Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans—the main lineage found in Rio de Janeiro hospitals—to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.

Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South Africa

Meat products have been implicated in many listeriosis outbreaks globally, however there is a dearth of information on the diversity of L. monocytogenes isolates circulating in food products in South Africa. The aim of this study was to investigate the population structure of L. monocytogenes isolated in the meat value chain within the South African market. Based on whole-genome sequence analysis, a total of 217 isolates were classified into two main lineage groupings namely lineages I (n = 97; 44.7%) and II (n = 120; 55.3%). The lineage groups were further differentiated into IIa (n = 95, 43.8%), IVb (n = 69, 31.8%), IIb (n = 28, 12.9%), and IIc (n = 25, 11.5%) sero-groups. The most abundant sequence types (STs) were ST204 (n = 32, 14.7%), ST2 (n = 30, 13.8%), ST1 (n = 25, 11.5%), ST9 (n = 24, 11.1%), and ST321 (n = 21, 9.7%). In addition, 14 clonal complex (CCs) were identified with over-representation of CC1, CC3, and CC121 in “Processed Meat-Beef”, “RTE-Poultry”, and “Raw-Lamb” meat categories, respectively. Listeria pathogenic islands were present in 7.4% (LIPI-1), 21.7% (LIPI-3), and 1.8% (LIPI-4) of the isolates. Mutation leading to premature stop codons was detected in inlA virulence genes across isolates identified as ST121 and ST321. The findings of this study demonstrated a high-level of genomic diversity among L. monocytogenes isolates recovered across the meat value chain control points in South Africa.

Variability of the Bacillus anthracis tryptophan operon

BackgroundBacillus anthracis is a causal agent of a zoonotic disease relevant for many countries, and is an agent of bioterrorism. Meanwhile, the reasons for the dependence on tryptophan of some strains with altered virulence have not been established with an almost complete absence of information on the tryptophan operon of this pathogen. In this study, we report gene variability and the structure of the tryptophan operon in B. anthracis strains of the three main lineages.ResultsFor in silico analysis we used 112 B. anthracis genomes, including 68 of those available at the GenBank database and 44 sequenced at our institute. The B. anthracis tryptophan operon has an ancestral structure with a complete set of seven partially overlapping genes. The results show that the variability of all seven tryptophan operon genes is determined by the presence of single nucleotide polymorphisms and InDels. The trpA genes of strains of the main lineage B and trpG genes of strains of the C lineage are pseudogenes and the proteomes lack the corresponding enzymes of the biosynthetic pathway, which may explain the dependence of the strains of line B on tryptophan. ConclusionIn this study, the differences in tryptophan operon genes for B. anthracis strains belonging to different main lineages were demonstrated for the first time. Mutation in the gene of the tryptophan synthase subunit alpha can explain the dysfunction of this enzyme and the dependence on tryptophan in strains of the main lineage B. Identified features suggest a further study of the dependence on tryptophan in B. anthracis strains of the main lineage B and may be of interest from the point of view of intraspecific evolution of the anthrax pathogen.

Portraits of the grand knez Vukan in the endowments of Nemanjić's family in the 13th century

The portrait of grand knez Vukan, the only modern and fragmentarily preserved one, was located on the North wall of the tower of the main entrance to the Studenica monastery. It is assumed that there was a composition on the North wall of the main entrance in which Simeon with his three sons approaches the Mother of God and Christ. There is a possibility that Vukan, as one of the ktetors of Studenica, was shown in the ktetor's composition. Since then, Vukan has been shown only with Stefan in compositions that illustrate scenes from the Life of Saint Simeon, in Radoslav's narthex and monasteries Gradac and Sopoćani. Due to the usurpation of Stefan's supremacy, Vukan became a sinner who broke his father's vow to live in harmony with his brother. However, after the end of the civil war, the brothers reconciled: Vukan repented for everything that he had done, and Stefan forgave him everything. The peace between them was established by Sava's arrival with the relics of Saint Simeon. Saint Sava arranged the reconciliation of the brothers, and he laid the ideal of brotherly love and harmony in the basis of the ruling ideology of Nemanjić's dynasty. He wanted to emphasize this through paintings, fitting the portraits of his brothers into the iconographic program of the frescoes of the Studenica monastery, and he introduced their names in the founder's inscription. After the frescoes created in 1208/9. Vukan was painted where it made sense, as someone who, in agreement with his brother Stefan, transfers theirs father's relics. Since he does not belong to the main lineage of the dynasty, his portrait wasn't painted in the family compositions of Nemanjićs in the 13th century.

A new genus of cynipid inquiline, Lithosaphonecrus Tang, Melika & Bozsó (Hymenoptera: Cynipidae: Synergini), with description of four new species from Taiwan and China

The cynipid inquilines genus Saphonecrus is known to be a polyphyletic group with distinct lineages. One lineage is associated with Synophrus in the Western Palaearctic on section Cerris oaks. Another involves the type species of Saphonecrus, S. connatus, and represents a distinct and probably early-diverging lineage with a Palaearctic distribution on white oaks. The third main lineage is predominantly Asian, and associated with Quercus subgenus Cyclobalanopsis and Quercus section Cerris and the oak-related Fagaceae including Lithocarpus. This third lineage shows large diversity, and includes the genus Ufo, the European lineage of S. undulatus and S. haimi, and the herein described new genus, Lithosaphonecrus Tang, Melika & Bozsó, known from Taiwan and China, with four new species: L. formosanus Melika & Tang, L. dakengi Tang & Pujade-Villar, L. huisuni Tang, Bozsó & Melika and L. yunnani Tang, Bozsó & Melika. All the four described species are associated only with Lithocarpus. Descriptions, diagnoses, biology, and host associations for the new genus and species are given, as well as a key to species and cynipid inquilines genera. All taxa are supported by morphological and molecular data.

Things held in common: Memory, space and the reconstitution of community life

This article presents the hard work, and eventual failure, of the elder branch of the main lineage within a village of steel producers to reaffirm local identity through the recreation of a common ritual space dedicated to the spirit of the village's founder, original artisan, and their ancestor. It presents this process as a struggle over the meanings and representations of community and space in a time of rapid social and economic transformation. The ultimate failure of this struggle, which only becomes evident after 15 years, has affirmed something else: the spaces of practice associated with the village's public administration and family-based commercial interests.

Evolution of the Sabin Strain of Type 3 Poliovirus in an Immunodeficient Patient during the Entire 637-Day Period of Virus Excretion

ABSTRACT A 20-year-old female hypogammaglobulinemic patient received monotypic Sabin 3 vaccine in 1962. The patient excreted type 3 poliovirus for a period of 637 days without developing any symptoms of poliomyelitis, after which excretion appeared to have ceased spontaneously. The evolution of Sabin 3 throughout the entire period of virus excretion was studied by characterization of seven sequential isolates from the patient. The isolates were analyzed in terms of their antigenic properties, virulence, sensitivity for growth at high temperatures, and differences in nucleotide sequence from the Sabin type 3 vaccine. The isolates followed a main lineage of evolution with a rate of nucleotide substitution that was very similar to that estimated for wild-type poliovirus during person-to-person transmission. There was a delay in the appearance of antigenic variants compared to sequential type 3 isolates from healthy vaccines, which could be one of the possible explanations for the long-term excretion of virus from the patient. The distribution of mutations in the isolates identified regions of the virus possibly involved in adaptation for growth in the human gut and virus persistence. None of the isolates showed a full reversion of the attenuated and temperature-sensitive phenotypes of Sabin 3. Information of this sort will help in the assessment of the risk of spread of virulent polioviruses from long-term excretors and in the design of therapies to stop long-term excretion. This will make an important contribution to the decision-making process on when to stop vaccination once wild poliovirus has been eradicated.

Conodont biostratigraphy and depositional history of strata comprising the Niagaran sequence (Silurian) in the northern part of the Cincinnati Arch region, west-central Ohio, and evolution of Kockelella walliseri (Helfrich)

The Dayton, Osgood, and Laurel Formations and the Euphemia, Springfield, and basal part of the Cedarville Dolomites near the axis of the Cincinnati Arch in northeast Preble County, Ohio, belong in the uppermost part of the Ozarkodina sagitta rhenana to lower part of the Ozarkodina? crassa Chronozone and are late early to middle Wenlockian in age. The Dayton–Cedarville succession on the eastern flank of the Cincinnati Arch in north-central Greene County, Ohio, belongs in the uppermost part of the Pterospathodus celloni to upper part of the Ancoradella ploeckensis Chronozone and is late Llandoverian to early middle Ludlovian in age.The sea transgressed across the exposed and eroded Brassfield Formation to begin deposition of the Dayton Formation on the eastern flank of the Cincinnati Arch in Greene County, Ohio, during the late Llandoverian and completely flooded all of west-central Ohio by the late early Wenlockian. The region remained covered by a sea of fluctuating depth during deposition of the Dayton Formation–Cedarville Dolomite succession from the Wenlockian through early middle Ludlovian.Kockelella walliseri (Helfrich) evolved from K. ranuliformis (Walliser) during the middle Wenlockian (upper part of Ozarkodina sagitta rhenana Chronozone) by development of a lateral process adjacent to the cusp on the Pa element and by minor modification of the Pb element and some of the ramiform elements. Specimens from upper Llandoverian and lower Wenlockian strata previously assigned to K. walliseri belong to a different species, Kockelella sp. A Fordham, 1991. The evolutionary trends in the K. walliseri lineage, progressive restriction of the basal cavity and increasing development of the length of the lateral processes in the Pa element, parallel the trends in the K. amsdeni–K. stauros–K. variabilis lineage and resulted in the divergence of Kockelella cf. K. stauros Bischoff, 1986, from the main lineage in the middle Wenlockian.