Sequence variability of Campylobacter temperate bacteriophages

<p>Abstract</p> <p>Background</p> <p>Prophages integrated within the chromosomes of <it>Campylobacter jejuni </it>isolates have been demonstrated very recently. Prior work with <it>Campylobacter </it>temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of <it>Campylobacter </it>prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of <it>C. jejuni </it>prophages, we investigated the distribution of prophage DNA within a <it>C. jejuni </it>population assessed the DNA and protein sequence variability within a subset of the putative prophages found.</p> <p>Results</p> <p>Southern blotting of <it>C. jejuni </it>DNA using probes from genes within the three putative prophages of the <it>C. jejuni </it>sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for 5 or more of the 7 <it>Campylobacter </it>Mu-like phage 1 (CMLP 1, also designated <it>Campylobacter jejuni </it>integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to <it>C. jejuni </it>sequenced strains, as well as promoter regions characteristic of <it>C. jejuni</it>. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or if they represented remnant prophage DNA in the bacterial chromosomes.</p> <p>Conclusion</p> <p>These putative prophages form a family of phages with conserved sequences, and appear to be adapted to <it>Campylobacter</it>. There was evidence for recombination among groups of prophages, suggesting that the prophages had a mosaic structure. In many of these properties, the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of enteric bacteria that are responsible for contributions to virulence and host adaptation.</p

Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada

<p>Abstract</p> <p>Background</p> <p><it>Salmonella enterica </it>serovar Heidelberg ranks amongst the most prevalent causes of human salmonellosis in Canada and an increase in resistance to extended spectrum cephalosporins (ESC) has been observed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance. This study examined the genetic relationship between <it>S</it>. Heidelberg isolates from livestock, abattoir, retail meat, and clinical human specimens to determine whether there was a link between the emergence of MDR <it>S</it>. Heidelberg in chicken agri-food sources and the simultaneous increase of MDR <it>S</it>. Heidelberg in human clinical samples.</p> <p>Results</p> <p>Chromosomal genetic homogeneity was observed by pulsed-field gel electrophoresis (PFGE), DNA sequence-based typing (SBT) and DNA microarray-based comparative genomic hybridization (CGH). Sixty one percent of isolates were indistinguishable by PFGE conducted using <it>Xba</it>I and <it>Bln</it>I restriction enzymes. An additional 15% of isolates had PFGE patterns that were closely related to the main cluster. SBT did not identify DNA polymorphisms and CGH revealed only genetic differences between the reference <it>S</it>. Typhimurium strain and <it>S</it>. Heidelberg isolates. Genetic variation observed by CGH between <it>S</it>. Heidelberg isolates could be attributed to experimental variation. Alternatively, plasmid content was responsible for differences in antimicrobial susceptibility, and restriction fragment length polymorphism (RFLP) analyses followed by replicon typing identified two divergent plasmid types responsible for ESC resistance.</p> <p>Conclusion</p> <p>Due to the overall limited genetic diversity among the isolates, it was not possible to identify variable traits that would be suitable for source tracking between human and agri-food isolates of <it>S</it>. Heidelberg in Canada.</p

Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13

<p>Abstract</p> <p>Background</p> <p><it>Salmonella enterica </it>serovar Enteritidis has emerged as a significant foodborne pathogen throughout the world and is commonly characterized by phage typing. In Canada phage types (PT) 4, 8 and 13 predominate and in 2005 a large foodborne PT13 outbreak occurred in the province of Ontario. The ability to link strains during this outbreak was difficult due to the apparent clonality of PT13 isolates in Canada, as there was a single dominant pulsed-field gel electrophoresis (PFGE) profile amongst epidemiologically linked human and food isolates as well as concurrent sporadic strains. The aim of this study was to perform comparative genomic hybridization (CGH), DNA sequence-based typing (SBT) genomic analyses, plasmid analyses, and automated repetitive sequence-based PCR (rep-PCR) to identify epidemiologically significant traits capable of subtyping <it>S</it>. Enteritidis PT13.</p> <p>Results</p> <p>CGH using an oligonucleotide array based upon chromosomal coding sequences of <it>S. enterica </it>serovar Typhimurium strain LT2 and the <it>Salmonella </it>genomic island 1 successfully determined major genetic differences between <it>S</it>. Typhimurium and <it>S</it>. Enteritidis PT13, but no significant strain-to-strain differences were observed between <it>S</it>. Enteritidis PT13 isolates. Individual loci (<it>safA </it>and <it>fliC</it>) that were identified as potentially divergent in the CGH data set were sequenced in a panel of <it>S</it>. Enteritidis strains, and no differences were detected between the PT13 strains. Additional sequence-based typing was performed at the <it>fimA</it>, <it>mdh</it>, <it>manB</it>, <it>cyaA</it>, <it>citT</it>, <it>caiC</it>, <it>dmsA</it>, <it>ratA </it>and STM0660 loci. Similarly, no diversity was observed amongst PT13 strains. Variation in plasmid content between PT13 strains was observed, but macrorestriction with B<it>gl</it>II did not identify further differences. Automated rep-PCR patterns were variable between serovars, but <it>S</it>. Enteritidis PT13 strains could not be differentiated.</p> <p>Conclusion</p> <p>None of the methods identified any significant variation between PT13 strains. Greater than 11,300 base pairs of sequence for each of seven <it>S</it>. Enteritidis PT13 strains were analyzed without detecting a single polymorphic site, although diversity between different phage types of <it>S</it>. Enteritidis was observed. These data suggest that Canadian <it>S</it>. Enteritidis PT13 strains are highly related genetically.</p

Emergence of Multidrug-resistant Salmonella Paratyphi B dT+, Canada

We document an increase in the number of multidrug-resistant Salmonella enterica serovar Paratyphi B dT+ identified in Canada. Most of these strains harbor Salmonella genomic island 1 (SGI1). Further studies are needed to determine factors contributing to the observed emergence of this multidrug-resistant strain

The O28 Antigen Gene Clusters of Salmonella enterica

A 10 kb O-antigen gene cluster was sequenced from a Salmonella enterica subsp. enterica Dakar O28 reference strain and from two S. Pomona serogroup O28 isolates. The two S. Pomona O antigen gene clusters showed only moderate identity with the S. Dakar O28 gene cluster, suggesting that the O antigen oligosaccharides may contain one or more sugars conferring the O28 epitope but may otherwise be different. These novel findings are absolutely critical for the correct interpretation of molecular serotyping assays targeting genes within the O antigen gene clusters of these Salmonella serotypes and suggest the possibility that the O antigen gene clusters of other Salmonella serovars may also be heterogenous

Chronic adiponectin deficiency leads to Alzheimer’s disease-like cognitive impairments and pathologies through AMPK inactivation and cerebral insulin resistance in aged mice

(a) Immunoblotting analysis of IRβ in the hippocampus and frontal cortex of 18-month old wildtype and APN-KO mice. (b) Densitometric analysis of the ratio of IRβ. Mean ± S.E.M.; ***p < 0.001, n.s. statistically not significant; Scale bar: 100 μm. (JPG 30 kb

Rationalisation and Validation of an Acrylamide-Free Procedure in Three-Dimensional Histological Imaging

201810_a bcmapublished_fina

Association between the risk of seizure and COVID-19 vaccinations: A self-controlled case-series study

OBJECTIVE: The risk of seizure following BNT162b2 and CoronaVac vaccinations has been sparsely investigated. This study aimed to evaluate this association. METHOD: Patients who had their first seizure-related hospitalization between February 23, 2021 and January 31, 2022 were identified in Hong Kong. All seizure episodes happening on the day of vaccination (day 0) were excluded since clinicians validated that most of the cases on day 0 were syncopal episodes. Within-individual comparison using a modified self-controlled case series analysis was applied to estimate the incidence rate ratio (IRR) with 95% confidence intervals (CI) of seizure using conditional Poisson regression. RESULTS: We identified 1656 individuals who had their first seizure-related hospitalization (BNT162b2: 426; CoronaVac: 263; unvaccinated: 967) within the observation period. The incidence of seizure was 1.04 (95% CI: 0.80-1.33) and 1.11 (95% CI: 0.80-1.50) per 100,000 doses of BNT162b2 and CoronaVac administered respectively. 16 and 17 individuals received second dose after having first seizure within 28 days after first dose of BNT162b2 and CoronaVac vaccinations, respectively. None had recurrent seizures after the second dose. There was no increased risk during day 1-6 after the first (BNT162b2: IRR=1.39, 95% CI=0.75-2.58; CoronaVac: IRR=1.19, 95% CI=0.50-2.83) and second doses (BNT162b2: IRR=1.36, 95% CI 0.72-2.57; CoronaVac: IRR=0.71, 95% CI=0.22-2.30) of vaccinations. During 7-13, 14-20- and 21-27-days post-vaccination, no association was observed for both vaccines. SIGNIFICANCE: The findings demonstrated no increased risk of seizure following BNT162b2 and CoronaVac vaccinations. Future studies will be warranted to evaluate the risk of seizure following COVID-19 vaccinations in different populations with subsequent doses to ensure the generalizability

Laboratory Diagnosis of SARS

The virologic test results of 415 patients with severe acute respiratory syndrome (SARS) were examined. The peak detection rate for SARS-associated coronavirus occurred at week 2 after illness onset for respiratory specimens, at weeks 2 to 3 for stool or rectal swab specimens, and at week 4 for urine specimens. The latest stool sample that was positive by reverse transcription–polymerase chain reaction (RT-PCR) was collected on day 75 while the patient was receiving intensive care. Tracheal aspirate and stool samples had a higher diagnostic yield (RT-PCR average positive rate for first 2 weeks: 66.7% and 56.5%, respectively). Pooled throat and nasal swabs, rectal swab, nasal swab, throat swab, and nasopharyngeal aspirate specimens provided a moderate yield (29.7%–40.0%), whereas throat washing and urine specimens showed a lower yield (17.3% and 4.5%). The collection procedures for stool and pooled nasal and throat swab specimens were the least likely to transmit infection, and the combination gave the highest yield for coronavirus detection by RT-PCR. Positive virologic test results in patient groups were associated with mechanical ventilation or death (p < 0.001), suggesting a correlation between viral load and disease severity