Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit

Background: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates

Draft genome sequences of three newly identified species in the genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T

Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described species in the Cronobacter genus, which is associated with serious infections of neonates. This is the first report of draft genome sequences for these species

Draft genome sequence of the earliest Cronobacter sakazakii sequence type 4 strain, NCIMB 8272

The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with severe cases of neonatal meningitis and persistence in powdered infant formula. For genome sequencing of the earliest deposited culture collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272, originally isolated from milk powder in 1950

Draft genome sequence of "Candidatus Cronobacter colletis" NCTC 14934T, a new species in the genus Cronobacter

Members of the Cronobacter genus are associated with serious infections in neonates. This is the first report of the draft genome sequence for the newly proposed species Cronobacter colletis

Draft genome sequence of a meningitic isolate of Cronobacter sakazakii clonal complex 4, strain 8399

The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine sequence types, is associated with severe cases of neonatal meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4) strains have been sequenced. C. sakazakii strain 8399, isolated from a case of neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

The Use of Ships\u27 Protests for Reconstruction of Synoptic-Scale Weather and Tropical Storm Identification in the Late Eighteenth Century

Ships’ protests have been used for centuries as legal documents to record and detail damages and indemnify Captains from fault. We use them in this article, along with data extracted through forensic synoptic analysis (McNally, 1994, 2004) to identify a tropical or subtropical system in the North Atlantic Ocean in 1785. They are shown to be viable sources of meteorological information. By comparing a damaging storm in New England in 1996, which included an offshore tropical system, with one reconstructed in 1785, we demonstrate that the tropical system identified in a ship’s protest played a significant role in the 1785 storm. With both forensic reconstruction and anecdotal evidence, we are able to assess that these storms are remarkably identical. The recurrence rate calculated in previous studies of the 1996 storm is 400–500 years. We suggest that reconstruction of additional years in the 1700s would provide the basis for a reanalysis of recurrence rates, with implications for future insurance and reinsurance rates. The application of the methodology to this new data source can also be used for extension of the hurricane database in the North Atlantic basin, and elsewhere, much further back into history than is currently available

Increase in bacteraemia cases in the East Midlands region of the UK due to MDREscherichia coliST73: high levels of genomic and plasmid diversity in causative isolates

Objectives: To determine the population structure of E. coli ST73 isolated from human bacteraemia and urinary tract infections. Methods: The genomes of 22 E.coli ST73 isolates were sequenced using the Illumina HiSeq platform. High resolution SNP typing was used to create a phylogenetic tree. Comparative genomics were also performed using a pangenome approach. In silico and S1-PFGE plasmid profiling was conducted, and isolates were checked for their ability to survive exposure to human serum. Results: E.coli ST73 isolates circulating in clinically unrelated episodes show a high degree of diversity at a whole genome level, though exhibit conservation in gene content, particularly in virulence associated gene carriage. The isolates also contain a highly diverse plasmid pool that confers multi-drug resistance via carriage of CTX-M genes. All strains are highly serum resistant and uniformly carry genes shown to be essential for serum resistance. Conclusions: Our data shows that a rise in incidence of multi-drug resistant E.coli ST73 clinical isolates is not due to a circulating outbreak strain as in E.coli ST131. Rather the ST73 circulating strains are distantly related and carry a diverse set of resistance plasmids. This suggests that the evolutionary events behind emergence of drug resistant E.coli differ between lineages

Paisatges funeraris i diversitat a Anglaterra i a Gal·les: l'establiment d'una agenda = Deathscapes and diversity in England and Wales: setting an agenda

Aquest article se centra en una dimensió poc discutida, però important, de les experiències dels migrants i les minories a Anglaterra i Gal·les: els cementiris i crematoris de què disposen. Basat en una àmplia investigació amb comunitats locals i proveïdors de serveis en quatre ciutats casos d’estudi, aquest article ex-plora les diverses necessitats funeràries culturals i religioses a Anglaterra i Gal·les, els reptes que hi estan associats i les formes en què tant les comunitats com els proveïdors de serveis (p. ex.: planifica-dors i directors funeraris) hi responen. Destaquen vuit temes clau: i)l’oferta de cementiris; ii)l’oferta de crematoris; iii)l’oferta desigual per diferents grups migrants i minoritaris; iv)la diversitat en la diversitat; v)els canvis de patrons de repatriació;vi)el foment del diàleg;vii)la comprensió entre professionals icomunitats, i viii)la planificació dels cementiris com aespais de trobada.Este artículo se centra en una dimensión poco discutida pero importante de las experiencias de los migrantes y las mi-norías en Inglaterra y Gales: los cemen-terios y crematorios de que disponen. Basándose en una amplia investigación con comunidades locales y proveedores de servicios en cuatro ciudades casos de estudio, este artículo explora las diver-sas necesidades funerarias culturales y religiosas en Inglaterra y Gales, los retos asociados a estas y las formas en que tanto las comunidades como los provee-dores de servicios (p. ej.: planificadores y directores funerarios) responden a ellos. Destacan ocho temas clave: i)la oferta de cementerios; ii)la oferta de crematorios; iii)la oferta desigual por diferentes grupos migrantes y minoritarios; iv)la diversidad en la diversidad;v)los cambios de patrones de repatri-ación; vi)el fomento del diálogo;vii)la comprensión entre profesionalesy comunidades, y viii)la planificación de los cementerios como espacios de encuentro.This paper focuses on a little discussed but important dimension of migrant and minority experiences in England and Wales: cemetery and crematoria provi-sion. Based on extensive research with local communities and service providers in four case study towns, this paper explores the varied cultural and religious funerary needs in England and Wales, the associated challenges and the ways in which both communities and service providers (e.g. cemetery managers, town planners and funeral directors) respond to them. It highlights seven key themes, namely:i)cemetery provision;ii)crematorium provision;iii)unequal provision across migrantand minority groups;iv)diversity within diversity;v)changing patterns of repatriation; vi)fostering dialogue;vii)understanding between profession-als and communities; and viii)planning for cemeteries as spacesof encounter. / Este artículo se centra en una dimensión poco discutida pero importante de las experiencias de los migrantes y las mi-norías en Inglaterra y Gales: los cemen-terios y crematorios de que disponen. Basándose en una amplia investigación con comunidades locales y proveedores de servicios en cuatro ciudades casos de estudio, este artículo explora las diver-sas necesidades funerarias culturales y religiosas en Inglaterra y Gales, los retos asociados a estas y las formas en que tanto las comunidades como los provee-dores de servicios (p. ej.: planificadores y directores funerarios) responden a ellos. Destacan ocho temas clave: i)la oferta de cementerios; ii)la oferta de crematorios; iii)la oferta desigual por diferentes grupos migrantes y minoritarios; iv)la diversidad en la diversidad;v)los cambios de patrones de repatri-ación; vi)el fomento del diálogo;vii)la comprensión entre profesionalesy comunidades, y viii)la planificación de los cementerios como espacios de encuentro. / This paper focuses on a little discussed but important dimension of migrant and minority experiences in England and Wales: cemetery and crematoria provi-sion. Based on extensive research with local communities and service providers in four case study towns, this paper explores the varied cultural and religious funerary needs in England and Wales, the associated challenges and the ways in which both communities and service providers (e.g. cemetery managers, town planners and funeral directors) respond to them. It highlights seven key themes, namely:i)cemetery provision;ii)crematorium provision;iii)unequal provision across migrantand minority groups;iv)diversity within diversity;v)changing patterns of repatriation; vi)fostering dialogue;vii)understanding between profession-als and communities; and viii)planning for cemeteries as spacesof encounter