 39 of the 78 predicted gene products. A single-step growth curve revealed that fBC-Eco01 has a latent period of 30 minutes and a burst size of 175 plaque-forming units (PFU) per infected cell. Genomic analysis indicated that fBC-Eco01 is a member of the subfamily Guernseyvirinae. It is most closely related to a group of phages of the genus Kagunavirus that infect Enterobacter, Raoultella, and Escherichia strains.