Diverse CRISPRs Evolving in Human Microbiomes

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR–associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes

The Australasian COVID-19 Trial (ASCOT) to assess clinical outcomes in hospitalised patients with SARS-CoV-2 infection (COVID-19) treated with lopinavir/ritonavir and/or hydroxychloroquine compared to standard of care: A structured summary of a study protocol for a randomised controlled trial

Objectives: To determine if lopinavir/ritonavir +/- hydroxychloroquine will reduce the proportion of participants who survive without requiring ventilatory support, 15 days after enrolment, in adult participants with non-critically ill SARS-CoV-2 infection. Trial design: ASCOT is an investigator-initiated, multi-centre, open-label, randomised controlled trial. Participants will have been hospitalised with confirmed COVID-19, and will be randomised 1:1:1:1 to receive lopinavir /ritonavir, hydroxychloroquine, both or neither drug in addition to standard of care management. Participants: Participants will be recruited from >80 hospitals across Australia and New Zealand, representing metropolitan and regional centres in both public and private sectors. Admitted patients will be eligible if aged ≥ 18 years, have confirmed SARS-CoV-2 by nucleic acid testing in the past 12 days and are expected to remain an inpatient for at least 48 hours from the time of randomisation. Potentially eligible participants will be excluded if admitted to intensive care or requiring high level respiratory support, are currently receiving study drugs or their use is contraindicated due to allergy, drug interaction or comorbidities (including baseline QTc prolongation of 470ms for women or 480ms for men), or death is anticipated imminently

Bilateral Neck Pyomyositis Caused by Staphylococcus capitis and Staphylococcus saccharolyticus in a Diabetic Adult

We report a case of pyomyositis of the paraspinal neck muscles caused by two coagulase-negative staphylococci: Staphylococcus capitis and Staphylococcus saccharolyticus. Inflammation in the spermatic cords was an additional feature of this infection. Treatment with six weeks of first-generation cephalosporin therapy resulted in complete clinical and radiological resolution

Severe Clostridium difficile infection in New Zealand associated with an emerging strain, PCR-ribotype 244

Aim To compare disease severity and clinical outcome of Clostridium difficile infection (CDI) due to PCR-ribotype (RT) 244 with CDI due to other strains present in Auckland. Method A retrospective, case-control study was conducted. Ten cases with CDI due to RT 244 were compared with 20 controls infected with other C. difficile strains. RT 244 isolates were further analysed for antimicrobial susceptibility, binary toxin genes and mutations in the tcdC gene. Results Cases were significantly more likely to have severe disease than controls (OR 9.33; p=0.015). 50% of cases had community-associated CDI compared with 15% of controls (p=0.078). All RT 244 isolates produced binary toxin and had a single-base pair deletion in tcdC at position 117. Conclusion C. difficile RT 244 is a newly recognised strain in New Zealand. It shares several features that characterise RT 027. Given its propensity to cause severe community-associated disease, a heightened awareness of this strain is needed to ensure early testing in patients admitted from the community with identified risk factors for CDI

Epidemiology of blood-borne viruses: a study of healthy blood donors in Southern Pakistan

There are only a few published reports regarding the prevalence of hepatitis B virus, hepatitis C virus and human immunodeficiency virus in Pakistani blood donors. The true extent of the prevalence of these viral infections in healthy adults in unclear. We examined blood donors attending the Aga Khan University Hospital and blood donation camps in the cities of Karachi and Hyderabad, Pakistan for the presence of hepatitis B surface antigen (HBsAg), antibodies to hepatitis C virus (anti-HCV) and human immunodeficiency virus (anti-HIV). Relationship of anti HCV to the surrogate marker alanine aminotransferase (ALT) was also examined. Prevalence of HBsAg was found to be 2.28% (1,173/51,257), anti HCV was 1.18%(198/16,705) and that of anti HIV to be 0.02% (10/51,257). Higher rate of prevalence of HBsAg and anti HCV was observed in the younger age group of 21 to 30 years. Male to female ratio for HBsAg was 2.5:1 and for anti HCV 1:1. Seropositivity for HBsAg was significantly greater than anti HCV (p \u3c 0.0001). No clear relationship was found between high ALT (\u3e55 U/l) and anti HCV positivity. Further examination of seropositive samples for HIV revealed only one donor to be positive by Western blot also. Prevalence of hepatitis B and C in the adult blood donor population in Southern Pakistan is higher than western countries but is similar to regional countries. This study also suggested that high ALT is not a useful surrogate marker for hepatitis C virus. Prevalence of HIV in this donor population is very low and is comparable to the western countries