Pan-genome analysis is a powerful method to explore genomic heterogeneity and diversity of bacterial species. Here we present a pan-genome analysis of the genus
Francisella
, comprising a dataset of ...63 genomes and encompassing clinical as well as environmental isolates from distinct geographic locations. To determine the evolutionary relationship within the genus, we performed phylogenetic whole-genome studies utilizing the average nucleotide identity, average amino acid identity, core genes and non-recombinant loci markers. Based on the analyses, the phylogenetic trees obtained identified two distinct clades, A and B and a diverse cluster designated C. The sizes of the pan-, core-, cloud-, and shell-genomes of
Francisella
were estimated and compared to those of two other facultative intracellular pathogens,
Legionella
and
Piscirickettsia
.
Francisella
had the smallest core-genome, 692 genes, compared to 886 and 1,732 genes for
Legionella
and
Piscirickettsia
respectively, while the pan-genome of
Legionella
was more than twice the size of that of the other two genera. Also, the composition of the
Francisella
Type VI secretion system (T6SS) was analyzed. Distinct differences in the gene content of the T6SS were identified.
In silico
approaches performed to identify putative substrates of these systems revealed potential effectors targeting the cell wall, inner membrane, cellular nucleic acids as well as proteins, thus constituting attractive targets for site-directed mutagenesis. The comparative analysis performed here provides a comprehensive basis for the assessment of the phylogenomic relationship of members of the genus
Francisella
and for the identification of putative T6SS virulence traits.
The Hypoxylaceae (Xylariales, Ascomycota) is a diverse family of mainly saprotrophic fungi, which commonly occur in angiosperm-dominated forests around the world. Despite their importance in forest ...and plant ecology as well as a prolific source of secondary metabolites and enzymes, genome sequences of related taxa are scarce and usually derived from environmental isolates. To address this lack of knowledge thirteen taxonomically well-defined representatives of the family and one member of the closely related Xylariaceae were genome sequenced using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing. The workflow leads to high quality draft genome sequences with an average N50 of 3.0 Mbp. A backbone phylogenomic tree was calculated based on the amino acid sequences of 4912 core genes reflecting the current accepted taxonomic concept of the Hypoxylaceae. A Percentage of Conserved Proteins (POCP) analysis revealed that 70% of the proteins are conserved within the family, a value with potential application for the definition of family boundaries within the order Xylariales. Also,
Hypomontagnella spongiphila
is proposed as a new marine derived lineage of
Hypom. monticulosa
based on in-depth genomic comparison and morphological differences of the cultures. The results showed that both species share 95% of their genes corresponding to more than 700 strain-specific proteins. This difference is not reflected by standard taxonomic assessments (morphology of sexual and asexual morph, chemotaxonomy, phylogeny), preventing species delimitation based on traditional concepts. Genetic changes are likely to be the result of environmental adaptations and selective pressure, the driving force of speciation. These data provide an important starting point for the establishment of a stable phylogeny of the Xylariales; they enable studies on evolution, ecological behavior and biosynthesis of natural products; and they significantly advance the taxonomy of fungi.
Four strains belonging to the family of
were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as ...Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2
, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as
. The sequence similarity of these three ISS strains, designated as IF7SW-B2
, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for
gene, with the closest being
SE2.11
. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of
The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described
species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus
The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble
and
since they assimilate similar sugars as sole carbon substrate when compared to other
species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C
-ω7
and C
-ω6
. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2
, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus
, and the name
sp. nov. is proposed. The type strain is IF7SW-B2
(NRRL B-65601
and LMG 32165
).
Introduction and hypothesis
Vaginal delivery may lead to levator ani muscle (LAM) injury or avulsion. Episiotomy may reduce obstetric anal sphincter injury in operative vaginal delivery, but may ...increase the risk of LAM injury. Our aim was to assess whether lateral episiotomy in vacuum extraction (VE) in primiparous women causes LAM injury.
Methods
A prospective cohort study of 58 primiparous women with episiotomy nested within an ongoing multicenter randomized controlled trial of lateral episiotomy versus no episiotomy in VE (EVA trial) was carried out in Sweden. LAM injury was evaluated using 3D endovaginal ultrasound 6–12 months after delivery and Levator Ani Deficiency (LAD) score. Episiotomy scar properties were measured. Characteristics were described and compared using Chi-squared tests. We stipulated that if a lateral episiotomy cuts the LAM, ≥50% would have a LAM injury. Among those, ≥50% would be side specific. We compared the observed prevalence with a test of one proportion.
Results
Twelve (20.7%, 95% CI 10.9–32.9) of 58 women had a LAD (
p
< 0.001, compared with the stipulated 50%). Six (50.0%, 95% CI 21.1% to 78.9%) of 12 women had a LAD on the episiotomy side, including those with bilateral LAD (
p
= 1.00). Two (16.7%, 95% CI 2.1% to 48.4%) of 12 women had a LAD exclusively on the episiotomy side (
p
= 0.02).
Conclusions
There was no excessive risk of cutting the LAM while performing a lateral episiotomy. LAD was not seen in women with episiotomies shorter than 18 mm.
spp. have primarily been reported as non-pathogenic, plant-probiotic bacteria, despite the presence of some opportunistic human pathogens in the genus. Here, three Gram-stain negative, rod-shaped, ...non-spore-forming bacteria, designated as strains CPCC 101365
, CPCC 101269
, and CPCC 101426 were isolated from surface-sterilized medicinal plant roots of a mulberry plant in Chuxiong of the Yunnan Province, freshwater from Erhai Lake in the Yunnan Province, and sandy soils in the Badain Jaran desert in Inner Mongolia Autonomous Region, China, respectively. The 16S rRNA gene sequences analysis of these isolates in comparison with sequences from the GenBank database indicated that they belong to the genus
, with nucleotide similarities of 96.52-99.92% to identified
members. Phylogenetic analysis based on 16S rRNA gene and genome sequences confirmed that the isolates are members of the genus
. Values for genomic average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; < 70%) indicated that strains CPCC 101365
and CPCC 101269
were well-differentiated from validly described
species, while strain CPCC 101426 shared high ANI (97.7%) and dDDH (78.3%) identity with its closest phylogenetic neighbor,
JCM 13256
. The three genomes were approximately 3.1-4.0 Mbp in size and their G + C content ranged in 66.2-70.2%, with values slightly differing between CPCC 101365
(3.4 Mbp; 70.2%), CPCC 101269
(4.0 Mbp; 66.4%), and CPCC 101426 (3.1 Mbp; 66.2%). Genes encoding enzymes involved in the biosynthesis of
(IAA) and siderophores were identified in the genomes of the three isolates, suggesting that these strains might serve roles as plant-growth promoting microorganisms. The polar lipid fractions of the three isolates primarily comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The predominant cellular fatty acid was iso-C
:
, with moderate amounts of antesio-C
, iso-C
, iso C
9c/C
10-methyl, iso-C
, and C
7
/C
6
. These results indicated that polyphasic characteristics of strains CPCC 101365
and CPCC 101269
differed from other identified
species and that strain CPCC 101426 was affiliated with the species
. Accordingly, two novel species of the genus
were consequently proposed, corresponding to
sp. nov. (type strain CPCC 101365
= DY006
= KCTC 82900
) and
sp. nov. (type strain CPCC 101269
= K32
= KCTC 82901
).
Members of the genus
, and particularly
, are opportunistic human pathogens, but not enough research has evaluated the identification of environmental
spp. However, most
spp. serves as plant-probiotic bacteria.In this study, we obtained and characterized three
strains from different ecosystems. Based on phenotypic differences, chemotaxonomic properties, ANI and dDDH identity values, and phylogenetic analyses, two novel
species are proposed for the strains identified here. The encoding genes related to plant-growth promotion in the genomes of the newly recovered
spp. were retrieved. Follow-on experiments confirmed that these strains produced the important plant hormone IAA. Thus, these
spp. could considerably contribute to shaping and maintaining ecological stability in plant-associated environments, particularly while acting as plant-probiotic microorganisms.
Obstetrical levator ani muscle avulsion is detected after 10%–30% of vaginal deliveries and is associated with pelvic organ prolapse later in life. However, the mechanism by which levator avulsion ...may contribute to prolapse is unknown.
This study investigated the extent by which size of the levator hiatus and pelvic muscle weakness may explain the association between levator avulsion and pelvic organ prolapse.
This was a supplementary study of a longitudinal cohort of parous women enrolled 5–10 years after first delivery and assessed annually for prolapse (defined as descent beyond the hymen) for up to 9 annual visits. For this substudy, vaginally parous participants were assessed for levator avulsion using 3-dimensional transperineal ultrasound. Ultrasound was performed at a median interval of 11 years from delivery. Ultrasound volumes also were used to measure levator hiatus area with Valsalva. Pelvic muscle strength was measured with perineometry. Women with and without pelvic organ prolapse were compared for levator avulsion, levator hiatus area, and pelvic muscle strength, using multivariable logistic regression yielding a measure of mediation. Bootstrap methods were used to calculate the confidence interval corresponding to the measure of mediation by hiatus area and pelvic muscle strength.
Prolapse was identified in 109 of 429 (25%) and was significantly associated with levator avulsion (odds ratio, 4.17; 95% confidence interval, 2.28–7.31). Prolapse also was associated with levator hiatus area (odds ratio, 1.52 per 5 cm2; 95% confidence interval, 1.34–1.73) and inversely with muscle strength (odds ratio, 0.87 per 5 cm H2O; 95% confidence interval, 0.81–0.94). In a multivariable logistic model including levator avulsion, levator hiatus area, and strength, the association between levator avulsion and prolapse was substantially attenuated and indeed was no longer statistically significant (odds ratio, 1.75; 95% confidence interval, 0.91–3.39). Hiatus area and strength mediated 61% (95% confidence interval, 34%–106%) of the association between avulsion and prolapse. Furthermore, since the 95% confidence interval for this estimate contained 100%, it cannot be ruled out that the 2 markers fully mediate the effect of avulsion on prolapse.
The strong association between pelvic organ prolapse and levator avulsion can be explained to a large extent by a larger levator hiatus and weaker pelvic muscles after levator avulsion.
Disease outbreaks of bacterial leaf spot and blight of pepper and tomato often occur in both transplant- and field-production systems worldwide. In some cases, the outbreaks are caused by novel ...bacterial species. Characterization of these novel bacterial species are critical in developing diagnostic assays and identifying management options for pathogen monitoring and sustainable production, respectively. We characterized strains belonging to novel
Pseudomonas
species that are responsible for outbreaks in pepper and tomato both in transplant-houses and in production fields in Georgia, USA. Phylogenomic analyses and whole genome sequence indices demonstrated that the pepper and tomato strains belonged to
P. capsici
. The whole-genome comparison revealed that 13
Pseudomonas
strains from diverse isolation sources that were curated in NCBI were indeed
P. capsici
indicating a potential wide-host range for this bacterial species. Our greenhouse-based host-range assay also indicated that
P. capsici
strains were pathogenic on pepper, tomato, eggplant, cabbage, lettuce, and watermelon corroborating a wide-host-range. A phylogenetic tree inferred from the whole genome sequence data showed that the
P. capsici
strains from Georgia (pepper and tomato) were genetically diverse, and were closely related to tomato
P. capsici
strains from Florida. Genomic presence of traditional bacterial virulence factors in
P. capsici
strains was also determined.
Pseudomonas
capsici
strains encode one set of type I secretion system, two sets of type II secretion systems, one set of type III secretion system, two sets of type V secretion systems, three sets of type VI secretion systems, and various secondary metabolite gene clusters including lipopeptides. In
in-vitro
assays, it was demonstrated that six out of seven
P. capsici
strains (pepper and tomato strains from Georgia) were not sensitive to 0.8 mM CuSO
4
. When the genomes of copper-tolerant strains were compared with the copper-sensitive strains, it was observed that the former strains encode a cluster of genes related to copper tolerance, which were absent in the genomes of copper-sensitive strains. Considering the ability of
P. capsici
strains to infect a range of vegetable hosts and possession of a wide range of bacterial virulence factors, secondary metabolites, and copper-tolerance genes, we envision that the management of this pathogen might potentially be a challenge.
Introduction
Levator ani muscle avulsions potentially increase recurrence after anterior colporrhaphies. We aimed at evaluating the impact of avulsions on anatomical and patient‐reported outcomes ...1 year after the Manchester procedure for primary anterior compartment pelvic organ prolapse.
Material and methods
Prospective cohort study of 189 women undergoing the Manchester procedure between October 2014 and January 2017. Avulsions were diagnosed by transperineal ultrasound. Women with and without avulsions were compared for 1‐year postoperative outcomes; Pelvic Organ Prolapse Quantification measurements, subjective satisfaction (1—worse to 4—cured), failure (new prolapse treatment), response to validated questionnaires on pelvic floor distress and sexual function, and a composite outcome (subjectively cured and optimal anterior compartment outcome (stage 0‐I)). Optimal mid‐compartment outcome was defined as cervix ≥5 cm above the hymen. Factors potentially associated with poor anatomical outcomes (anterior compartment stage ≥II) or pelvic floor distress were analyzed using regression analyses.
Results
Fewer women with avulsions (present in 50.8%) obtained optimal mid‐compartment outcomes (88.2% vs 77.1%; P = 0.05). The groups were otherwise similar in terms of mid‐compartment reduction, anterior compartment results, failure rate, subjective satisfaction, pelvic floor/sexual symptoms, and combined optimal subjective and anatomical outcome. Only preoperative anterior compartment stage ≥III was associated with poor anatomical outcome (P < 0.01). A high preoperative symptom score was associated with a high postoperative symptom score (P < 0.001).
Conclusions
Although fewer women with avulsions obtained optimal mid‐compartment results, avulsions had no impact on other anatomical or symptomatic outcomes 1 year after the Manchester procedure for primary anterior compartment prolapse.
Background
Puborectalis muscle rupture usually arises from peri-partum perineal trauma and may result in anterior, middle compartment prolapses, posterior compartment prolapse which includes ...rectocele and rectal prolapse, with or without associated anal sphincter damage. Patients with puborectalis muscle and levator ani rupture may present some form of incontinence or evacuation disorder, sexual dysfunction or pelvic organ descent. However, the literature on this subject is scarce. The aim of our study was to evaluate management and treatment of functional disorders associated with puborectalis and/or pubococcygei rupture at the level of the insertion in the pubis in a cohort of patients referred to a tertiary care coloproctology center.
Methods
We conducted a prospective cohort study of patients with levator ani and puborectalis muscle avulsion in the Proctology and Pelvic Floor Unit, Division of Digestive Surgery of the University Hospitals of Geneva from January 2001 to November 2018. Clinical examination, anoscopy and ultrasound were performed on a routine basis. Rupture of the levator ani muscle was diagnosed by clinical examination and ultrasound. A Wexner incontinence score was completed before and 6 months after surgery. Levator ani muscle repair was performed using a transvaginal approach.
Results
Fifty-two female patients (median age 56 ± 11.69 SD years, range 38–86 years) were included in the study. Thirty-one patients (59.6%) had anal incontinence, 25 (48.1%) urinary incontinence, 28 (53.9%) dyschezia (obstructive defecation or excessive straining to defecate), 20 (38.5%) dyspareunia, 17 (32.7%) colpophony, and 13 (25.0%) impaired sensation during sexual intercourse. Deviation of the anus on the side opposite the lesion was observed in 50 patients (96.2%), confirmed with clinical examination and both endoanal and perineal ultrasound. Out of these 52 patients, levator ani rupture (including puborectalis rupture) were categorized into right sided, 43 (82.69%), left sided, 7 (13.46%) and bilateral, 2 (3.85%). Levator ani muscle repair was performed in all patients, associated with posterior repair and levatorplasty in 26 patients (50%) and with sphincteroplasty in 34 patients (63.4%). Four patients (7.7%) experienced postoperative complications: significant postoperative pain (
n
= 3; 5.77%), urinary retention (
n
= 2; 3.85%), hematoma (
n
= 1; 1.92%), and perineal abscess (
n
= 1; 1.92%). Forty-one patients (78.8%) had full restoration of normal puborectalis muscle function (Wexner score: 0/20) after surgery, and overall, all patients had an improvement in the Wexner score and in sexual function. Dyschezia was reported by 28 patients (53.9%) preoperatively, resolved in 18 (64.3%) and improved by 50% or more in 10 (35.71%).
Conclusions
Diagnosis of levator ani and puborectalis muscle rupture requires careful history taking, clinical examination, endoanal and perineal ultrasound. Surgical repair improved anal continence as well as sexual function in all patients. Transvaginal levator ani repair seems to be well tolerated with good short-term results.
PDF
