SEARCH · Search bioRxiv

Results for “Epidemiology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources

bioRxiv2024

An epidemiological description of rabies outbreaks in Zambia from 2013 to 2023.

BackgroundIn Zambia, a dog bite is the most common rabies exposure. There is limited information on rabies outbreaks in jackals in Zambia. We investigated all rabies cases in Zambia and narrowed down on jackal bites in Mungwi district to determine a temporal trend and buffer zones for rabies. MethodsThe risk of exposure included all humans and animals bitten by jackals, data were collected by interviewing jackal bite victims and collecting brain specimen samples from animals. Risk of spread was determined by estimating the distance jackals strayed into human population and the Rabies Vaccination Coverage (RVC) in the district. The RVC was determined by dividing vaccinated dogs by dog population. The incidence rate (IR) and a Sens slope was used to determine a trend of RVC and the rabies cases in Zambia. QGIS was used to produce a heatmap and rabies risk zones. Direct Fluorescent Antibody technique was used to test for rabies. ResultsZambia had recorded a total of 224 rabies cases with a mean (SD) of 22.4 (16) rabies cases and a positivity rate of 65.4% (25.7) per year from 2013 to 2022. Lusaka and Copperbelt provinces recorded the highest rabies cases. The rabies incidence rate was 2.3 rabies cases per 10,000 dogs in Zambia. The cases had reduced from 2013 to 2021 with a Sens slope of -0.74 (p = 0.02). At least 227 animal bites were recorded (two jackals and 225 dog bites) in Mungwi District. 94% (213) of the victims needed Post Exposure Prophylaxis. The victims median age was 20 (Interquartile range=12-38) years. The accumulative RVC from 2018-2022 (611/7777), was 0.11 (95% CI: -0.4-0.7, p=0.46) annual slope increase with 1.60% mean (Standard deviation = 0.34). One rabies heatmap and three risk-level zones (low, medium and high) were produced, and two jackals and one goat specimens were positive. ConclusionsA risk-based surveillance and enhanced vaccination of dogs in high-risk areas through a one health approach is critical for rabies control in Zambia.

pathology↗

bioRxiv2024

Chromosomal curing drives prophage evolution and bacterial epidemiology

Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recombination (HR). This process may provide an evolutionary advantage to cells through enabling "chromosomal curing": the deletion of integrative mobile genetic elements (MGEs). However, many such MGEs are sensitive to RecA-DNA filaments, triggering activation of a lifecycle that may enable them to evade HR-mediated deletion. Despite >40% of isolates containing prophage integrated at a site that inhibits transformation, three representative prophage were identified in naturally-competent pneumococci to test this hypothesis. These encompassed representatives with C1-type and ImmAR-type regulatory systems, found in almost all pneumococcal prophage. All three prophage were deleted by HR with an efficiency similar to the transfer of base substitutions. Mutations that impaired a C1-regulated prophage increased this deletion rate, reflecting this element being activated by RecA-DNA filaments imported during transformation, likely preferentially killing cells that induce competence. ImmAR-regulated prophage instead responded to transient stimuli by excising as deletion-resistant pseudolysogens, only driving cell lysis in response to sustained stimuli. This was likely a consequence of these prophage reacting to multiple signals, as they differed in their response to both RecA and the DNA-binding protein and competence repressor DprA. One prophage constitutively elevated host DprA levels, thereby reducing transformation by preventing induction of the competence machinery. Hence these data are consistent with an evolutionary arms race between prophage and the competence machinery, resulting in bacterial diversification though HR being impeded by MGEs preventing their own elimination from the chromosome.

microbiology↗

bioRxiv2024

EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens

This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently >1.1 million bacterial isolates, more recently including Streptococcus spp. and Mycobacterium tuberculosis. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualising bacterial genomic population structures, based on pre-computed hierarchical clusters. Access to data and analysis tools is provided through an enhanced graphical user interface and a new application programming interface (RESTful API). EnteroBase is now being developed and operated by an international consortium, to accelerate the development of the platform and ensure the longevity of the resources built. EnteroBase can be accessed at https://enterobase.warwick.ac.uk as well as https://enterobase.dsmz.de. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/608032v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@88ff78org.highwire.dtl.DTLVardef@3c426eorg.highwire.dtl.DTLVardef@2d8481org.highwire.dtl.DTLVardef@5644bb_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Preliminary report on the molecular epidemiology of mpox, South Africa 2024

Mpox is an emerging viral infection and has since May 2022 been reported in a multi-country outbreak involving predominantly previously non-endemic countries. In addition, the number of cases of mpox is also rising in some endemic countries in Western and Central Africa. The disease is a notifiable medical condition in South Africa, with no cases reported before 2022. However, in 2022, coinciding with the peak of a multi-country mpox outbreak, five mpox cases were diagnosed in the country. Genomic sequencing and analysis revealed the presence of a monkeypox virus variant, which was circulating during the multi-country outbreak, namely Clade IIb sub-lineage B.1.7 (hMPXV). After the fifth case was reported in 2022, there were no cases detected for the following 20 months. In May 2024, mpox cases were again detected in South Africa leading to concerns that the virus may have been silently transmitting in the country since 2022. Genomic sequencing and analysis for 22 mpox cases reported during May to September 2024, were compared with sequences obtained from mpox cases reported in South Africa in 2022, and cases that have been reported globally. It was found that the sequences of the 2024 cases analysed in this study, clustered with Clade IIb hMPXV and sub-lineage B.1.20 and B.1.6 sequences. The results indicate that the detection of mpox cases in South Africa was an extension of the ongoing multi-country outbreak. Detection of different sub-lineages of hMPXV indicates reintroductions of the virus in the country since 2022, with local transmission of Clade IIb B1.20 hMPXV.

microbiology↗

bioRxiv2025

Large-scale global molecular epidemiology of antibiotic resistance determinants in Streptococcus pneumoniae

BackgroundStreptococcus pneumoniae is a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts. AimLeveraging on publicly available whole-genome sequencing data, we aimed to investigate the presence and distribution patterns of antibiotic resistance in S. pneumoniae with a focus on multi-drug resistance and serotype distribution. MethodsMetadata and genomes were obtained from the National Center for Biotechnology Information Pathogen Detection database. Curation and harmonization were performed in R and SPSS. Data on resistance patterns was defined according to AMRFinderPlus and a combination of prediction tools were employed for in silico serotyping. ResultsAnalyses involved 75,161 genomes totaling 122,673 gene/allele counts from 14 antibiotic classes. Multi-drug resistance was observed in 16.7% of isolates with the highest increasing rates in Asia and South America. Within antibiotic classes, increase in macrolide resistance genes was highlighted, particularly in the proportion of genomes presenting mefA/msrD. Over a third of isolates with serotypes 19F, 23F, 15A, 6B, and 19A showed multi-drug resistance. We further observed the highest significant increases in the presence of resistance in 33F, 22F, 10A, and 23A. Serotype 13, not included in any vaccine formulation, presented high multi-drug resistance rates with a strong increasing trend. ConclusionsThe findings of this study highlight variations in resistance determinants globally and across serotypes over time. Collectively these data underscore the added value of utilizing public whole-genome sequencing data to investigate the effectiveness and repercussions of treatment and vaccination strategies on managing antibiotic resistance.

microbiology↗

bioRxiv2025

Genomic epidemiology of enteropathogenic Escherichia coli (EPEC) in southwestern Nigeria

BackgroundEnteropathogenic Escherichia coli (EPEC) are etiological agents of diarrhea. We studied the genetic diversity and virulence factors of EPEC in southwestern Nigeria, where this pathotype is rarely characterized. Methodology/ Principal findingsEPEC isolates (n=96) recovered from recent southwestern Nigeria diarrhea case-control studies were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes and quality was evaluated using QUAST. Virulencefinder, SeroTypefinder, and Resfinder were used to identify virulence genes, serotypes, and resistance genes, while multilocus sequence typing was done by STtyping. Single nucleotide polymorphisms (SNPs) were called out of whole genome alignment using SNP-sites and a phylogenetic tree was constructed using IQtree. Thirty-nine of the 96 (40.6%) EPEC isolates were from cases of diarrhea. Nine isolates from diarrhea patients and four from healthy controls were typical EPEC, harboring bundle-forming pilus (bfp) genes whilst the rest were atypical EPEC. Fifteen isolates were EPEC-EAEC hybrids. Atypical serotypes O71:H19 (16, 16.6%), O108:H21 (6, 6.3%), O157:H39 (5, 5.2%), and O165:H9 (4, 4.2%) were most prevalent; only 8(8.3%) isolates belonged to classical EPEC serovars. The largest clade comprised ST517 isolates, of O71:H19 and O165:H9 serovars harboring multiple siderophore and serine protease autotransporter genes. An O71:H19 subclade comprised isolates <10 SNPs apart, representing a likely outbreak involving 15 children, four presenting with diarrhea. Conclusion/ SignificanceLikely outbreaks, of typical O119:H6(ST28) and atypical O127:H29(ST7798) were additionally identified. EPEC circulating in southwestern Nigeria are diverse and differ substantially from well-characterized lineages seen previously elsewhere. EPEC carriage and outbreaks could be commonplace but are largely undetected, hence, unreported, and require genomic surveillance for identification.

microbiology↗

bioRxiv2025

Sero-epidemiology of Rift Valley fever virus in ruminant livestock in The Gambia

Rift Valley fever (RVF) virus is a globally significant zoonotic pathogen primarily transmitted by mosquitoes, causing abortion storms and neonatal mortality in ruminant livestock and haemorrhagic encephalitis in humans. Although localized RVF outbreaks occur frequently in the West Africa Sahel, the complex interplay between vectors, ruminant hosts, human behaviours, and ecoclimatic factors driving these outbreaks remains unclear. In 2022, we conducted a cross-sectional study across The Gambia that collected serum samples linked to questionnaire data from 202 randomly selected livestock-owning households to estimate population-level seroprevalence, investigate the patterns of, and identify risk factors associated with RVFV seropositivity in ruminant livestock. Design adjusted seroprevalence estimates were 36.8% (95% Confidence Interval [CI]: 31.6-40.0) for cattle (n = 1416), 2.1% (95% CI: 0.5-3.7) for goats (n = 1101) and 4.3% (95% CI: 1.2-7.4) for sheep (n = 1085) using the IDScreen(R) RVF c-ELISA assay. The intracluster correlation coefficients for RVFV seropositivity at the herd level were 0.13 (95% CI: 0.09-0.18) in cattle and 0.22 (95% CI: 0.06-0.31) in small ruminants on the logit scale. Risk factors associated with RVFV seropositivity were investigated using a LASSO regression, with transhumant movement to the Gambia river valley, increasing age, introduction of new ruminants, and proximity to water identified as most strongly associated with seropositivity. By fitting the serologic data to a catalytic force of infection (FOI) model, age-independent FOI estimates of 0.12 (95% Credible Interval [CrI]: 0.10-0.16) for cattle and 0.013 (95% CrI: 0.01-0.02) for small ruminants were obtained. The observed patterns of RVFV seropositivity indicate widespread and endemic viral circulation, with livestock management practices and the Gambia river floodplains likely sustaining transmission. The high seroprevalence in cattle raises concerns that sporadic outbreaks may have occurred unnoticed or unreported, underscoring the critical need for comprehensive One Health surveillance to identify potential clinical cases.

ecology↗

bioRxiv2025

A SHERLOCK toolbox for the eco-epidemiological surveillance of animal African trypanosomosis reveals a similar parasite diversity in domestic pigs in two ancient sleeping sickness foci in Western Africa.

Animal African trypanosomosis (AAT), caused by protist parasites of the genus Trypanosoma, puts upward of a million head of livestock at risk across 37 countries in Africa. The economic impact of AAT and the presence of human-infectious trypanosomes in animals place a clear importance on improving diagnostics for animal trypanosomes to map the distribution of the veterinary parasites and identify reservoirs of human-infectious trypanosomes. We have adapted the CRISPR-based detection toolkit SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for trypanosomatid parasites responsible for AAT (SHERLOCK4AAT) including Pan- trypanosomatid, Trypanozoon, T. vivax, T. congolense, T. theileri, T. simiae and T. suis assays. To test the applicability of this technique in the field, we analysed dried blood spots collected from 200 farm and 224 free-ranging pigs in endemic and historical human African trypanosomiasis foci in Guinea and Cote dIvoire, respectively. The results revealed that SHERLOCK4AAT can detect and discriminate between trypanosome species involved in multiple infections with a high sensitivity. 62.7 % [58.1, 67.3] of pigs were found infected with at least one trypanosome species. T. brucei gambiense, a human-infectious trypanosome, was found in one animal at both sites, highlighting the risk that these animals may act as persistent reservoirs. These data suggest that, due to their proximity to humans and their attractiveness to tsetse flies, pigs could act as sentinels to monitor T. b. gambiense circulation using the SHERLOCK4AAT toolbox.

microbiology↗

bioRxiv2025

Molecular epidemiology of Theileria parva in Eastern Democratic Republic of Congo: Implications to the introduction of the Muguga Cocktail vaccine for East Coast Fever

East Coast Fever (ECF) is one of the most economically important tick-borne diseases of cattle in Eastern, Central, and Southern Africa, caused by the intracellular protozoan parasite Theileria parva (T. parva). This study investigated the prevalence and genetic diversity of T. parva populations in the eastern Democratic Republic of Congo (DRC) to inform immunization strategies against ECF. By employing PCR and DNA sequencing techniques, in conjunction with surveys assessing Knowledge and Practices, as well as conducting an immunization and field challenge trial, the findings suggest the existence of Rhipicephalus appendiculatus ticks in the provinces of South-Kivu, North Kivu, and Ituri. This underscores a possible threat of disease transmission in these areas. Molecular analyses uncovered diverse T. parva populations with varying antigenic profiles, challenging the assumption of uniformity despite Muguga cocktail-like appearances. Moreover, phylogenetic analyses suggested limited similarity between T. parva populations and the Muguga cocktail vaccine. Microsatellite analysis and field challenge trials supported the notion of multiple populations, highlighting the current vaccines limitations against field strains. This study has the potential to significantly contribute to understanding T. parva dynamics in the region, emphasizing the complexities of vaccine strain selection and stressing the importance of continuous monitoring and adaptive control strategies in the face of evolving parasite populations.

molecular biology↗

bioRxiv2025

Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

The study investigates global genomic surveillance of Cryptococcus neoformans over three decades to elucidate genetic diversity, incorporating serotypes, molecular types, STs and mating types, phylogenomics, virulence-associated determinants, antifungal resistance, and pangenome profiles. Across 139 study genomes, the isolates exhibited nineteen distinct sequence types (STs), among which ST5 (63%) was the most prevalent. The predominance of MAT mating type 91% mirrors enhanced virulence, environmental adaptability and clonal expansion, enabling its persistence without MATa (9%) counterparts. The phylogenomic analysis revealed, there is no distinct clustering of isolates from clinical and environmental settings, indicating a high level of genome conservation across sources. Core-accessory genome partitioning and ortholog-based clustering revealed clonal population dominance of the VNI lineage across continents, alongside clear divergence from the VNIV lineage. Virulence gene analysis highlighted conserved expression of capsular genes, phospholipase gene, iron acquisition genes and superoxide dismutase genes, while point mutations and aneuploidy in ERG11 and AFR1 suggested potential azole-resistance mechanisms. This study delivers a holistic assessment of global genomic diversity in the C. neoformans population, emphasising evolutionary conservation, lineage-specific divergence, and adaptability to environment, host and anti-fungal treatments.

bioinformatics↗

bioRxiv2018

epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

The increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

genomics↗

bioRxiv2018

Pathogens, parasites, and parasitoids of ants: a synthesis of parasite biodiversity and epidemiological traits

1.Ants are among the most ecologically successful organisms on Earth, with a global distribution and diverse nesting and foraging ecologies. Ants are also social organisms, living in crowded, dense colonies that can range up to millions of individuals. Understanding the ecological success of the ants requires understanding how they have mitigated one of the major costs of social living-infection by parasitic organisms. Additionally, the ecological diversity of ants suggests that they may themselves harbor a diverse, and largely unknown, assemblage of parasites. As a first step, we need to know the taxonomic and functional diversity of the parasitic organisms infecting ants. To that end, we provide a comprehensive review of the parasitic organisms infecting ants by collecting all extant records. We synthesize major patterns in parasite ecology by categorizing how parasites encounter their ant hosts, whether they require host death as a developmental necessity, and how they transmit to future hosts.\n\nWe report 1,415 records of parasitic organisms infecting ants, the majority of which come from order Diptera (34.8%), phylum Fungi (25.6%), and order Hymenoptera (25.1%). Most parasitic organisms infecting ants are parasitoids (89.6%), requiring the death of their host as developmental necessity and most initially encounter their hosts in the extranidal environment (68.6%). Importantly, though most parasitic organisms infecting ants only need a single host to complete their life cycle (89.2%), the vast majority need to leave the nest before transmission to the next ant host can occur (88.3%), precluding ant-to-ant transmission within the nest. With respect to the host, we only found records for 9 out of 17 extant ant sub-families, and for 82 out of the currently recognized 334 ant genera. Though there is likely bias in the records reported, both host and parasite ecological traits and evolutionary histories underlie the pattern of ant-parasite association reported here. This work provides a foundation for future work that will begin to untangle the ecological drivers of ant-parasite relationships and the evolutionary implications thereof.

ecology↗

bioRxiv2018

DETECTION AND MOLECULAR EPIDEMIOLOGY OF HUMAN BOCAVIRUS IN CHILDREN WITH ACUTE GASTROENTERITIS FROM BRAZIL

Human Bocavirus (HBoV) is a recently discovered virus and was first detected in the nasopharyngeal aspirate samples and after in stool samples, suggesting that HBoV may be a causative agent for human enteric infections. Due to absence of treatment options, there is a need to understand the disease-causing mechanism of these viruses. The aim of this was to demonstrate the prevalence of HBoV from children less than 10 years with acute gastroenteritis in Brazil, during November 2011 to November 2012. Stool samples from hospitalized children [≤] 10 years who presented symptoms of acute gastroenteritis were analyzed for the presence of HBoV DNA by nested-PCR. HBoV- positivity was detected in 24.0% (54/225) of samples. Two peaks of HBoV detection were observed, during November 2011 and July to September 2012. Co-infections between HBoV and rotavirus A were identified in 50.0% (27/54) of specimens. Phylogenetic analysis identified the presence of HBoV-1 (94.8%), HBoV-2 (2.6%) and HBoV-3 (2.6%) species, with only minor variations among them. Further investigations are necessary to improve the knowledge on the role of HBoV in gastrointestinal infections.

microbiology↗

bioRxiv2018

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

Syphilis is a sexually transmitted infection caused by Treponema pallidum subspecies pallidum and may lead to severe complications. Recent years have seen striking increases in syphilis in many countries. Previous analyses have suggested one lineage of syphilis, SS14, may have expanded recently, indicating emergence of a single pandemic azithromycin-resistant cluster. We used direct sequencing of T. pallidum combined with phylogenomic analyses to show that both SS14- and Nichols-lineages are simultaneously circulating in clinically relevant populations in multiple countries. We correlate the appearance of genotypic macrolide resistance with multiple independently evolved SS14 sub-lineages and show that genotypically resistant and sensitive sub-lineages are spreading contemporaneously, incompatible with the notion that SS14-lineage expansion is driven purely by macrolide resistance. These findings inform our understanding of the current syphilis epidemic by demonstrating how macrolide resistance evolves in Treponema subspecies and provide a warning on broader issues of antimicrobial resistance.

genomics↗

bioRxiv2018

Molecular epidemiology of Colombian Histoplasma capsulatum isolates shows their polyphyletic behavior and point out raw chicken manure as one of the infections sources

The thermally dimorphic fungus Histoplasma capsulatum is the causative agent of histoplasmosis, which is the most prevalent endemic mycosis in America. The replacement of organic matter in agro-ecosystems is necessary in the tropics, and the use of organic fertilizers has increased. Cases and outbreaks due to the presence of the fungus in these components have been reported. In Colombia, chicken manure is the most common raw material in the organic fertilizers production. In this work, we reached the isolation of the fungus from a chicken manure. Then, we were able to compare genetically 3 environmental isolates with 42 Colombian human clinical isolates. The genetic comparison showed the environmental isolates grouping together with the clinical isolates. This result suggests chicken manure as one of the infection source with H. capsulatum. Also, the phylogenetic analysis using another H. capsulatum isolates from databases showed that the Colombian isolates widely distributed in the relation tree. This result pointed out the great genetic diversity among H. capsulatum Colombian population.

microbiology↗

bioRxiv2018

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

BackgroundBovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen.\n\nMethodsMycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes.\n\nResultsMycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR=2.7,p=0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001,OR=124.4,95% CI=30.1-508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana.\n\nConclusionOur data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups.

microbiology↗

bioRxiv2019

Genomic and epidemiological evidence of a dominant Panton-Valentine leucocidin-positive Methicillin Resistant Staphylococcus aureus lineage in Sri Lanka with spread to the United Kingdom and Australia

ObjectiveTo undertake the first detailed genomic analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Sri Lanka.\n\nMethodsA prospective observational study was performed on 94 MRSA isolates collected over a four month period from the Anuradhapura Teaching Hospital, Sri Lanka. Screening for mecA, mecC and the Panton-Valentine leucocidin (PVL)-associated lukS-PV/lukF-PV genes and molecular characterisation by spa typing was undertaken. Whole genome sequencing (WGS) and phylogenetic analysis was performed on selected multilocus sequence type (MLST) clonal complex 5 (CC5) isolates from Sri Lanka, England, Australia and Argentina.\n\nResultsAll 94 MRSA harboured the mecA gene. Nineteen spa types associated with nine MLST clonal complexes were identified. Most isolates were from skin and soft tissue infections (76.9%), with the remainder causing more invasive disease. Sixty two (65.9%) of isolates were PVL positive with the majority (56 isolates; 90.3%) belonging to a dominant CC5 lineage. This lineage, PVL-positive ST5-MRSA-IVc, was associated with community and hospital-onset infections. Based on WGS, representative PVL-positive ST5-MRSA-IVc isolates from Sri Lanka, England and Australia formed a single phylogenetic clade, suggesting wide geographical circulation.\n\nConclusionsWe present the most detailed genomic analysis of MRSA isolated in Sri Lanka to date. The analysis identified a PVL-positive ST5-MRSA-IVc that dominates MRSA clinical infections in Sri Lanka. Furthermore, transmission of the strain has occurred in the United Kingdom and Australia.

microbiology↗

bioRxiv2019

Work Flows for Cellular Epidemiology, From Conception to Translation

The authors have withdrawn their manuscript after issues with the cell viability validation (Fig. 8) were found. In the interest of furthering science and ensuring that clinical decisions are based on best practices and evidence, the issue is described in more detail in the peer-reviewed, published paper: https://www.frontiersin.org/articles/10.3389/fphys.2021.647603/full Knothe Tate ML, Srikantha A, Wojek C, Zeidler D (2021) Connectomics of Bone to Brain-- Probing Physical Renderings of Cellular Experience, Frontiers in Physiology 12: 1018, doi: 10.3389/fphys.2021.647603 As noted in that published work: "Osteocyte coordinates can be extracted from the YOLO classified image set, enabling high throughput analyses of massive datasets, which in the future could include other cellular inhabitants of tissues including blood cells, immune cells, chondrocytes, etc. While the method shows great promise for automated detection of cells, the greatest limitation of the method is the definition of appropriate and unbiased classifiers. The definition of osteocytes as pyknotic and viable based on the number of cell processes was shown to be flawed in a parallel study testing the assumption using biochemical based viability measures (Anastopolous and Knothe Tate, 2021)." Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

physiology↗