Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide, with contaminated chicken meat considered to represent a major source of human infection. Biosecurity measures ...can reduce C. jejuni shedding rates of housed chickens, but the increasing popularity of free-range and organic meat raises the question of whether the welfare benefits of extensive production are compatible with food safety. The widespread assumption that the free-range environment contaminates extensively reared chickens has not been rigorously tested. A year-long survey of 64 free-range broiler flocks reared on two sites in Oxfordshire, UK, combining high-resolution genotyping with behavioural and environmental observations revealed: (i) no evidence of colonization of succeeding flocks by the C. jejuni genotypes shed by preceding flocks, (ii) a high degree of similarity between C. jejuni genotypes from both farm sites, (iii) no association of ranging behaviour with likelihood of Campylobacter shedding, and (iv) higher genetic differentiation between C. jejuni populations from chickens and wild birds on the same farm than between the chicken samples, human disease isolates from the same region and national samples of C. jejuni from chicken meat.
Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with ...research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.
The myeloid restricted membrane glycoprotein, CD33, is a member of the recently characterized âsialic acid-binding immunoglobulin-related
lectinâ family. Although CD33 can mediate sialic ...acid-dependent cell interactions as a recombinant protein, its function in
myeloid cells has yet to be determined. Since CD33 contains two potential immunoreceptor tyrosine-based inhibition motifs
in its cytoplasmic tail, we investigated whether it might act as a signaling receptor in myeloid cells. Tyrosine phosphorylation
of CD33 in myeloid cell lines was stimulated by cell surface cross-linking or by pervanadate, and inhibited by PP2, a specific
inhibitor of Src family tyrosine kinases. Phosphorylated CD33 recruited both the protein-tyrosine phosphatases, SHP-1 and
SHP-2. CD33 was dephosphorylated in vitro by the co-immunoprecipitated tyrosine phosphatases, suggesting that it might also be an in vivo substrate. The first CD33 phosphotyrosine motif is dominant in CD33-SHP-1/SHP-2 interactions, since mutating tyrosine 340
in a CD33-cytoplasmic tail fusion protein significantly reduced binding to SHP-1 and SHP-2 in THP-1 lysates, while mutation
of tyrosine 358 had no effect. Furthermore, the NH 2 -terminal Src homology 2 domain of SHP-1 and SHP-2, believed to be essential for phosphatase activation, selectively bound
a CD33 phosphopeptide containing tyrosine 340 but not one containing tyrosine 358. Finally, mutation of tyrosine 340 increased
red blood cell binding by CD33 expressed in COS cells. Hence, CD33 signaling through selective recruitment of SHP-1/SHP-2
may modulate its ligand(s) binding activity.
Non-typeable (NT) or capsule-deficient,
Haemophilus influenzae (
Hi) is a common commensal of the upper respiratory tract of humans and can be pathogenic resulting in diseases such as otitis media, ...sinusitis and pneumonia. The lipopolysaccharide (LPS) of NT
Hi is a major virulence factor that displays substantial intra-strain and inter-strain variation of its oligosaccharide structures. To investigate the genetic basis of LPS variation we sequenced internal regions of each of seven genes required for the biosynthesis of either the inner or the outer core oligosaccharide structures. These sequences were obtained from 25 representative NT
Hi isolates from episodes of otitis media. We found abundant evidence of recombination among LPS genes of NT
Hi, a finding in marked contrast to previous analyses of biosynthetic genes for capsular polysaccharide, a well-documented virulence factor of
Hi. We found mosaic sequences, linkage equilibrium between loci and a lack of congruence between gene trees. These high rates were not confined to LPS genes since evidence for similar amounts of recombination was also found in eight housekeeping genes in a subset of the same 25 isolates. These findings provide a population based foundation for a better understanding of the role of NT
Hi LPS as a virulence factor and its potential as a candidate vaccine.
Summary
Campylobacter jejuni
is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry.
C. jejuni
lineages vary in host range and ...prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST‐characterised isolates, we sequenced 600
C. jejuni
and
C. coli
isolates from various stages of poultry processing and clinical cases. A genome‐wide association study (GWAS) in
C. jejuni
ST‐21 and ST‐45 complexes identified genetic elements over‐represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease‐associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for
cj1377c
in formate metabolism,
nuoK
in aerobic survival and oxidative respiration, and
cj1368‐70
in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major
C. jejuni
lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.
Importance
Gaps in readiness for indirect supervision have been identified for essential responsibilities encountered early in residency, presenting risks to patient safety. Core Entrustable ...Professional Activities (EPAs) for entering residency have been proposed as a framework to address these gaps and strengthen the transition from medical school to residency.
Objective
To assess progress in developing an entrustment process in the Core EPAs framework.
Design, Setting, and Participants
In this quality improvement study in the Core EPAs for Entering Residency Pilot, trained faculty made theoretical entrustment determinations and recorded the number of workplace-based assessments (WBAs) available for each determination in 2019 and 2020. Four participating schools attempted entrustment decision-making for all graduating students or a randomly selected subset of students. Deidentified, individual-level data were merged into a multischool database.
Interventions
Schools implemented EPA-related curriculum, WBAs, and faculty development; developed systems to compile and display data; and convened groups to make theoretical summative entrustment determinations.
Main Outcomes and Measures
On an EPA-specific basis, the percentage of students for whom an entrustment determination could be made, the percentage of students ready for indirect supervision, and the volume of WBAs available were recorded.
Results
Four participating schools made 4525 EPA-specific readiness determinations (2296 determinations in 2019 and 2229 determinations in 2020) for 732 graduating students (349 students in 2019 and 383 students in 2020). Across all EPAs, the proportion of determinations of “ready for indirect supervision” increased from 2019 to 2020 (997 determinations 43.4% vs 1340 determinations 60.1%; 16.7 percentage point increase; 95% CI, 13.8-19.6 percentage points;
P
< .001), as did the proportion of determinations for which there were 4 or more WBAs (456 of 2295 determinations with WBA data 19.9% vs 938 42.1%; 22.2 percentage point increase; 95% CI, 19.6-24.8 percentage points;
P
< .001). The proportion of EPA-specific data sets considered for which an entrustment determination could be made increased from 1731 determinations (75.4%) in 2019 to 2010 determinations (90.2%) in 2020 (14.8 percentage point increase; 95% CI, 12.6-16.9 percentage points;
P
< .001). On an EPA-specific basis, there were 5 EPAs (EPA 4 orders, EPA 8 handovers, EPA 10 urgent care, EPA 11 informed consent, and EPA 13 patient safety) for which few students were deemed ready for indirect supervision and for which there were few WBAs available per student in either year. For example, for EPA 13, 0 of 125 students were deemed ready in 2019 and 0 of 127 students were deemed ready in 2020, while 0 determinations in either year included 4 or more WBAs.
Conclusions and Relevance
These findings suggest that there was progress in WBA data collected, the extent to which entrustment determinations could be made, and proportions of entrustment determinations reported as ready for indirect supervision. However, important gaps remained, particularly for a subset of Core EPAs.
The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to ...develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.
Summary
The contribution of wild birds as a source of human campylobacteriosis was investigated in
O
xfordshire,
U
nited
K
ingdom (
UK
) over a 10 year period. The probable origin of human
C
...ampylobacter jejuni
genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the
STRUCTURE
algorithm. Wild bird‐attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (
P
= 0.934) but varied seasonally, with wild bird‐attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (
P
= 0.003). The highest proportion of wild bird‐attributed illness occurred in
A
ugust (
P
< 0.001), with a significantly lower proportion in
N
ovember (
P
= 0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for
T
urdidae
‐attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the
UK
as a whole in this respect, these data suggest that the national burden of wild bird‐attributed isolates could be in the order of 10 000 annually.
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