Michael Strinden - Academia.edu (original) (raw)
Papers by Michael Strinden
As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout... more As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout parts of southern Africa they are thought to be of little conservation risk. As such, this species is seldom studied and relatively little is known of their behavior and biology. This research partially addresses this lack of knowledge by investigating the oral microbiome for potential zoonoses. Real-time PCR was used for the detection of Mycobacterium tuberculosis and M. leprae whereas next generation MiSeq Illumina sequencing was conducted on the 16S ribosomal RNA gene (16S rRNA) with a universal primer set which amplified the variable V3 and V4 regions to quantify the amount of different bacterial taxa. Major bacterial taxa of each tested oral microbiome were isolated, and those with potential for causing disease in humans and domestic animals were identified. The results illustrated a potential core microbiome for all O. crassicaudatus consisting of three separate bacterial taxa: Ma...
As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout... more As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout parts of southern Africa they are thought to be of little conservation risk. As such, this species is seldom studied and relatively little is known of their behavior and biology. This research partially addresses this lack of knowledge by investigating the oral microbiome for potential zoonoses. Real-time PCR was used for the detection of Mycobacterium tuberculosis and M. leprae whereas next generation MiSeq Illumina sequencing was conducted on the 16S ribosomal RNA gene (16S rRNA) with a universal primer set which amplified the variable V3 and V4 regions to quantify the amount of different bacterial taxa. Major bacterial taxa of each tested oral microbiome were isolated, and those with potential for causing disease in humans and domestic animals were identified. The results illustrated a potential core microbiome for all O. crassicaudatus consisting of three separate bacterial taxa: Ma...
Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major hu... more Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru under the GPLv3 open source licence.
Current Opinion in Microbiology, 2019
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 20... more The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-inanswer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
As Otolemur crassicaudatus and Galago moholi are ubiquitous throughout part of South Africa they ... more As Otolemur crassicaudatus and Galago moholi are ubiquitous throughout part of South Africa they are thought to be at little conservation risk. However, this has resulted in a situation where these species are seldom studied. This thesis addresses this lack of knowledge about these two species by investigating the oral microbiome of each for potential zoonoses. This is an important undertaking due to the widespread nature of these species which could provide an avenue for potential zoonoses to spread. In order to assess the oral microbiome, two genetic sequencing methods were utilized. Real-time PCR was utilized to search for mycobacterial contributors to the oral microbiome such as Mycobacterium tuberculosis and Mycobacterium leprae. Next-gen Illumina sequencing of the 16s region was chosen as an effective method to get an overall quantification of the amount of different bacterial contributors. Through these two methods major bacterial contributors of each tested oral microbiome were isolated and those with potential for causing illness in humans or domestic animals were identified. The results illustrated a potential core microbiome for all Otolemur crassicaudatus consisting of three separate bacterial contributors; Mannheimia caviae, Porphyromonas catonia, and Gemella cunicula. While all tested O. crassicaudatus exhibited these three contributors the rest of the oral microbiome was made of different contributors in varying amounts. The qPCR (real-time PCR) for mycobacteria (tuberculosis and leprosy) yielded negative results despite several potential initial amplifications. Despite qPCR findings several potentially pathogenic bacterial strains were discovered through next-gen 16s sequencing. These included Fusobacterium naviforme, Streptococcus bovis, and Gemella cunicula; all of which are known to cause disease in human hosts. A number of other bacterial strains with both human and non-human health risks were discovered in wild O. crassicaudatus as well as in captive sampled Galago moholi. These findings thus form the basis for several future avenues of potential research to assess any real zoonotic risks from these galagos to the broader human and animal populations of southern Africa
As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout... more As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout parts of southern Africa they are thought to be of little conservation risk. As such, this species is seldom studied and relatively little is known of their behavior and biology. This research partially addresses this lack of knowledge by investigating the oral microbiome for potential zoonoses. Real-time PCR was used for the detection of Mycobacterium tuberculosis and M. leprae whereas next generation MiSeq Illumina sequencing was conducted on the 16S ribosomal RNA gene (16S rRNA) with a universal primer set which amplified the variable V3 and V4 regions to quantify the amount of different bacterial taxa. Major bacterial taxa of each tested oral microbiome were isolated, and those with potential for causing disease in humans and domestic animals were identified. The results illustrated a potential core microbiome for all O. crassicaudatus consisting of three separate bacterial taxa: Ma...
As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout... more As the southern thick-tailed or greater galago (Otolemur crassicaudatus) is ubiquitous throughout parts of southern Africa they are thought to be of little conservation risk. As such, this species is seldom studied and relatively little is known of their behavior and biology. This research partially addresses this lack of knowledge by investigating the oral microbiome for potential zoonoses. Real-time PCR was used for the detection of Mycobacterium tuberculosis and M. leprae whereas next generation MiSeq Illumina sequencing was conducted on the 16S ribosomal RNA gene (16S rRNA) with a universal primer set which amplified the variable V3 and V4 regions to quantify the amount of different bacterial taxa. Major bacterial taxa of each tested oral microbiome were isolated, and those with potential for causing disease in humans and domestic animals were identified. The results illustrated a potential core microbiome for all O. crassicaudatus consisting of three separate bacterial taxa: Ma...
Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major hu... more Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru under the GPLv3 open source licence.
Current Opinion in Microbiology, 2019
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 20... more The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-inanswer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
As Otolemur crassicaudatus and Galago moholi are ubiquitous throughout part of South Africa they ... more As Otolemur crassicaudatus and Galago moholi are ubiquitous throughout part of South Africa they are thought to be at little conservation risk. However, this has resulted in a situation where these species are seldom studied. This thesis addresses this lack of knowledge about these two species by investigating the oral microbiome of each for potential zoonoses. This is an important undertaking due to the widespread nature of these species which could provide an avenue for potential zoonoses to spread. In order to assess the oral microbiome, two genetic sequencing methods were utilized. Real-time PCR was utilized to search for mycobacterial contributors to the oral microbiome such as Mycobacterium tuberculosis and Mycobacterium leprae. Next-gen Illumina sequencing of the 16s region was chosen as an effective method to get an overall quantification of the amount of different bacterial contributors. Through these two methods major bacterial contributors of each tested oral microbiome were isolated and those with potential for causing illness in humans or domestic animals were identified. The results illustrated a potential core microbiome for all Otolemur crassicaudatus consisting of three separate bacterial contributors; Mannheimia caviae, Porphyromonas catonia, and Gemella cunicula. While all tested O. crassicaudatus exhibited these three contributors the rest of the oral microbiome was made of different contributors in varying amounts. The qPCR (real-time PCR) for mycobacteria (tuberculosis and leprosy) yielded negative results despite several potential initial amplifications. Despite qPCR findings several potentially pathogenic bacterial strains were discovered through next-gen 16s sequencing. These included Fusobacterium naviforme, Streptococcus bovis, and Gemella cunicula; all of which are known to cause disease in human hosts. A number of other bacterial strains with both human and non-human health risks were discovered in wild O. crassicaudatus as well as in captive sampled Galago moholi. These findings thus form the basis for several future avenues of potential research to assess any real zoonotic risks from these galagos to the broader human and animal populations of southern Africa