Sequence of a Coxiella endosymbiont of the tick Amblyomma nuttalli suggests a pattern of convergent genome reduction in the Coxiella genus.

Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to the Coxiella genus, which also includes the human pathogen Coxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete co-cladogenesis with the tick hosts. Here we report the genome sequence of a novel Coxiella, endosymbiont of the African tick Amblyomma nuttalli, and the ensuing comparative analyses. Its size (~1 Mb) is intermediate between symbionts of Rhipicephalus species and other Amblyomma species. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent of Coxiella burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous among Coxiella endosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities among Coxiella endosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects

Molecular identification of Contracaecum rudolphii A and B (Nematoda: Anisakidae) from cormorants collected in a freshwater ecosystem of the pre-alpine area in Northern Italy

Contracaecum rudolphii (s.l.) is a complex of sibling species with different genetic structure and ecological preference. This study reports the presence of specimens of Contracaecum rudolphii (s.l.) from sedentary and wintering cormorants (Phalacrocorax carbo sinensis) from the pre-mountain area of the Alps in Northern Italy, an important crossroads for most of the bird migration routes. A total of 48 specimens of cormorants collected from two adjacent freshwater habitats were analysed and C. rudolphii nematodes were retrieved in 100% of the examined specimens. A subsamples of 115 C. rudolphii individuals were genetically characterized and found to belong to the sibling species C. rudolphii B (n = 90) and C. rudolphii A (n = 25). C. rudolphii B were retrieved from both locations and included adults as well as larvae, while only adults of C. rudolphii A were detected, and in just one location. As expected for a freshwater environment, C. rudolphii B constitutes the largest sibling fraction, indicating that this likely is the endemic species, while cormorants originating from the breeding brackish lagoons and marine coastal environments of central and northern Europe could have brought C. rudolphii A from their breeding sites or migration stopovers

Multiple Klebsiella pneumoniae KPC Clones Contribute to an Extended Hospital Outbreak

The circulation of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant problem worldwide. In this work we characterize the isolates and reconstruct the spread of a multi-clone epidemic event that occurred in an Intensive Care Unit in a hospital in Northern Italy. The event took place from August 2015 to May 2016 and involved 23 patients. Twelve of these patients were colonized by CRKP at the gastrointestinal level, while the other 11 were infected in various body districts. We retrospectively collected data on the inpatients and characterized a subset of the CRKP isolates using antibiotic resistance profiling and whole genome sequencing. A SNP-based phylogenetic approach was used to depict the evolutionary context of the obtained genomes, showing that 26 of the 32 isolates belong to three genome clusters, while the remaining six were classified as sporadic. The first genome cluster was composed of multi-resistant isolates of sequence type (ST) 512. Among those, two were resistant to colistin, one of which indicating the insurgence of resistance during an infection. One patient hospitalized in this period was colonized by two strains of CRKP, both carrying the blaKPC gene (variant KPC-3). The analysis of the genome contig containing the blaKPC locus indicates that the gene was not transmitted between the two isolates. The second infection cluster comprised four other genomes of ST512, while the third one (ST258) colonized 12 patients, causing five clinical infections and resulting in seven deaths. This cluster presented the highest level of antibiotic resistance, including colistin resistance in all 17 analyzed isolates. The three outbreaking clones did not present more virulence genes than the sporadic isolates and had different patterns of antibiotic resistance, however, were clearly distinct from the sporadic ones in terms of infection status, being the only ones causing overt infections

SeqDeχ : a sequence deconvolution tool for genome separation of endosymbionts from mixed sequencing samples

In recent years, the advent of NGS technology has made genome sequencing much cheaper than in the past; the high parallelization capability and the possibility to sequence more than one organism at once have opened the door to processing whole symbiotic consortia. However, this approach needs the development of specific bioinformatics tools able to analyze these data. In this work, we describe SeqDex, a tool that starts from a preliminary assembly obtained from sequencing a mixture of DNA from different organisms, to identify the contigs coming from one organism of interest. SeqDex is a fully automated machine learning-based tool exploiting partial taxonomic affiliations and compositional analysis to predict the taxonomic affiliations of contigs in an assembly. In literature, there are few methods able to deconvolve host-symbiont datasets, and most of them heavily rely on user curation and are therefore time consuming. The problem has strong similarities with metagenomic studies, where mixed samples are sequenced and the bioinformatics challenge is trying to separate contigs on the basis of their source organism; however, in symbiotic systems, additional information can be exploited to improve the output. To assess the ability of SeqDex to deconvolve host-symbiont datasets, we compared it to state-of-the-art methods for metagenomic binning and for host-symbiont deconvolution on three study cases. The results point out the good performances of the presented tool that, in addition to the ease of use and customization potential, make SeqDex a useful tool for rapid identification of endosymbiont sequences

Description of klebsiella spallanzanii sp. Nov. and of klebsiella pasteurii sp. nov

Klebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), Klebsiella oxytoca (Ko2), K. huaxiensis (Ko8) and K. grimontii (Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human faeces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4 and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T, DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T, DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow faeces and farm surfaces, while strains of K. pasteurii were found in faecal carriage from humans, cows and turtles

Molecular screening for bacterial pathogens in ticks (Ixodes ricinus) collected on migratory birds captured in northern Italy

Migratory birds have an important role in transporting ticks and associated tick-borne pathogens over long distances. In this study, 2,793 migratory birds were captured by nets in a ringing station, located in northern Italy, and checked for the presence of ticks. Two-hundred and fifty-one ticks were identified as nymphs and larvae of Ixodes ricinus (Linnaeus, 1758) and they were PCR-screened for the presence of bacteria belonging to Borrelia burgdorferi sensu lato, Rickettsia spp., Francisella tularensis and Coxiella burnetii. Four species of Borrelia (B. garinii, B. afzelii, B. valaisiana and B. lusitaniae) and three species of Rickettsia (R. monacensis, R. helvetica and Candidatus Rickettsia mendelii) were detected in 74 (30%) and 25 (10%) respectively out of 251 ticks examined. Co-infection with Borrelia spp. and Rickettsia spp. in the same tick sample was encountered in 7 (7%) out of the 99 infected ticks. We report for the first time the presence of Candidatus Rickettsia mendelii in I. ricinus collected on birds in Italy. This study, besides confirming the role of birds in dispersal of I. ricinus, highlights an important route by which tick-borne pathogens might spread across different countries and from natural environments towards urbanised areas

The Genomes of Four Meyerozymacaribbica Isolates and Novel Insights into the Meyerozymaguilliermondii Species Complex

Yeasts of the Meyerozyma guilliermondii species complex are widespread in nature and can be isolated from a variety of sources, from the environment to arthropods to hospital patients. To date, the species complex comprises the thoroughly studied and versatile M. guilliermondii, and the hard to distinguish M. caribbica, and Candida carpophila Here we report the whole-genome sequencing and de novo assembly of four M. caribbica isolates, identified with the most recent molecular techniques, derived from four Diptera species. The four novel assemblies present reduced fragmentation and comparable metrics (genome size, gene content) to the available genomes belonging to the species complex. We performed a phylogenomic analysis comprising all known members of the species complex, to investigate evolutionary relationships within this clade. Our results show a compact phylogenetic structure for the complex and indicate the presence of a sizable core set of genes. Furthermore, M. caribbica, despite a broad literature on the difficulties of discerning it from M. guilliermondii, seems to be more closely related to C. carpophila Finally, we believe that there is evidence for considering these four genomes the first published for the species M. caribbica Raw reads and assembled contigs have been made public to further the studies on these organisms

Draft Genome Sequence of Clostridium tyrobutyricum Strain DIVETGP, Isolated from Cow's Milk for Grana Padano Production

We announce the draft genome sequence of Clostridium tyrobutyricum strain DIVETGP. This strain was isolated from cow's milk used for Grana Padano cheese production. The genome was obtained using Illumina HiSeq technology and comprises 45 contigs for 3,018,999\ua0bp, with a G+C content of 30.8%

Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis

We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n = 15) and food, feed, animal, and environmental sources (n = 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB-BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system