Haneummycin, a new 22-membered macrolide lactam antibiotic, produced by marine-derived Streptomyces sp. KM77-8.

A new antibiotic named haneummycin (1) was isolated from a culture broth of marine-derived Streptomyces sp. KM77-8 by solvent extraction and HPLC using a C4 column. The structure of 1 was elucidated including relative stereochemistry as a new 22-membered macrolide lactam associated with a cyclopentanone and three sugars by various spectroscopic analyses, such as MS and NMR. Compound 1 displayed significant antibacterial activities against Gram-positive bacteria including vancomycin-resistant Enterococcus faecium (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) with both MIC values of 8.0 µg ml-1.

A Culture Supernatant from an Actinomycete sp. Affects Biofilm Formation and Virulence Expression of Candida auris.

The multidrug-resistant pathogen Candida auris is characterized by its aggregation under certain conditions, which affects its biofilm formation, drug susceptibility, and pathogenicity. Although the innate tendency to aggregate depends on the strain, the mechanism regulating C. auris aggregation remains unclear. We found that the culture supernatant from one of the 95 Actinomyces strains isolated from a deep-sea environment (IMAs2016D-66) inhibited C. auris aggregation. The cells grown in the presence of IMAs2016D-66 exhibited reduced hydrophobicity, biofilm formation, and enhanced proteolytic activity. In addition, the efflux pump activity of the fluconazole-resistant C. auris strain LSEM 3673 was stimulated by IMAs2016D-66, whereas no significant change was observed in the fluconazole-susceptible strain LSEM 0643. As the relationship between aggregative tendency and virulence in C. auris is still unclear, IMAs2016D-66 can serve as a tool for investigating regulatory mechanisms of phenotype switching and virulence expression of C. auris. Understanding of phenotype switching may help us not only to understand the pathogenicity of C. auris, but also to design new drugs that target the molecules regulating virulence factors.

Rifampicin exerts anti-mucoviscous activity against hypervirulent Klebsiella pneumoniae via binding to the RNA polymerase ß subunit.

OBJECTIVES: In hypervirulent Klebsiella pneumoniae (hvKP), the hypermucoviscous capsule is known to be a major virulence determinant. We previously discovered that rifampicin (RFP), a bactericidal drug that binds to and inhibits the ß subunit of RNA polymerase (RpoB), elicits anti-mucoviscous activity against hvKP by suppressing rmpA, a regulator of capsule production. Here, we aimed to determine whether RFP exerts this effect at sub-growth-inhibitory concentrations via its binding to RpoB. METHODS: Five spontaneous RFP-resistant mutants (R1-R5) were prepared from an hvKP clinical isolate and subjected to whole genome sequencing and mucoviscosity analyses. Subsequently, a two-step allelic exchange procedure was used to create a rpoB mutant R6 and revertants with wild-type rpoB from R1-R5 (named R1'-R5'). Transcription levels of rmpA and the capsular polysaccharide polymerase gene magA and capsule thickness of R1-R5 and R1'-R5' grown without or with RFP were evaluated by quantitative reverse transcription polymerase chain reaction and microscopic observation using India ink staining. RESULTS: R1-R5 all had non-synonymous point mutations in rpoB and were highly resistant to the bactericidal effects and anti-mucoviscous activity of RFP. While the properties of R6 were similar to those of R1-R5, the responses of R1'-R5' to RFP were identical to those of the wild type. rmpA and magA transcription levels and capsule thickness correlated well with the mucoviscosity levels. CONCLUSIONS: RFP exerts anti-mucoviscous activity by binding to RpoB. The mechanism of how this causes rmpA suppression remains to be explored.

Siderophore production as a biomarker for Klebsiella pneumoniae strains that cause sepsis: A pilot study.

BACKGROUND/PURPOSE: Klebsiella pneumoniae bacteremia-induced sepsis is a clinically important condition with a high mortality rate and various known virulence factors. However, studies on the association of these virulence factors with the occurrence of K. pneumoniae bacteremia-induced sepsis are scarce. We aimed to investigate clinical variables and virulence factors in patients with K. pneumoniae bacteremia-induced sepsis. METHODS: We retrospectively reviewed the medical records of 76 patients with K. pneumoniae bacteremia between January 2012 and July 2017. Patients were divided into sepsis (n = 25) and non-sepsis (n = 51) groups. Patient background characteristics, antimicrobial regimens, and prognosis were evaluated. We assessed the distribution of virulence factors related to K. pneumoniae, such as mucoviscosity, capsular polysaccharide, and siderophores. Siderophore production levels were determined by measuring the orange halo zone on chrome azurol S agar plate assay. RESULTS: There were no intergroup differences in male-to-female ratio and age. Multivariable analysis revealed that siderophore production level (p < 0.01) was an independent predictor of K. pneumoniae bacteremia-induced sepsis. Furthermore, the optimal cut-off point of siderophore production to predict sepsis was 9.6 mm (sensitivity, 86%; specificity, 76%; AUC, 0.81). CONCLUSION: Siderophore production was an independent predictor of sepsis caused by K. pneumoniae bacteremia. The optimal cut-off point for siderophore production for sepsis occurrence prediction was 9.6 mm. To improve outcomes, patients with K. pneumoniae bacteremia-induced sepsis with high siderophore production levels should be managed prudently.

Genomic characterization of triple-carbapenemase-producing Acinetobacter baumannii.

OBJECTIVES: To characterize Acinetobacter baumannii OCU_Ac16a, a clinical isolate co-harbouring three acquired carbapenemase genes, bla NDM-1, bla TMB-1, and bla OXA-58, and assess the clinical significance of so-called multiple-carbapenemase producers. METHODS: OCU_Ac16a and its close relative, OCU_Ac16b, which lacks the bla NDM-1, were isolated from sputum cultures of a patient at Osaka City University Hospital. We subjected these strains to whole-genome analysis, particularly focusing on the genetic context of each carbapenemase gene. The transmissibility and functionality of each carbapenemase gene were analysed by conjugation and transformation experiments and antimicrobial susceptibility tests. RESULTS: bla TMB-1 was located in a class 1 integron on the chromosome, whereas bla NDM-1 and bla OXA-58 were found on plasmids named pOCU_Ac16a_2 and pOCU_Ac16a_3, respectively. pOCU_Ac16a_2 (which exhibited highly efficient self-transmissibility) and pOCU_Ac16a_3 (which did not show transmissibility but could be introduced into another A. baumannii strain via electroporation) could both confer carbapenem resistance (MICs ≥512 and ≥32 mg/L, respectively) on the recipient strain. The functionality of bla TMB-1 was evident from the high resistance of OCU_Ac16b to ceftazidime and cefepime (MICs ≥256 and 48 mg/L, respectively), and the high resistance of OCU_Ac16a to cefiderocol (MIC 32 mg/L) could be explained by the additive effect of bla NDM-1 and bla TMB-1. CONCLUSIONS: Our data revealed the genomic organization of OCU_Ac16a and demonstrated that all the carbapenemase genes are functional, each contributing to the extremely high broad-spectrum resistance of OCU_Ac16a to ß-lactams. As multiple-carbapenemase producers can be serious health threats as drug-resistant pathogens and disseminators of carbapenemase genes, close attention should be paid to their emergence.

Complete Genome Sequence of Acinetobacter pittii OCU_Ac17, Isolated from Human Venous Blood.

Acinetobacter pittii isolate OCU_Ac17 was obtained from the venous blood of a patient at a hospital in Japan. We present its complete 4.108-Mbp genome sequence (1 chromosome plus 3 plasmids), analyzed by combining long-read (Flongle) and short-read (MiniSeq) sequencing.

Complete Genome Sequence of a Clinical Isolate of Acinetobacter baumannii Harboring 11 Plasmids.

Here, we report the complete genome sequence of an Acinetobacter baumannii isolate harboring 11 plasmids, obtained at a hospital in Japan in 2016. The complete 4.07-Mbp genome sequence (1 chromosome and 11 plasmids) was analyzed by a combination of long-read (Flongle) and short-read (NovaSeq 6000) sequencing.

Complete Genome Sequence of Polycladomyces abyssicola JIR-001T, Isolated from Hemipelagic Sediment in Deep Seawater.

Here, we report the complete genome sequence of Polycladomyces abyssicola strain JIR-001, which we isolated from hemipelagic sediment in deep seawater. The genome, generated by combining long-read (Flongle) and short-read (NovaSeq) sequencing data, is 3,197,230 bp, with a mean G+C content of 52.0%.

Cryptic fungal diversity revealed in deep-sea sediments associated with whale-fall chemosynthetic ecosystems.

In this study, sediments from whale-fall chemosynthetic ecosystems (two different sites, one naturally occurring at 4200 m water depth in South Atlantic Ocean and one artificially immersed at 100 m water depth in Kagoshima Bay, Japan) were investigated by Ion Torrent PGM sequencing of the ITS region of ribosomal RNA to reveal fungal communities in these unique marine environments. As a result, a total of 107 (897 including singletons) Operational Taxonomic Units (OTUs) were obtained from the samples explored. Composition of the 107 OTUs at the phylum level among the five samples from two different whale-fall sites was assigned to Ascomycota (46%), Basidiomycota (7%), unidentified fungi (21%), non-fungi (10%), and sequences with no affiliation to any organisms in the public database (No-match) (16%). The high detection of the unidentified fungi and unassigned fungi was revealed in the whale-fall environments in this study. Some of these unidentified fungi are allied to early diverging fungi and they were more abundant in the sediments not directly in contact with whalebone. This study suggests that a cryptic fungal community exists in unique whale-fall ecosystems.

Nutritional status positively impacts humoral immunity against its Mycobacterium tuberculosis, disease progression, and vaccine development.

Nutritional status contributes to the regulation of immune responses against pathogens, and malnutrition has been considered as a risk factor for tuberculosis (TB). Mycobacterium tuberculosis (Mtb), the causative agent of TB, can modulate host lipid metabolism and induce lipid accumulation in macrophages, where the bacilli adopt a dormant phenotype. In addition, serum lipid components play dual roles in the regulation of and protection from Mtb infection. We analyzed the relationship between nutritional status and the humoral immune response in TB patients. We found that serum HDL levels are positively correlated with the serum IgA specific for Mtb antigens. Analysis of the relationship between serum nutritional parameters and clinical parameters in TB patients showed that serum albumin and CRP levels were negatively correlated before treatment. We also observed reduced serum LDL levels in TB patients following treatment. These findings may provide insight into the role of serum lipids in host immune responses against Mtb infection. Furthermore, improving the nutritional status may enhance vaccination efficacy.

Complete Genome Sequence of Acinetobacter baumannii ATCC 19606T, a Model Strain of Pathogenic Bacteria Causing Nosocomial Infection.

Acinetobacter baumannii ATCC 19606T, which is often used in genetic studies as a routine model microorganism, belongs to sequence type 52 (ST52), showing beta-lactam resistance. We present the complete 3.996-Mbp genome sequence (1 chromosome plus 2 plasmids), generated by combining long-read (MinION) and short-read (MiniSeq) sequencing data.

Clinical and virulence factors related to the 30-day mortality of Klebsiella pneumoniae bacteremia at a tertiary hospital: a case-control study.

Klebsiella pneumoniae bacteremia is a critical clinical presentation that is associated with high mortality. However, extremely few studies have investigated the virulence factors related to mortality of K. pneumoniae bacteremia in patients. The present study elucidated clinical and virulence factors associated with the 30-day mortality of K. pneumoniae bacteremia at a tertiary hospital. The medical records of 129 patients with K. pneumoniae bacteremia admitted to Osaka City University Hospital between January 2012 and December 2018 were retrospectively reviewed. Patient background characteristics, antimicrobial regimens, and prognosis were evaluated. Additionally, virulence factors were assessed using multiplex polymerase chain reaction to elucidate their association with K. pneumoniae. The 30-day mortality was 10.9% in patients with K. pneumoniae bacteremia. The male-to-female ratio, age, and underlying disease did not differ between the non-survivor and survivor groups. Multivariate analysis showed that sepsis (odds ratio (OR), 7.46; p = 0.005) and iutA (OR, 4.47; p = 0.046) were independent predictors associated with the 30-day mortality of K. pneumoniae bacteremia. Despite the relatively low 30-day mortality of patients with K. pneumoniae bacteremia, the treatment of those with sepsis and those infected with K. pneumoniae harboring iutA may require careful management for improving their outcomes.

Clinical characteristics of bacteremia caused by hypermucoviscous Klebsiella pneumoniae at a tertiary hospital.

This study aimed to assess the predictive factors of bacteremia due to hypermucoviscous Klebsiella pneumoniae (hvKP), as well as the mortality. The medical records of 114 patients with K. pneumoniae bacteremia who were divided into the hvKP (n = 24) and non-hvKP (n = 90) groups and were retrospectively reviewed. The male-to-female ratio, age, and underlying disease did not differ between the 2 groups. Mortality was higher among patients in the hvKP bacteremia group than in the non-hvKP bacteremia group (29.2% vs 6.7%). Multivariate analysis showed that the independent predictors associated with hvKP bacteremia were abscess (P = 0.01) and no antibiotic exposure (P = 0.02); thus, early assessment of these conditions is important. For patients with a history of abscess and no antibiotic exposure, it is necessary to administer treatment while keeping the risk of hvKP in mind.

Discovery of anti-mucoviscous activity of rifampicin and its potential as a candidate antivirulence agent against hypervirulent Klebsiella pneumoniae.

A recent increase in the incidence of hypervirulent Klebsiella pneumoniae (hvKP) infections, especially those caused by a sublineage of clonal group CG23 (CG23-I), is raising serious health concerns worldwide. The high virulence of hvKP is, at least in part, attributed to the overproduction of capsular polysaccharide (CPS), which is triggered by a positive regulator of capsular polysaccharide synthesis (cps) genes, named rmpA (regulator of mucoid phenotype A). Although extensive research has been conducted on the mechanisms of hvKP virulence, no study has focused on the development of antivirulence therapeutics. This study attempted to identify and validate an antimicrobial agent able to suppress hvKP hypermucoviscosity. A total of 18 commercially available antimicrobial agents, including ß-lactams, quinolones and aminoglycosides, were tested. Rifampicin (RFP) was found to have strong anti-mucoviscous activity against CG23-I hvKP even at subinhibitory concentrations. Polysaccharide extracts from hvKP showed substantially lowered viscosity when cells were grown with RFP. Moreover, microscopic observations demonstrated that RFP treatment results in a drastic reduction in the thickness of the CPS layer around hvKP cells. RFP treatment decreased transcript levels of rmpA and rmpA-regulated cps genes, indicating that RFP suppresses mucoviscosity of hvKP through inhibition of rmpA transcription. These data suggest that RFP may serve as a potential antivirulence agent for refractory hvKP infection.

Molecular and epidemiological analysis of IMP-1 metallo-ß-lactamase-producing Klebsiella pneumoniae in a tertiary care hospital in Japan.

This study investigated the molecular and phenotypic characteristics of carbapenemase-producing Klebsiella pneumoniae, and identified the risk factors underlying its acquisition. We evaluated K. pneumoniae isolated in Nagasaki University Hospital between January 2009 and June 2015. The presence of carbapenemase genes and plasmid characteristics were investigated. We performed multilocus sequence typing (MLST), and generated a dendrogram based on the results of pulsed-field gel electrophoresis (PFGE) for carbapenemase-producing strains. We also performed a case-control study of patients. Of the 88 K. pneumoniae strains that showed minimum inhibitory concentration ≥1 µg/mL for imipenem and/or meropenem, and that were available from our bacterial collection, 18 had the IMP-type carbapenemase gene, all of which were IMP-1 according to sequencing analysis. Strains included seven different sequence types (STs), of which the most common was ST1471. A dendrogram showed the significant similarity of some strains with relationships in PFGE patterns, STs, and the wards in which they were isolated. Plasmid incompatibility group was similar among the IMP-1 producers. Regarding risk factors, multivariate analysis showed that liver disease and previous uses of carbapenems and anti-fungal drugs were significant factors for the acquisition of IMP-1-producing strains. Our results demonstrate that IMP-1 is a major carbapenemase produced by K. pneumoniae. The PFGE results indicated the possibility of transmission in the hospital. The identified risk factors should be considered for appropriate antibiotic therapy and infection-control measures.

Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan.

Sphingobium sp. strain YG1 is a lignin model dimer-metabolizing bacterium newly isolated from sediment in Kagoshima, Japan, at a depth of 102 m. Here, we report the complete genome nucleotide sequence of strain YG1.

Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002T.

We report the 3.2-Mb draft genome sequence of Brevundimonas denitrificans strain TAR-002T, isolated from deep-sea floor sediment. The draft genome sequence of strain TAR-002T consists of 3,231,216 bp in 44 contigs, with a G+C content of 68.47%, 3,866 potential coding sequences (CDSs), 3 rRNAs, and 45 tRNAs.

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode.

The purpose of this study was to develop a novel electrical retrieval method (ER method) for living sponge-associated microorganisms from marine sponges frozen at -80 °C. A -0.3-V vs. Ag/AgCl constant potential applied for 2 h at 9 °C induced the attachment of the sponge-associated microorganisms to an indium tin oxide/glass (ITO) or a gallium-doped zinc oxide/glass (GZO) working electrode. The electrically attached microorganisms from homogenized Spirastrella insignis tissues had intact cell membranes and showed intracellular dehydrogenase activity. Dead microorganisms were not attracted to the electrode when the homogenized tissues were autoclaved for 15 min at 121 °C before use. The electrically attached microorganisms included cultivable microorganisms retrieved after detachment from the electrode by application of a 9-MHz sine-wave potential. Using the ER method, we obtained 32 phyla and 72 classes of bacteria and 3 archaea of Crenarchaeota thermoprotei, Marine Group I, and Thaumarchaeota incertae sedis from marine sponges S. insignis and Callyspongia confoederata. Employment of the ER method for extraction and purification of the living microorganisms holds potential of single-cell cultivation for genome, transcriptome, proteome, and metabolome analyses of bioactive compounds producing sponge-associated microorganisms.

Involvement of flocculin in negative potential-applied ITO electrode adhesion of yeast cells.

The purpose of this study was to develop novel methods for attachment and cultivation of specifically positioned single yeast cells on a microelectrode surface with the application of a weak electrical potential. Saccharomyces cerevisiae diploid strains attached to an indium tin oxide/glass (ITO) electrode to which a negative potential between -0.2 and -0.4 V vs. Ag/AgCl was applied, while they did not adhere to a gallium-doped zinc oxide/glass electrode surface. The yeast cells attached to the negative potential-applied ITO electrodes showed normal cell proliferation. We found that the flocculin FLO10 gene-disrupted diploid BY4743 mutant strain (flo10Δ /flo10Δ) almost completely lost the ability to adhere to the negative potential-applied ITO electrode. Our results indicate that the mechanisms of diploid BY4743 S. cerevisiae adhesion involve interaction between the negative potential-applied ITO electrode and the Flo10 protein on the cell wall surface. A combination of micropatterning techniques of living single yeast cell on the ITO electrode and omics technologies holds potential of novel, highly parallelized, microchip-based single-cell analysis that will contribute to new screening concepts and applications.

Draft Genome Sequence of Aneurinibacillus tyrosinisolvens LL-002T, Which Possesses Some Pseudouridine Synthases.

We report the 5.7-Mb draft genome sequence of Aneurinibacillus tyrosinisolvens strain LL-002(T), isolated from organic- and methane-rich sea sediments. The draft genome sequence of strain LL-002(T) consists of 5,693,818 bp in 136 contigs, with a G+C content of 44.5%, 5,946 potential coding sequences (CDS), 2 rRNAs, and 39 tRNAs.