Biology subjects

Cleary, D. W.

Publications and source records attributed to Cleary, D. W..

4 recordsLinked to original sources

bioRxiv2025

The road less travelled: Exploring the genomic characteristics and antimicrobial resistance potential of Acinetobacter baumannii from the indigenous Orang Asli community in Peninsular Malaysia

Acinetobacter baumannii is widely recognized as a multidrug-resistant pathogen, but with most public genome datasets biased toward hospital-derived isolates. Little is thus known about A. baumannii isolates from healthy individuals from the community. This study analysed genome sequences from nine A. baumannii isolates obtained from the upper respiratory tract of healthy individuals of the indigenous Orang Asli community in their rural settlements located in the east coast of Peninsular Malaysia. Genomic analysis revealed all nine A. baumannii isolates to be genetically distinct and included three new sequence types (STs) under the Pasteur scheme and six novel STs under the Oxford scheme. Notably, one isolate, A. baumannii 19064, belonged to Global Clone 8 (GC8), a lineage associated with clinical infections. Core genome phylogeny indicated that the Orang Asli community isolates were interleaved with several non-GC clinical isolates from the tertiary hospital within the same state. This is suggestive of the potential of these community isolates to cause infections under conducive conditions. This is also attested by the identification of several virulence factors in their genomes. All nine isolates carried various intrinsic blaOXA-51-like class D {beta}-lactamase genes and class C Acinetobacter-derived cephalosporinase (ADC) blaADC genes but remained susceptible to meropenem. Two isolates, A. baumannii 19053 and 19062, were tetracycline resistant but minocycline susceptible and harboured the tet(39)-tetR gene pair within mobile pdif modules located on distinct Rep_3 family plasmids. Only one isolate, A. baumannii 19055, is plasmid-free; the rest mainly harboured cryptic Rep_3-type plasmids, often containing identifiable pdif modules. These findings highlight the clinical relevance of A. baumannii strains residing in healthy individuals, particularly in isolated communities that are seldom accessible to public health. Despite their remote location, the Orang Asli A. baumannii isolates possess virulence factors and antibiotic resistance genes similar to those found in hospital settings. This underscores the importance of genomic surveillance of commensal pathogens, and taking this road which is less travelled can help inform broader epidemiological insights and guide future public health strategies.

microbiology↗

bioRxiv2023

Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions.

BackgroundThe skin microbiome is increasingly recognised as a critical component of the innate skin immune response and is central to the pathogenesis of many inflammatory skin disorders including atopic dermatitis. Previous studies have not looked in detail at the impact of changing both sampling methodology and hypervariable region sequencing for skin microbiome analysis. ObjectivesWe set out to undertake a detailed analysis comparing microbe population diversity and resolution at the single species level by swab, tape, scrape and scrape then swab sampling assayed by hypervariable region sequencing. MethodsIn triplicate samples from the antecubital fossa were taken from healthy volunteers for 16s RNA analysis by primer amplification for hypervariable regions 1-3, and 3-4. ResultsAlpha (phylogenetic) diversity was the greatest with tape sampling and V1-3 analysis, whereas for V4, tape and swab were equivalent. Scrape sampling showed lower alpha diversity at both V1-3 and V4. All measures of beta diversity showed the scrape methodology yielded a lesser diversity than the others. Phyla composition was similar across all sampling methodologies. Minor differences in composition were noted between V1-3 and V4 sequencing, but V1-3 was optimal for identification of firmicutes (including staphylococci). ConclusionsIn the methodological planning of skin microbiome analysis skin scientists need to consider the microbes of interest to choose the optimal hypervariable region to sequence, and harmonisation of methodological approaches would be beneficial to the field. For detection of staphylococci on flexural skin, we would recommend tape sampling with analysis of V1-3. Whats already known about this topic?O_LIPrevious microbiome studies have utilised many different methodologies, but a detailed comparison of their utility in skin research has not been undertaken C_LIO_LIMethodological choices in skin microbiome analysis affect both sensitivity to detect diversity and sensitivity to identify at a species level C_LIO_LIOptimisation to detect diversity and species identification can require different approaches C_LI What does this study add?O_LIOur study compared a matrix the four most widely utilised skin sampling methodologies and the two principle means for hypervariable gene analysis. C_LIO_LIWe show that alpha diversity is optimal with tape sampling C_LIO_LIAdditionally, in contrast to gut microbiome analyses, in the skin hypervariable region V1-3 analysis is superior to V4 when the species of interest are staphylococci. C_LI

microbiology↗

bioRxiv2017

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae

Between 2008/09 and 2012/13 the molecular epidemiology of non-typeable Haemophilus influenzae (NTHi) carriage in children <5 years of age was determined; a period that included pneumococcal conjugate vaccine (PCV) 13 introduction. Significantly increased carriage in post-PCV13 years was observed and lineage-specific associations with S. pneumoniae were observed before and after PCV13 introduction. NTHi were characterised into eleven discrete, temporally stable lineages, congruent with current knowledge regarding the clonality of NTHi. This increase could not be linked to the expansion of a particular clone and demonstrates different dynamics to before PCV13 implementation during which time NTHi co-carried with vaccine serotype pneumococci.

microbiology↗

bioRxiv2017

Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study

Respiratory tract infections (RTI) are responsible for over 4 million deaths per year worldwide with pathobiont carriage a required precursor to infection. Through a cross-sectional community-based nasal self-swabbing study we sought to determine carriage epidemiology for respiratory pathogens amongst bacteria (Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonas aeruginosa and Neisseria meningitidis) and viruses (RSV, Influenza viruses A and B, Rhinovirus/Enterovirus, Coronavirus, Parainfluenza viruses 1-3 and Adenovirus (ADV)). Carriage of bacterial and viral species was shown to vary with participant age, recent RTI and the presence of other species. The spatial structure of microbial respiratory communities was less nested (more disordered) in the young (0-4 years) and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X2 = 20.42, p = 0.002), indicating spatial clumping of species consistent with facilitative relationships amongst them. Deviations from a neutral model of ecological niches were observed for samples collected in the summer and from older individuals (those aged 5-17, 18-64 and [≥]65 years) but not in samples collected from winter, younger individuals (those aged 0-4 years), individuals with recent RTI and individuals without recent RTI, demonstrating the importance of both neutral and niche processes in respiratory community assembly. The application of epidemiological methods and ecological theory to sets of respiratory tract samples has yielded novel insights into the factors that drive microbial community composition, such as seasonality and age, as well as species patterns and interactions within the nose.

microbiology↗