Granulicatella adiacens Endocarditis of a Bioprosthetic Aortic Valve

Infective endocarditis (IE) is relatively uncommon; however, when it is diagnosed, it is usually among those with known cardiac valvular abnormalities. The most common pathogens that cause endocarditis are streptococci (mainly viridans), enterococci, and other streptococci species. An extremely rare pathogen that could cause IE is Granulicatella. This gram-positive coccus classically inhabits human mucosal surfaces and only rarely causes disease. We present an incredibly rare case of a 74-year-old female with a bioprosthetic aortic valve replacement, who presented with headache and weakness and was subsequently found to have recurrent Granulicatella adiacens infective endocarditis.

Development of a long-read next generation sequencing workflow for improved characterization of fastidious respiratory mycoplasmas

Mycoplasma cynos and Mycoplasma felis are often associated with canine and feline infectious respiratory disease in dogs and cats, respectively. Mycoplasmas have a reduced genome and dearth of many biosynthetic pathways, making them dependent on rich medium for growth. Due to this fastidious nature, mycoplasmas have been historically underdiagnosed. The aim of this study was to develop a cost-effective and accurate sequencing workflow for genotypic characterization of clinical isolates of M. cynos and M. felis using a rapid long-read sequencing platform. We explored the following critical aspects of bacterial whole genome sequencing, including: (i) five solid and liquid-based culture approaches based on a specialized media formulation for Mycoplasma culture, (ii) three DNA extraction methods modified for long-read sequencing purposes, and (iii) two de novo assembly platforms, Flye and Canu, as key components of a bioinformatics pipeline. DNA extraction method 1, a solid-phase and column-based kit with enzymatic lysis, provided the best DNA quality and concentration followed by high coverage and sequencing contiguity. This was obtained with a culture volume of 45 ml in modified Hayflick's broth incubated for 48 h. DNA extracted directly from colonies on agar or from small broth volumes (6 ml) did not meet the criteria required for long-read sequencing. Overall, Flye generated more contiguous assemblies than the Canu assembler and was more time efficient. This 4-5 day sample-to-sequence workflow provides the scientific and clinical communities with a more comprehensive tool than laborious conventional methods for complete genomic characterization of M. cynos and M. felis clinical isolates.

Proof of Concept of Culturomics Use of Time of Care

Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including Faecalibacterium prausnitzii, Akkermansia muciniphila, Christensenella minuta, and Phascolarctobacterium faecium. Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.

Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum

Candidatus Liberibacter solanacearum (Lso) haplotype D (LsoD) is a suspected bacterial pathogen, spread by the phloem-feeding psyllid Bactericera trigonica Hodkinson and found to infect carrot plants throughout the Mediterranean. Haplotype D is one of six haplotypes of Lso that each have specific and overlapping host preferences, disease symptoms, and psyllid vectors. Genotyping of rRNA genes has allowed for tracking the haplotype diversity of Lso and genome sequencing of several haplotypes has been performed to advance a comprehensive understanding of Lso diseases and of the phylogenetic relationships among the haplotypes. To further pursue that aim we have sequenced the genome of LsoD from its psyllid vector and report here its draft genome. Genome-based single nucleotide polymorphism analysis indicates LsoD is most closely related to the A haplotype. Genomic features and the metabolic potential of LsoD are assessed in relation to Lso haplotypes A, B, and C, as well as the facultative strain Liberibacter crescens. We identify genes unique to haplotype D as well as putative secreted effectors that may play a role in disease characteristics specific to this haplotype of Lso.

Potato purple top disease associated with the novel subgroup 16SrII-X phytoplasma

Potato (Solanum tuberosum) is a very economically important perennial tuberous crop in Saudi Arabia. Potato plants displaying symptoms associated with potato purple top disease, such as aerial tubers and purple and small leaves, were observed in Al-Bukairiyah, Fowlq and Buraydah, Al-Tarafiyah, Qassim governorate, Saudi Arabia. In this study, we examined samples taken from 12 symptomatic potato plants and confirmed the presence of phytoplasma DNA. Analysis of the 16S rRNA-encoding sequences revealed that the symptomatic plants were infected with phytoplasma belonging to the peanut witches'-broom group (16SrII). Sequencing of the 16S rRNA- encoding gene, computer-simulated RFLP analysis and phylogenetic analysis revealed the presence of a novel representative of the 16SrII-X subgroup. The present study identified potato plants as a novel host for novel phytoplasma strains belonging to the pigeon pea witches'-broom group in Saudi Arabia.

Parallel detection of lactobacillus and bacterial vaginosis-associated bacterial DNA in the chorioamnion and vagina of pregnant women at term

BACKGROUND

The majority of early preterm births are associated with intrauterine infections, which are thought to occur when microbes traffic into the uterus from the lower genital tract and seed the placenta. Bacterial vaginosis (BV) is associated with heterogeneous bacterial communities in the vagina and is linked to preterm birth. The extent to which trafficking into the uterus of normal and BV-associated vaginal bacteria occurs is unknown. The study objective was to characterize in parallel the distribution and quantities of bacteria in the vagina, uterus, and placental compartments.

METHODS

Pregnant women at term (≥37 weeks) presenting for delivery were recruited prospectively. Swabs were collected in parallel from the vagina, chorioamnion. Choriodecidual swabs were collected if a cesarean section was performed. Samples were analyzed by culture, broad-range 16S rRNA gene PCR, and bacterial species-specific quantitative PCR (qPCR) for DNA from Lactobacillus and a panel of BV-associated bacteria. Results were correlated with placental histopathology.

RESULTS

Of the 23 women enrolled, 15 were delivered by cesarean section (N = 10 without labor; N = 5 in labor) and eight were delivered vaginally. BV was diagnosed in two women not in labor. Placental histopathology identified chorioamnionitis or funisitis in six cases [1/10 (10%) not in labor; 5/13 (38%) in labor]. Among non-laboring women, broad-range 16S qPCR detected bacteria in the chorioamnion and the choriodecidua (4/10; 40%). Among laboring women, Lactobacillus species were frequently detected in the chorioamnion by qPCR (4/13; 31%). In one case, mild chorioamnionitis was associated with qPCR detection of similar microbes in the chorioamnion and vagina (e.g. Leptotrichia/Sneathia, Megasphaera), along a quantitative gradient.

CONCLUSIONS

Microbial trafficking of lactobacilli and fastidious bacteria into the chorioamniotic membranes and choriodecidua occurs at term in normal pregnancies. In one case, we demonstrated a quantitative gradient between multiple bacterial species in the lower genital tract and placenta. Not all bacterial colonization is associated with placental inflammation and clinical sequelae. Further studies of the role of placental colonization with Lactobacillus in normal pregnancy and fastidious bacteria in chorioamnionitis may improve prevention and treatment approaches for preterm labor.

Delineation of a novel subgroup 16SrXIII-J phytoplasma, a 'Candidatus Phytoplasma hispanicum'-related strain, based on computer-simulated RFLP and phylogenetic analysis

Symptoms of fruit phyllody and slow growth, which are suggestive of phytoplasma infection, were observed in strawberry plants cultivated in commercial fields. In order to provide evidence of association of phytoplasma with affected plants, assays for detecting and identifying were performed through computer-simulated restriction fragment length polymorphism (RFLP) and phylogenetic analysis. Total DNA was extracted from symptomatic and asymptomatic samples and used as template in nested PCR primed by the primers P1/Tint followed by R16F2n/16R2. Amplified DNA fragments of 1.2 kb from the 16S rRNA gene revealed the presence of phytoplasma in all symptomatic samples. Molecular detection was confirmed by electron transmission microscopy, which evidenced pleomorphic bodies in the phloem vessels. Nucleotide sequence representative of the strawberry phytoplasma shared 97.2 to 99 % similarity with phytoplasmas currently classified as members of the distinct subgroups within the 16SrXIII group. Similarity coefficient (F) values ranged from 0.70 to 0.92, indicating that strawberry phytoplasma delineates a new strain in addition to 'Candidatus Phytoplasma hispanicum'-related strains. The evolutionary tree displayed that this strain emerges as a new branch in relation to those previously described. The novel strain, designated SFP (strawberry fruit phyllody) phytoplasma represents the new 16SrXIII-J subgroup and its sequence, denominated SFP-Br02, was deposited in the GenBank database (EU719108). These findings contribute for the knowledge of the genetic diversity existing among members of the group 16SrXIII and establishes strawberry as an additional host of representatives of this group in Brazil.

Possible Role of Rickettsia felis in Acute Febrile Illness among Children in Gabon

Infection is widespread but most prevalent among young, rural residents with fever.

Rickettsia felis has been reported to be a cause of fever in sub-Saharan Africa, but this association has been poorly evaluated in Gabon. We assessed the prevalence of this bacterium among children <15 years of age in 4 areas of Gabon; the locations were in urban, semiurban, and rural areas. DNA samples from 410 febrile children and 60 afebrile children were analyzed by quantitative PCR. Overall, the prevalence of R. felis among febrile and afebrile children was 10.2% (42/410 children) and 3.3% (2/60 children), respectively. Prevalence differed among febrile children living in areas that are urban (Franceville, 1.3% [1/77]), semiurban (Koulamoutou, 2.1% [3/141]), and rural (Lastourville, 11.2% [15/134]; Fougamou, 39.7% [23/58]). Furthermore, in a rural area (Fougamou), R. felis was significantly more prevalent in febrile (39.7% [23/58]) than afebrile children (5.0% [1/20]). Additional studies are needed to better understand the pathogenic role of R. felis in this part of the world.

A simple and novel method for retrieval of Pasteurellaceae from swab samples collected in the field

Traditionally it has been difficult or impossible to collect and preserve bacterial samples of especially fastidious bacteria in mixed primary cultures, unless the samples could be transported to a laboratory within approximately 24 h. Therefore, a simple novel method for preserving swab samples until bacterial isolation can be completed in the laboratory was developed and evaluated. Pasteurellaceae bacteria were used as a representative for fastidious bacteria. A 7.5% glucose serum medium was used as freeze medium. Swab samples were soaked in the medium a maximum of 2 h after collection and stored at −20°C. As a control study, 15 samples were collected from the oral cavity of a captive brown bear. One was immediately plated, while the remaining 12 swabs were stored at −20°C for 7 days and multiples of 30 days up to 330 days prior to plating. Two samples were stored without the medium for 7 and 30 days prior to plating. From a field setting in Greenland, eight polar bear samples were collected and subsequently stored for 240 to 259 days at −20°C before incubation. Pasteurellaceae bacteria were isolated and genotyped from all samples stored in the freeze medium, indicating that the medium enabled the bacteria to survive for at least 330 days at −20°C. The 100% recovery of target organisms in the polar bear samples even following lengthy storage and transport demonstrates that the method is very useful under remote field conditions.