Biology subjects

Seth-Smith, H. M.

Publications and source records attributed to Seth-Smith, H. M..

4 recordsLinked to original sources

bioRxiv2024

Genomic Analysis of Legionella pneumophila in the Drinking Water System of a Large Building over 25 Years

Legionella pneumophila, the causative agent of Legionnaires disease, is often found in the plumbing systems of buildings from where it can be transmitted to humans via inhalation or aspiration of contaminated water drops. Annual routine water sampling from the potable water system of an occupational healthcare building in Basel over 25 years was performed in accordance with national guidelines. Overall, 309 water samples were collected at 38 time points over the period of 25 years. L. pneumophila was recovered from 120 water samples (38.8%) from 26 time points. No clinical infections were recorded during this period. Initial decontamination measures were successful for approximately 12 years, after which an increase in the total number of Legionella colony forming units as well as of L. pneumophila-positive sites was noticed, in 2008. Whole genome sequencing (WGS) analysis of n=123 isolates from n=113 samples showed all L. pneumophila to be sequence type (ST)-45 (Sequence based typing scheme). The isolates are closely related, with only 408 single nucleotide polymorphisms (SNPs) among all isolates after the bioinformatic removal of recombination events. Over the 25 years, a single lineage deriving from a recent common ancestor colonized the water system of this building. The phylogeny of isolate genomes can be interpreted as inferring good water circulation, possible recolonization from a common source after cleaning, with genome evolution and insertion / loss of large elements evident. Regular monitoring of waterlines in healthcare settings helps to identify concentrations of Legionella spp. and WGS is recommended for detailed investigation. Data SummaryAll data is submitted to the ENA under project PRJEB79004 under accession numbers ERR13662450-ERR13662572. Impact StatementThis is the most detailed, long-term study of L. pneumophila in the water system of a single building recorded to date. The L. pneumophila isolates found in the building over the sampling period of 25 years were all closely related, belonging to ST45. SNP analysis suggested that the common ancestor of the cluster was from around 1938 (range 1911 to 1959), and movement of a large genomic island and plasmid transfer were observed. Despite several decontamination measures, it was impossible to completely eradicate Legionella spp. from the water system of the historic building. No infections could be attributed to the presence of L. pneumophila in this building. To mitigate the risk of Legionellosis from such buildings, awareness, regular water testing based on official national guidelines and recommendations, and other control measures, such as the use of sterile water for critical procedures can be recommended.

microbiology↗

bioRxiv2024

Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina

Whole genome analysis has provided us with insights into the evolution of Chlamydia trachomatis and recently into circulating strains which cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new ompA-genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), and then expanded globally. More recent work shows this outbreak diversifying into variants of described ompA-genotypes, with the same L2b genomic backbone. This study extends the investigation of LGV cases to Argentina and Finland. In 2017, an LGV outbreak was described in Argentina characterized by distinct genomic features shown by both ompA-genotyping and MLST analysis. We have obtained whole genome sequences from cultured isolates and clinical samples via SureSelect (Agilent) target enrichment. Based on ompA and phylogenetic analyses, we describe further diversity within the ompA-genotype L2b clade, illustrating the transmission dynamics in both Argentina and Finland. A key finding is that of a novel clade of Argentinian samples, characterised by a proposed new ompA-genotype L4. Additionally, we present the genome sequence of a non-LGV strain associated with anorectal proctitis. These findings contribute to the investigation of LGV evolution, particularly with the presence of the novel L4 lineage, and provide insights into genomic diversity and transmission dynamics of C. trachomatis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/624510v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3bd641org.highwire.dtl.DTLVardef@6f6866org.highwire.dtl.DTLVardef@2f1b6eorg.highwire.dtl.DTLVardef@b2137a_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementThe phylogeny of C. trachomatis has been described in several publications and has been clear for a decade. The evolution of this STI in the intervening years also informs a great deal about the transmission opportunities and selective pressures that the intracellular bacterium is under. Through genome sequencing, also directly from clinical samples, we provide the first LGV genomes from Argentina and Finland, and describe further evidence of global circulation of the ompA-genotype L2b lineage. We describe a fully novel lineage of LGV C. trachomatis, from Argentina, proposed as ompA-genotype L4. We also find evidence of a strain causing proctitis from the urogenital lineage. Together, these provide significant new findings in the investigation of C. trachomatis. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2020

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

Infecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, its local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. We find trends in transmission dynamics correlated positively with trends in temperature, but not relative humidity nor school holidays. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network, while school children likely drove the spread within the remaining transmission network. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities. Author summaryAs shown with the current SARS-CoV-2 pandemic, respiratory diseases can quickly spread around the globe. While it can be hugely important to understand how diseases spread around the globe, local spread is most often the main driver of novel infections of respiratory diseases such as SARS-CoV-2 or influenza. We here use genetic sequence data alongside patient information to better understand what the drives the local spread of influenza by looking at the 2016/2017 influenza season in Basel, Switzerland as an example. The genetic sequence data allows us to reconstruct the how the transmission dynamics changed over the course of the season, which we correlate to changes, but not humidity or school holidays. Additionally, the genetic sequence data allows us to see how individual cases are connected. Using patient information, such as age and household status our analyses suggest that the elderly mainly transmit within their own transmission network. Additionally, they suggest that school aged children, but not pre-school aged children are important drivers of the local spread of influenza.

evolutionary biology↗

bioRxiv2020

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.

microbiology↗