Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China

Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [bla _CTX-M-55 , bla _TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla _CTX-M-55 demonstrated that the flanking contexts of bla _CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.

Genomic characterization and production of antimicrobial lipopeptides by Bacillus velezensis P45 growing on feather by-products

AIMS

To investigate the potential of novel Bacillus velezensis P45 as an eco-friendly alternative for bioprocessing poultry by-products into valuable antimicrobial products.

METHODS AND RESULTS

The complete genome of B. velezensis P45 was sequenced using the Illumina MiSeq platform, showing 4455 protein and 98 RNA coding sequences according to the annotation on the RAST server. Moreover, the genome contains eight gene clusters for the production of antimicrobial secondary metabolites and 25 putative protease-related genes, which can be related to feather-degrading activity. Then, in vitro tests were performed to determine the production of antimicrobial compounds using feather, feather meal and brain-heart infusion (BHI) cultures. Antimicrobial activity was observed in feather meal and BHI media, reaching 800 and 3200 AU ml^-1 against Listeria monocytogenes respectively. Mass spectrometry analysis indicates the production of antimicrobial lipopeptides surfactin, fengycin and iturin.

CONCLUSIONS

The biotechnological potential of B. velezensis P45 was deciphered through genome analysis and in vitro studies. This strain produced antimicrobial lipopeptides growing on feather meal, a low-cost substrate.

SIGNIFICANCE AND IMPACT OF STUDY

The production of antimicrobial peptides by this keratinolytic strain may represent a sustainable alternative for recycling by-products from poultry industry. Furthermore, whole B. velezensis P45 genome sequence was obtained and deposited.

Emergence of Methicillin-Resistant Staphylococcus aureus ST239/241 SCCmec-III Mercury in Eastern Algeria

In this paper, we investigate the epidemiology of infections-associated Staphylococcusaureus (S. aureus) from the Medical Intensive Care Unit (MICU) at University Hospital Center of Constantine (UHCC) in Algeria, with a special emphasis on methicillin-resistant strains (MRSA) revealed by cefoxitin disks (30 μg), then confirmed by penicillin-binding protein (PBP2a) agglutination and real-time polymerase chain reaction (RT-PCR) targeting mecA and mecC genes. Staphylococcal Cassette Chromosome mec (SCCmec type), staphylococcal protein A (spa-type), multilocus sequence type (MLST), Panton-Valentine Leucocidin (PVL), and toxic shock syndrome toxin-1 (TSST-1) were further investigated in all isolates, and whole genome sequencing was performed for a selected subset of three hospital-acquired MRSA (HA-MRSA) isolates. A measurement of 80% out of the 50 S. aureus isolates were identified as HA-MRSA harbouring the mecA gene, and 72.5% of them were multidrug resistant (MDR). Twelve STs, four different SCCmec cassettes, fourteen spa types, ten isolates Panton-Valentine Leukocidin (PVL)-positive, and three isolates TSST-1 were identified. Interestingly, there was a high prevalence (n = 29; 72.5%) of a worrisome emerging clone: the HA-MRSA ST239/241 SCCmec-III mercury with PVL negative, resistant to β-lactams, aminoglycosides, quinolones, and tetracyclines. Other clones of HA-MRSA isolates were also identified, including PVL-positive ST80 SCCmec-IV/SCCmec-unknown (22.5%), ST34 SCCmec-V with TSST-1 positive (2.5%), and PVL-negative ST72 SCCmec-II (2.5%). Genome analysis enables us to describe the first detection of both PVL-negative HA-MRSA ST239/241 SCCmec-III mercury carrying ccrC, as well as SCCmec-V cassette, which dramatically changes the epidemiology of S. aureus infections in one of the hospitals in eastern Algeria.

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes

Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.

Genomic Epidemiology Reveals Multiple Introductions of Severe Acute Respiratory Syndrome Coronavirus 2 in Niigata City, Japan, Between February and May 2020

The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median C_t value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17–26 cycles), but after 10 days, the median C_t value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.

Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Background

We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods.

Results

We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach.

Conclusions

Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08115-x.

Pangenome inventory of Burkholderia sensu lato, Burkholderia sensu stricto, and the Burkholderia cepacia complex reveals the uniqueness of Burkholderia catarinensis

Here the pangenome analysis of Burkholderia sensu lato (s.l.) was performed for the first time, together with an updated analysis of the pangenome of Burkholderia sensu stricto, and Burkholderia cepacia complex (Bcc) focusing on the Bcc B. catarinensis specific features of its re-sequenced genome. The pangenome of Burkholderia s.l., Burkholderia s.s., and of the Bcc are open, composed of more than 96% of accessory genes, and more than 62% of unknown genes. Functional annotations showed that secondary metabolism genes belong to the variable portion of genomes, which might explain their production of several compounds with varied bioactivities. Taken together, this work shows the great variability and uniqueness of these genomes and reveals an underexplored unknown potential in poorly characterized genes. Regarding B. catarinensis 89^T, its genome harbors genes related to hydrolases production and plant growth promotion. This draft genome will be valuable for further investigation of its biotechnological potentials.

Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (-0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships

The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.

In Vitro Study of Biocontrol Potential of Rhizospheric Pseudomonas aeruginosa against Pathogenic Fungi of Saffron (Crocus sativus L.)

Plant rhizosphere soil contains a large number of plant-growth promoting rhizobacteria, which can not only resist the invasion of pathogenic microorganisms and protect plants from damage, but also promote the growth and development of plants. In this study, Pseudomonas aeruginosa strain YY322, isolated and screened from the rhizosphere soil of saffron (Crocus sativus L.), was found through a plate confrontation experiment to show highly effectual and obvious antagonistic activity against the pathogens of saffron, including Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, Penicillium citrinum and Stromatinia gladioli. In addition, the volatile organic compounds of strain YY322 had great antagonistic activity against these pathogens. Observation under a scanning electron microscope and transmission electron microscope reflected that strain YY322 had a significant effect on the hyphae and conidia of F. oxysporum and F. solani. Through the detection of degrading enzymes, it was found that P. aeruginosa can secrete protease and glucanase. The plant growth promoting performance was evaluated, finding that strain YY322 had the functions of dissolving phosphorus, fixing nitrogen, producing siderophore and producing NH3. In addition, whole genome sequencing analysis indicated that the YY322 genome is comprised of a 6,382,345-bp circular chromosome, containing 5809 protein-coding genes and 151 RNA genes. The P. aeruginosa YY322 genome encodes genes related to phenazine (phzABDEFGIMRS), hydrogen cyanide(HCN) (hcnABC), surfactin (srfAA), salicylate (pchA), biofilm formation (flgBCDEFGHIJKL, motAB, efp, hfq), and colonization (minCDE, yjbB, lysC). These results collectively indicated the role of P. aeruginosa YY322 in plant growth enhancement and biocontrol mechanisms. All in all, this study provides a theoretical basis for P. aeruginosa as the PGPR of saffron, paving the way for the subsequent development and utilization of microbial fertilizer.

The complete mitochondrial genome of Antestiopsis thunbergii (Gmelin, 1790) (Hemiptera: Pentatomidae) and its phylogenetic implication

The complete mitochondrial genome of Antestiopsis thunbergii was sequenced and was 15,391 bp long with a base composition of 43.03% A, 9.97% G, 13.04% C and 33.95% T. It contains 37 mitochondrial genes (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region). The genome structure, gene order, nucleotide composition, and codon usage of A. thunbergii were consistent with those of typical Pentatomidae insects. Phylogenetic analysis implied that A. thunbergii belonged to the family Pentatomidae, and each branch had a high Bayesian posterior probability value.

Identification of Diverse Toxin Complex Clusters and an eCIS Variant in Serratia proteamaculans Pathovars of the New Zealand Grass Grub (Costelytra Giveni) and Manuka Beetle (Pyronota Spp.) Larvae

The grass grub endemic to New Zealand, Costelytra giveni (Coleoptera: Scarabaeidae), and the manuka beetle, Pyronota festiva and P. setosa (Coleoptera: Scarabaeidae), are prevalent pest species. Through assessment of bacterial strains isolated from diseased cadavers of these insect species, 19 insect-active Serratia proteamaculans variants and a single Serratia entomophila strain were isolated. When independently bioassayed, these isolates differed in host range, the rate of disease progression, and 12-day mortality rates, which ranged from 60 to 100% of the challenged larvae. A Pyronota spp.-derived S. proteamaculans isolate caused a transient disease phenotype in challenged C. giveni larvae, whereby larvae appeared diseased before recovering to a healthy state. Genome sequence analysis revealed that all but two of the sequenced isolates contained a variant of the S. entomophila amber-disease-associated plasmid, pADAP. Each isolate also encoded one of seven distinct members of the toxin complex (Tc) family of insect-active toxins, five of which are newly described, or a member of the extracellular contractile injection (eCIS) machine family, with a new AfpX variant designated SpF. Targeted mutagenesis of each of the predicted Tc- or eCIS-encoding regions abolished or attenuated pathogenicity. Host-range testing showed that several of the S. proteamaculans Tc-encoding isolates affected both Pyronota and C. giveni species, with other isolates specific for either Pyronota spp. or C. giveni. The isolation of several distinct host-specific pathotypes of Serratia spp. may reflect pathogen-host speciation. IMPORTANCE New pathotypes of the insect pathogen Serratia, each with differing virulence attributes and host specificity toward larvae of the New Zealand manuka beetle and grass grub, have been identified. All of the Serratia proteamaculans isolates contained one of seven different insect-active toxin clusters or one of three eCIS variants. The diversity of these Serratia-encoded virulence clusters, resulting in differences in larval disease progression and host specificity in endemic scarab larvae, suggests speciation of these pathogens with their insect hosts. The differing virulence properties of these Serratia species may affect their potential infectivity and distribution among the insect populations. Based on their differing geographic isolation and pathotypes, several of these Serratia isolates, including the manuka beetle-active isolates, are likely to be more effective biopesticides in specific environments or could be used in combination for greater effect.

Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem

Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavors isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands were predicted for the five C. beijerinckii genomes. The existence of a large number of mobile genetic elements indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.

Isolation of a Virulent Aeromonas salmonicida subsp. masoucida Bacteriophage and Its Application in Phage Therapy in Turbot (Scophthalmus maximus)

Aeromonas salmonicida is an aquatic pathogen that can infect a variety of fish. Phage therapy has been applied to treat bacterial infections. In this study, we obtained three A. salmonicida subsp. masoucida phage isolates from sewage, and one phage (vB_AsM_ZHF) exhibited the best antibacterial effect, based on in vitro kinetics experiments. Sequencing indicated that the vB_AsM_ZHF genome is 161,887 bp (41.24% C+G content) with 237 predicted open reading frames. No antibiotic resistance or virulence genes were detected in the complete genome, which is a requirement for phage therapy safety. Intraperitoneal injection of phage vB_AsM_ZHF into turbot at 8 × 10⁴ PFU/fish rescued turbot from A. salmonicida subsp. masoucida injection and reduced the bacterial burden by 1 order of magnitude. Injection of vB_AsM_ZHF also decreased levels of inflammatory cell infiltration in muscle tissue, cytokines interleukin-1β (IL-1β), tumor necrosis factor alpha (TNF-α), and gamma interferon (IFN-γ) in serum and the expression of the inflammatory factors IL-1β, IL-6, IFN-γ, transforming growth factor β, TNF-α, and hepcidin in the liver, spleen, and head kidney of turbot. Phage vB_AsM_ZHF demonstrated antibacterial ability in vitro and in vivo and significantly reduced mortality in turbot challenged by A. salmonicida subsp. masoucida. This study revealed that phage vB_AsM_ZHF can effectively treat the infection caused by A. salmonicida subsp. masoucida in turbot. IMPORTANCE A. salmonicida is an aquatic pathogen that can infect different fish and causes economic loss to the global aquaculture industry. Clinical strains of A. salmonicida have developed multidrug resistance, and phage therapy is being evaluated for controlling bacterial infections. Phages are biological antibacterial agents and have the potential to be therapeutic agents against multidrug-resistant bacteria. In this study, three A. salmonicida subsp. masoucida phages were isolated from sewage, and their biological behaviors were characterized. The newly isolated phage vB_AsM_ZHF could inhibit A. salmonicida subsp. masoucida infection in vitro and in vivo, suggesting that it may be an alternative strategy to antibiotics for protecting fish against multidrug-resistant A. salmonicida subsp. masoucida in the aquaculture industry.

The complete mitochondrial genome of Ixodes vespertilionis (Acari: Ixodidae)

Ixodes vespertilionis is a tick parasitizing on the bodies of bats. In our study, the complete mitogenome of I. vespertilionis was determined by using Illumina sequencing technology. The mitogenome was 14,559 bp in size and was predicted to encode 37 genes including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region. The gene order of the mitogenome is identical to Argasidae and non-Australasian Prostriata. The phylogenetic analysis by the Maximum-likelihood method reveals that I. vespertilionis is phylogenetically closest to Ixodes simplex. These data provide novel reference for further studies on the population genetics and phylogenetics of ticks.

Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila

Background

How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS).

Results

We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT).

Conclusion

Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01124-y.

Genomic analysis of Burkholderia cenocepacia isolated from a liver abscess in a patient with cystic fibrosis

Burkholderia cenocepacia complex is associated with high transmissibility, virulence, and poor prognosis in cystic fibrosis (CF) patients. However, extrapulmonary infections are rare. We investigated the genome of a B. cenocepacia IIIA isolated from a liver abscess in a Brazilian CF patient and compared it to strain J2315. The whole genome was sequenced, and contigs were annotated by Rapid Annotation using Subsystem Technology. The Pathosystems Resource Integration Center was used to map antimicrobial and virulence genes. The genomic island (GIs) analysis was performed using two prediction methods, and the presence of putative plasmids and insertion sequences (ISs) was investigated. The isolate was confirmed as B. cenocepacia IIIA to ST-28 (ET12 lineage). A total of 64 genes for antimicrobial resistance and 47 genes related to virulence were identified. Among the virulence factors, there was a predominance of factors related to the invasion mechanism, to the flagellar biosynthesis protein, and to the RNA polymerase sigma factor for flagellar operon (cdpA). Two IS families (IS3 and IS5) and only one plasmid were found. On average 56 GIs were predicted by at least one of the methods applied. Comparative analysis showed resistance mechanisms and virulence factors revealing invasive determinants used by B. cenocepacia IIIA (ET12) in the process of disease spread to other infection sites (extrapulmonary) of highly virulent strains in CF patients.

Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity

Limosilactobacillus fermentum (ATCC 23271) was originally isolated from the human intestine and has displayed antimicrobial activity, primarily against Candida species. Complete genome sequencing and comparative analyses were performed to elucidate the genetic basis underlying its probiotic potential. The ATCC 23271 genome was found to contain 2,193,335 bp, with 2123 protein-coding sequences. Phylogenetic analysis revealed that the ATCC 23271 strain shares 941 gene clusters with six other probiotic strains of L. fermentum. Putative genes known to confer probiotic properties have been identified in the genome, including genes related to adhesion, tolerance to acidic pH and bile salts, tolerance to oxidative stress, and metabolism and transport of sugars and other compounds. A search for bacteriocin genes revealed a sequence 48% similar to that of enterolysin A, a protein from Enterococcus faecalis. However, in vitro assays confirmed that the strain has inhibitory activity on the growth of Candida species and also interferes with their adhesion to HeLa cells. In silico analyses demonstrated a high probability of the protein with antimicrobial activity. Our data reveal the genome features of L. fermentum ATCC 23271, which may provide insight into its future use given the functional benefits, especially against Candida infections.

Rejection of the reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum based on whole genome analysis

In 2014, Rahkila et al. transferred Leuconostoc gasicomitatum to Leuconostoc gelidum as L. gelidum subsp. gasicomitatum comb. nov. based on a 75 % DNA-DNA hybridization value. In the present study, the taxonomic status of L. gelidum subsp. gasicomitatum is re-evaluated by a polyphasic approach, including 16S rRNA, pheS, rpoA, recA, and atpA gene sequence analyses, phylogenomic treeing, analyses of ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization), fatty acid methyl ester analysis and a phenotypic characterization. On the basis of the ANI and dDDH values, we propose to reject the proposal of Rahkila et al. to reclassify L. gasicomitatum as L. gelidum subsp. gasicomitatum.

Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs

The increase of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) causes a threat to human health. LA-MRSA can be transmitted from animals to animal caretakers, which may further spread MRSA to communities and health care facilities. The objective of this work was to study the efficacy of phage treatment in the eradication of LA-MRSA from healthy carrier pigs. A total of 19 MRSA -positive weanling pigs were assigned to a test (n = 10) and a control group (n = 9). A phage cocktail containing three Staphylococcus phages, or a control buffer was administered to the nares and skin of the pigs three times every two days, after which the phage and MRSA levels in nasal and skin swab samples were monitored for a three-week period. The sensitivity of the strains isolated during the follow-up period to the phage cocktail and each phage individually was analyzed and the pig sera were tested for antibodies against the phages used in the cocktail. The phage treatment did not cause any side effects to the pigs. Phages were found in the skin and nasal samples on the days following the phage applications, but there was no reduction in the MRSA levels in the sampled animals. Phage-resistant strains or phage-specific antibodies were not detected during the experiment. The MRSA load in these healthy carrier animals was only 10-100 CFU/swab or nasal sample, which was likely below the replication threshold of phages. The effectiveness of phage treatment to eradicate MRSA from the pigs could thus not be (reliably) determined.

Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production

BACKGROUND

Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soil Clostridium isolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods.

RESULTS

Conditioned/spent media from all four Clostridium isolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth of Pseudomonas aeruginosa. FS01, FS2.2, and FS04 were active against Bacillus mycoides and FS03 reduced the growth of Bacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the species Paraclostridium bifermentans, Clostridium cadaveris, and Clostridium senegalense respectively, while FS03 may represent a novel species of the genus Clostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putative Clostridium toxin related genes in FS01 and FS2.2 genomes. No genes associated with the main Clostridium toxins were identified in the FS03 and FS04 genomes.

CONCLUSIONS

The presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonistic Clostridium spp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soil Clostridium spp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genus Clostridium.

Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems

Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.

The complete chloroplast genome of Saussurella borneensis (Orthoptera: Tetrigoidea) from China and its phylogenetic analysis

The mitochondrial genome (mitogenome) of Saussurella borneensis (Orthoptera: Tetrigoidea) was determined and analyzed. The complete mitochondrial genome is 16,006 bp in length, consisting of 37 genes, including 13 protein-coding (PCGs), 22 tRNA, 2 rRNA genes as well as an A + T-rich region. Ten PCGs initiated with a typical ATN codon (one with ATC, two with ATA, two with ATT, and five with ATG) and 13 terminated with complete stop codons. The overall nucleotide composition was 42.97% for A, 17.61% for C, 11.62% for G, and 27.8% for T. Phylogenetic analysis of S. borneensis fully resolved it in a basal branch sister to Tripetaloceroides tonkinensis. This data increase the bioinformatics of the Tetrigidae, and improves our understanding of the phylogenetic status of S. borneensis in the Tetrigoidea.

Proposal of Lactococcus garvieae subsp. bovis Varsha and Nampoothiri 2016 as a later heterotypic synonym of Lactococcus formosensis Chen et al. 2014 and Lactococcus formosensis subsp. bovis comb. nov

Currently, Lactococcus garvieae contains two subspecies: L. garvieae subsp. bovis and L. garvieae subsp. garvieae. In a study by Varsha and Nampoothiri, high pheS (99.7 %) and rpoA (99.6 %) sequence similarities indicated that L. garvieae subsp. bovis and Lactococcus formosensis probably have a close taxonomic relationship; low pheS (92.2 %) and rpoA (97.8 %) sequence similarities and relatively low DNA-DNA hybridization value (75.8 %) indicated that L. garvieae subsp. bovis and L. garvieae subsp. garvieae probably represent two different species. In the present study, the taxonomic relationships between L. garvieae subsp. bovis, L. garvieae subsp. garvieae and L. formosensis were re-examined based on sequence analyses of 16S rRNA, pheS, recA, rpoA and rpoB genes, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) values, average amino acid identity (AAI), fatty acid methyl ester analysis and phenotypic characterization. L. garvieae subsp. bovis LMG 30663^T exhibited 97.3 % ANI, 78.3 % dDDH and 96.4 % AAI values to L. formosensis NBRC 109475^T, higher than the threshold for species demarcation (95-96, 70 and 95-96 %, respectively), indicating that L. garvieae subsp. bovis LMG 30663^T and L. formosensis NBRC 109475^T belong to the same species. L. garvieae subsp. bovis LMG 30663^T had 91.2 % ANI, 43.3 % dDDH and 92.9-93.0% AAI values with the type strain of L. garvieae subsp. garvieae, indicating that they represent two different species. Because L. formosensis has been proposed and validated before L. garvieae subsp. bovis, L. garvieae subsp. bovis is transferred to L. formosensis as L. formosensis subsp. bovis comb. nov. The type strain of L. formosensis subsp. bovis is BSN307^T (=DSM 100577^T=MCC 2824^T=KCTC 21083^T=LMG 30663^T). The type strain of L. formosensis subsp. formosensis is 516^T (=NBRC 109475^T=BCRC 80576^T).

Spontaneous changes in somatic compatibility in Fusarium circinatum

Filamentous fungi grow by the elaboration of hyphae, which may fuse to form a network as a colony develops. Fusion of hyphae can occur between genetically different individuals, provided they share a common allele at loci affecting somatic compatibility. Diversity in somatic compatibility phenotypes reduces the frequency of hyphal fusion in a population, thereby slowing the spread of deleterious genetic elements such as viruses and plasmids, which require direct cytoplasmic contact for transmission. Diverse somatic compatibility phenotypes can be generated by recombining alleles through sexual reproduction, but this mechanism may not fully account for the diversity found in nature. For example, multiple compatibility phenotypes of Fusarium circinatum were shown to be associated with the same clonal lineage, which implies they were derived by a mutation rather than recombination through sexual reproduction. Experimental tests of this hypothesis confirmed that spontaneous changes in somatic compatibility can occur at a frequency between 5 and 8 per million spores. Genomic analysis of F. circinatum strains with altered somatic compatibility revealed no consistent evidence of recombination and supported the hypothesis that a spontaneous mutation generated the observed phenotypic change. Genes known to be involved in somatic compatibility had no mutations, suggesting that mutation occurred in a gene with an as yet unexplored function in somatic compatibility.

First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture

In this paper, we describe the first complete genome sequence of Providencia vermicola species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative P. vermicola P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including bla_CMY-6 and bla_NDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the bla_NDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.

Draft Genome Sequence of Stenotrophomonas maltophilia Strain PE591, a Polyethylene-Degrading Bacterium Isolated from Savanna Soil

We report the genome sequence of a polyethylene-degrading bacterial strain identified as Stenotrophomonas maltophilia strain PE591, which was isolated from plastic debris found in savanna soil. The genome was assembled in 16 scaffolds with a length of 4,751,236 bp, a GC content of 66.5%, and 4,432 predicted genes.

The complete mitochondrial genome of Haemaphysalis montgomeryi

The complete mitogenome of Haemaphysalis montgomeryi is reported for the first time in this study. The mitochondrial genome is 14,681 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The phylogenetic relations base on the maximum-likelihood (ML) method show that H. montgomeryi and the other members of the genus Haemaphysalis constitute a monophyletic group, confirming that H. montgomeryi belongs to the genus Haemaphysalis.

Genome analysis of Salmonella strains isolated from imported frozen fish in Burkina Faso

Purpose

Fish is an excellent source of protein and vitamins for humans, but improperly handled, fish can expose consumers to pathogenic bacteria. This study was aimed to isolate and characterize the genomes of Salmonella strains isolated from imported fish sold in the open market in Ouagadougou.

Methods

One hundred and fifty-nine fish were collected from open markets and were cultured for Salmonella. Antimicrobial susceptibility was determined by broth microdilution. Whole-genome sequencing was done to further study antibiotic resistance genes, plasmid replicons, and MSLT types. Serotyping was done using SeqSero 2.

Result

Out of the 159 fish samples analyzed, 30 (18.9%) were found to be contaminated with Salmonella. Among the isolated Salmonella strains, six different serotypes, Nima, Liverpool, Kokomlemle, Teshie, Derby, and Tennessee, were found using SeqSero2. Salmonella Tennessee was the predominant serotype. All the isolates possessed at least one resistance gene. The aac6-Iaa aminoglycoside resistance gene was the most prevalent gene found in the strains. The gene fosA7 was detected in three strains. All the S. Nima isolates were of Multilocus Sequence Type (MLST) 8086, S. Teshie isolate was ST 530; Liverpool was ST 1959; Derby was ST 7880; Kokomlemle was ST 2696. The Tennessee isolates gave two different STs including ST 8395 and 8398.

Conclusion

The presented results highlight the prevalence of Salmonella on imported fish purchased from the open markets. More attention should be paid regarding fish selling conditions in the country to prevent the potential health risk for consumers.

Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., isolated from traditional Chinese pickle and the gut of honeybee (Apis mellifera)

Thirteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that 12 of the 13 strains represented eight novel species belonging to the genera Apilactobacillus, Secundilactobacillus, Levilactobacillus and Lacticaseibacillus; strains HN36-1^T, 887-11^T, F79-211-2^T, 866-3^T, 6-5(1)^T, 13B17^T, 117-1^T and ZW152^T were designated as the type strains. Based upon the data of polyphasic characterization obtained in the present study, eight novel species, Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., are proposed and the type strains are HN36-1^T (=JCM 33867^T=CCTCC AB 2019385^T), 887-11^T (=NCIMB 15201^T=CCM 8950^T=JCM 33864^T=CCTCC AB 2018396^T), F79-211-2^T (=NCIMB 15254^T=JCM 33866^T=CCTCC AB 2019384^T), 866-3^T (=JCM 33863^T=CCTCC AB 2019383^T), 6-5(1)^T (=NCIMB 15229^T=CCM 8977^T=JCM 33564^T=CCTCC AB 2019168^T), 13B17^T (=NCIMB 15230^T=CCM 8979^T=JCM 33565^T=CCTCC AB 2019167^T), 117-1^T (=NCIMB 15232^T=CCM 8980^T=JCM 33567^T) and ZW152^T (=JCM 34363^T=CCTCC AB 2020299^T=LMG 32143^T=CCM 9110^T), respectively.

Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges

Two novel Rhodococcus strains, LHW50502^T and LHW51113^T, were isolated from marine sponges obtained on Xisha Island, Hainan Province, PR China. Rods and cocci, typical characteristics of the genus Rhodococcus, were observed. The strains contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall hydrolysates and galactose, arabinose, ribose and glucose as the whole-cell sugars. The major fatty acid identified was C_16 : 0. MK-8(H₄) was the predominat menaquinone of both strains. Stains LHW50502^T and LHW51113^T had almost identical (99.6 %) 16S rRNA gene sequences but shared relatively low similarities with previously characterized Rhodococcus species (well below 98.7 %). The results of phylogenetic analysis supported their closest relationship; however, the average nucleotide identity and digital DNA-DNA hybridization values between these two strains indicated that they belonged to distinct species. Taken together, the results of this study indicate that strains LHW50502^T and LHW51113^T represent two novel species of the genus Rhodococcus, for which the names Rhodococcus spongiicola sp. nov. (type strain LHW50502^T=DSM 106291^T=CCTCC AA 2018033^T) and Rhodococcus xishaensis sp. nov. (type strain LHW51113^T=DSM 106204^T=CCTCC AA 2018034^T) are proposed.

Whole Genome Analysis Detects the Emergence of a Single Salmonella enterica Serovar Chester Clone in Japan's Kanto Region

In Japan's Kanto region, the number of Salmonella enterica serovar Chester infections increased temporarily between 2014 and 2016. Concurrently with this temporal increase in the Kanto region, S. Chester isolates belonging to one clonal group were causing repetitive outbreaks in Europe. A recent study reported that the European outbreaks were associated with travelers who had been exposed to contaminated food in Morocco, possibly seafood. Because Japan imports a large amount of seafood from Morocco, we aimed to establish whether the temporal increase in S. Chester infections in the Kanto region was associated with imported Moroccan seafood. Short sequence reads from the whole-genome sequencing of 47 S. Chester isolates from people in the Kanto region (2014-2016), and the additional genome sequences from 58 isolates from the European outbreaks, were analyzed. The reads were compared with the complete genome sequence from a S. Chester reference strain, and 347 single nucleotide polymorphisms (SNPs) were identified. These SNPs were used in this study. Cluster and Bayesian cluster analyses showed that the Japanese and European isolates fell into two different clusters. Therefore, Φ PT and I A S values were calculated to evaluate genetic differences between these clusters. The results revealed that the Japanese and European isolates were genetically distinct populations. Our root-to-tip analysis showed that the Japanese isolates originating from one clone had accumulated mutations, suggesting that an emergence of this organism occurred. A minimum spanning tree analysis demonstrated no correlation between genetic and geographical distances in the Japanese isolates, suggesting that the emergence of the serovar in the Kanto region did not involve person-to-person contact; rather, it occurred through food consumption. The d N /d S ratio indicated that the Japanese strain has evolved under positive selection pressure. Generally, a population of bacterial clones in a reservoir faces negative selection pressure. Therefore, the Japanese strain must have existed outside of any reservoir during its emergence. In conclusion, S. Chester isolates originating from one clone probably emerged in the Kanto region via the consumption of contaminated foods other than imported Moroccan seafood. The emerging strain may have not established a reservoir for survival in the food supply chain resulting in its disappearance after 2017.

The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence

The reference sequences play an essential role in genome assembly, like type specimens in taxonomy. Those references are also samples obtained at some time and location with a specific method. How can we evaluate or discriminate uncertainties of the reference itself and assembly methods? Here we bootstrapped 50 random read data sets from a small circular genome of a Escherichia coli bacteriophage, phiX174, and tried to reconstruct the reference with 14 free assembly programs. Nine out of 14 assembly programs were capable of circular genome reconstruction. Unicycler correctly reconstructed the reference for 44 out of 50 data sets, but each reconstructed contig of the failed six data sets had minor defects. The other assembly software could reconstruct the reference with minor defects. The defect regions differed among the assembly programs, and the defect locations were far from randomly distributed in the reference genome. All contigs of Trinity included one, but Minia had two perfect copies other than an imperfect reference copy. The centroid of contigs for assembly programs except Unicycler differed from the reference with 75bases at most. Nonmetric multidimensional scaling (NMDS) plots of the centroids indicated that even the reference sequence was located slightly off from the estimated location of the true reference. We propose that the combination of bootstrapping a reference, making consensus contigs as centroids in an edit distance, and NMDS plotting will provide an evidential statistic way of genetic assembly for non-fragmented base sequences.

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene

Tests based on the d_N/d_S statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.

Bacteriophages fEV-1 and fD1 Infect Yersinia pestis

Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1.

The complete mitochondrial genome of Mactra quadrangularis (Mactridae)

The whole mitochondrial genome sequence of Mactra quadrangularis (Reeve, 1854) was determined. It had a total length of 16,848 bp and it contained 12 protein coding genes, 2 ribosome RNA genes, and 22 transfer RNA genes. The base composition was 25.75% A, 20.82% G, 11.53% C, and 41.90% T, respectively. Furthermore, state codon of ND4 was ATT; ND1 and CYTB were ATA; COX1 was GTG; ND5, COX2, ND4L, ND6, ND2, COX3, ATP6, and ND3 were ATG. Phylogenetic analysis demonstrated that M. quadrangularis was most closely related to Mactra chinensis. The mitochondrial genome will provide reference for the further investigation and research of M. quadrangularis.

Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From Egypt

In this study, multidrug-resistant (MDR) Escherichia coli isolates from retail food and humans assigned into similar Multilocus Sequence Types (MLST) were analyzed using whole genome sequencing (WGS). In silico analysis of assembled sequences revealed the existence of multiple resistance genes among the examined E. coli isolates. Of the six CTX-M-producing isolates from retail food, bla _CTX-M-14 was the prevalent variant identified (83.3%, 5/6). Two plasmid-mediated fosfomycin resistance genes, fosA3, and fosA4, were detected from retail food isolates (one each from chicken and beef), where fosA4 was identified in the chicken isolate 82CH that also carried the colistin resistance gene mcr-1. The bla _CTX-M-14 and fosA genes in retail food isolates were located adjacent to insertion sequences ISEcp1 and IS26, respectively. Sequence analysis of the reconstructed mcr-1 plasmid (p82CH) showed 96-97% identity to mcr-1-carrying IncI2 plasmids previously identified in human and food E. coli isolates from Egypt. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of chicken isolate 82CH, co-harboring mcr-1 and fosA4 genes, with a chicken E. coli isolate from China at the HC200 level (≤200 core genome allelic differences). As E. coli co-harboring mcr-1 and fosA4 genes has only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international E. coli lineages originating from both humans and food animals. Adopting WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens.

Isolation and plasmid characterisation of Salmonella enterica serovar Albany harbouring mcr-5 from retail chicken meat in Japan

The emergence of plasmid-mediated colistin resistance genes (mcr), which is occurring in numerous countries, is a worldwide concern, primarily because colistin is a last-resort antibiotic. Compared to E. coli, prevalence of mcr genes in Salmonella is unclear in Japan. Here we screened for mcr-1-5 genes in our collection of Salmonella strains isolated from retail meat products collected in Japan from 2012 through 2016. We found that Salmonella Albany strain 27A-368 encodes mcr-5 and that mcr genes were undetectable among the remaining 202 isolates. The resistance plasmid p27A-368 was transferred by conjugation to S. Infantis and was stably retained as a transconjugant. Whole-genome sequencing revealed that mcr-5 resided on a 115 kb plasmid (p27A-368). The plasmid backbone of p27A-368 is more similar to that of pCOV27, an ESBL-encoding plasmid recovered from avian pathogenic E. coli, rather than pSE13-SA01718 of S. Paratyphi B that encodes mcr-5. Further, mcr-5 is located on a transposon, and its sequence is similar to that of pSE13-SA01718. A phylogenetic tree based on single nucleotide variants implies a relationship between 27A-368 and S. Albany isolated in Southeast Asian countries.

Pangenome analysis and virulence profiling of Streptococcus intermedius

Background

Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank.

Results

We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an “open” pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB.

Conclusions

Based on the virulence gene content of 27 S. intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.

Empirical evaluation of methods for de novo genome assembly

Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and de novo assembly is a key initiative that has facilitated gene discovery and other studies. More powerful analytical algorithms are needed to work on the increasing amount of sequence data. We make a thorough comparison of the de novo assembly algorithms to allow new users to clearly understand the assembly algorithms: overlap-layout-consensus and de-Bruijn-graph, string-graph based assembly, and hybrid approach. We also address the computational efficacy of each algorithm's performance, challenges faced by the assem- bly tools used, and the impact of repeats. Our results compare the relative performance of the different assemblers and other related assembly differences with and without the reference genome. We hope that this analysis will contribute to further the application of de novo sequences and help the future growth of assembly algorithms.

Massive gene rearrangement in mitogenomes of phytoseiid mites

Mitochondrial (mt) gene sequences have been widely used to infer phylogeny in animals. The relative order of mt genes in the mitogenome can also be a useful marker for evolution, but the propensity of mt gene rearrangements vary tremendously among taxa. Ticks and mites in Acari exemplify this trend as some families retain the ancestral arthropod gene order, while others show highly divergent gene orders. Mites in Phytoseiidae, many of which are effective biological control agents, show some of the most divergent gene orders. However, the diversity of mitogenome order within this family is little known. We thus sequenced three mt genomes of phytoseiid mites from two of the most speciose genera: Amblyseius swirskii (Athias-Henriot), Amblyseius tsugawai (Ehara) and Neoseiulus womersleyi (Schicha). We find differences in mt GC skew and nucleotide composition, especially between N. womersleyi and the two Amblyseius species. Each species within Phytoseiidae (including three previously available sequences) present a unique gene order. Phytoseiid mitogenomes show some of the highest numbers of breakpoints when compared to the ancestral arthropod order (up to 33), as well as high numbers of breakpoints within the family (14-30). This suggests a history of massive, ongoing mitogenome rearrangements in the family. Phylogenetic analyses of mt sequences confirm that the degree of gene rearrangements follows phylogenetic relatedness. We discuss possible causes for the high degree of mt gene rearrangement within phytoseiid mites as well as selection in the mt and nuclear genome tied to the independent evolution of many diverse feeding strategies in the family. Finally, we suggest N. womersleyi should be used instead of the synonym Amblyseius pseudolongispinosus.

The complete chloroplast genome of Chimonobambusa hejiangensis

Chimonobambusa hejiangensis is of the unique edible bamboo specie of high quality in China. We studied the complete chloroplast(cp) genome of C. purpurea in this study. The cp genome of C. hejiangensis (GenBank accession: MW186792) was 138,911 bp in length, including a large single-copy (LSC) region of 82,498 bp, a small single-copy (SSC) region of 12,743 bp and a pair of inverted repeated (IR) regions of 21,835 bp. The genome contained 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Based on 39 cp genomes, we used the phylogenetic analysis to build phylogenetic tree, indicating that C. hejiangensis is closely related to C. tumidissinoda. Also, the phylogenetic relationship of lineages might be (Hsuehochloa + (((Shibataea clade + Arundinaria clade) + Indocalamus wilsonii) + ((Bergbambos + Indocalamus) + (((African alpine bamboos + Gaoligongshania) + (Chimonocalamus + Kuruna))+(Thamnocalamus + Phyllostachys clade))))). It could be devoted to phylogenetic analysis of Arundinarieae.

Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus

Bacillus cereus is a common food-borne pathogen that is responsible for important outbreaks of food poisoning in humans. Diseases caused by B. cereus usually exhibit two major symptoms, emetic or diarrheic, depending on the toxins produced. It is assumed that after the ingestion of contaminated vegetables or processed food, spores of enterotoxigenic B. cereus reach the intestine, where they germinate and produce the enterotoxins that are responsible for food poisoning. In our study, we observed that sporulation is required for the survival of B. cereus in leaves but is dispensable in ready-to-eat vegetables, such as endives. We demonstrate that vegetative cells of B. cereus that are originally impaired in sporulation but not biofilm formation are able to reach the intestine and cause severe disorders in a murine model. Furthermore, our findings emphasise that the number of food poisoning cases associated with B. cereus is underestimated and suggest the need to revise the detection protocols, which are based primarily on spores and toxins.

Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan

Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.

Five Mitochondrial Genomes of the Genus Eysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae)

Simple Summary

Pentatominae is the largest subfamily in the Pentatomidae, and most of its species are considered important agricultural pests. The phylogenetic relationships of tribes within Pentatominae remain controversial despite the fact that many studies have been performed using various molecular markers. In this study, five mitogenomes of the genus Eysarcoris were sequenced and analyzed, and the phylogenetic relationships of tribes within Pentatominae were reconstructed. The gene arrangement of the five mitochondrial genomes were found to be conserved and identical to other heteropteran mitogenomes. Differences in start codon usage and tandem repeats within control regions were found between E. gibbosus and the other four Eysarcoris species. In addition, the phylogenetic analyses showed that E. gibbosus is the first diverging clade within Eysarcorini. The results support the proposal to transfer E. gibbosus to the Stagonomus, another genus of Eysarcorini. Our results clarified the phylogenetic relationships among tribes of Pentatominae and laid a foundation for the further studies of Pentatominae.

Abstract

Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.

Molecular epidemiology of Enterobacter cloacae complex isolates with reduced carbapenem susceptibility recovered by blood culture

The Enterobacter cloacae complex (ECC) is one of the most common causes of bacteremia and leads to poor clinical outcomes. The aim of this study was to clarify the antimicrobial susceptibility profiles and genetic backgrounds of non-carbapenemase-producing reduced-carbapenem-susceptible (RCS) ECC blood isolates in Japan using agar dilution antimicrobial susceptibility testing, whole-genome sequencing, and quantitative polymerase chain reaction for assays of ampC, ompC and ompF transcripts. Forty-two ECC blood isolates were categorized into RCS and carbapenem-susceptible groups based on imipenem minimum inhibitory concentration. RCS ECC blood isolates belonged to distinct species and sequence types and produced varying class C β-lactamases. The E. roggenkampii, E. asburiae, and E. bugandensis isolates belonged only to the RCS group. Some E. hormaecheii ssp. steigerwaltii isolates of the RCS group exhibited AmpC overexpression caused by amino acid substitutions in AmpD and AmpR along with ompF gene downregulation. These findings suggest that non-carbapenemase-producing RCS ECC blood isolates are genetically diverse.

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria)

Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.

The complete plastome sequence of Pinellia peltata Pei (Araceae)

The complete plastome of Pinellia peltata is reported in this study. The whole plstome contains 164,293 bp, including a large single copy region (90,089 bp) and a small single copy region (24,871 bp), which were separated by a pair of inverted repeat regions (24,881 bp of IRB and 24,982 bp of IRA). Totally, 130 genes were identified, containing 86 coding-protein, 8 rRNA (4 rRNA species), and 36 tRNA genes. Phylogenetic analysis based on common protein coding genes of 10 Araceae species showed that P. peltata is original than other species in the genus Pinellia. The whole plastome of P. peltata and other species should facilitate further works for the genus Pinellia about genetic diversity, phylogenetic analysis, and so on.