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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 19 recordsLinked to original sources

bioRxiv2018

Redesign of an Undergraduate General Microbiology Lab to Include Authentic Discovery-Driven Research on Cucumber Fermentations

Many undergraduate introductory microbiology laboratory courses teach basic principles of bacteriology using classical protocol-based experiments, with limited critical thinking and inquiry-based learning practices. We initiated a comprehensive redesign in our General Microbiology Laboratory course to promote scientific critical and creative thinking, while strengthening core microbiology concepts and skills. As part of the redesign, a series of authentic discovery-driven labs, based on cucumber fermentations, were developed as an independent research module within the course curriculum. Integrating discovery-driven labs allowed students to be engaged problem solvers, applying the scientific process to develop hypotheses, design experiments, utilize quantitative reasoning, and effectively communicate results. The inquiry-guided research project was developed to evaluate the minimum concentration of salt (NaCl) required in fermentation brine to safely, and effectively, ferment cucumbers. Over 5 weeks, students assess different aspects of the fermentation process, including quantifying bacterial populations with differential and selective media, measuring pH and glucose concentration of brine solutions, and characterizing the microbial metabolic potential. Additionally, students isolate an unknown bacterium from their fermentations, identifying and characterizing the isolate using 16S rRNA gene sequencing and metabolic tests. Throughout the research project, students collect, graph, and analyze their observations, culminating in students creating and presenting a scientific research poster. With this lab redesign, students generate new knowledge contributing to our understanding of microbial ecology within food fermentations, learn core microbiology skills and techniques, and develop critical and creative thinking skills. The impact of their research is valuable to science educators, researchers, and industry partners.

scientific communication and education↗

bioRxiv2015

Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar

Advances in whole genome sequencing (WGS) platforms and DNA library preparation have led to the development of methods for high throughput sequencing of bacterial genomes at a relatively low cost (Loman et al. 2012; Medini et al. 2008). WGS offers unprecedented resolution for determining degrees of relatedness between strains of bacterial pathogens and has proven a powerful tool for microbial population studies and epidemiological investigations (Harris et al. 2010; Lienau et al. 2011; Holt et al. 2009; Ashton, Peters, et al. 2015). The potential utility of WGS to public health microbiology has been highlighted previously (Koser et al. 2012; Kwong et al. 2013; Reuter et al. 2013; Joensen et al. 2014; Nair et al. 2014; Bakker et al. 2014; DAuria et al. 2014). Here we report, for the first time, the routine use of WGS as the primary test for identification, surveillance and outbreak investigation by a national reference laboratory. We present data on how this has revolutionised public health microbiology for one of the most common bacterial pathogens in the United Kingdom, the Salmonellae.\n\nDATA SUMMARY1. PHE Salmonella sequencing data is deposited in the Sequence Read Archive in BioProject PRJNA248792.\n\nIMPACT STATEMENTThe first human genome cost around $3 billion, and took around 10 years to complete. Advances in DNA sequencing technology (also referred to as whole genome sequencing (WGS)) allow the same feat to be accomplished today for less than $10000 and less than 2 weeks. This remarkable improvement in technology has also led to a step change in microbiology, increasing our understanding of the evolution of major human pathogens such as Yersinia pestis, Salmonella Typhi and Mycobacterium tuberculosis. While these kinds of academic studies provide unparalleled context for public health action, until now, this approach has not been routinely employed at the frontline. At Public Health England, WGS has been implemented for routine public health identification, characterisation and typing of an important human pathogen, Salmonella, replacing methods that have changed little over the last 100 years. Analysis of WGS data has identified outbreaks that were previously undetectable and been used to infer rare antimicrobial resistance patterns. This paper will serve as a notification to the community of the methods PHE are using, and will be of great use to other public health labs considering switching to WGS.

Microbiology↗

bioRxiv2018

Fresh Snowfall Microbiology and Chemistry are Driven by Geography in Storm-Tracked Events

Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in-silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfalls geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual deposits of up to ~10 kg of bacterial / archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the everything is everywhere hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.\n\nImportanceSnowfall is commonplace to the temperate and polar regions of the world. As an interface between the atmosphere, hydrosphere and earth, snow is responsible for high annual deposits of moisture globally, and, can serve as a water bank in the form of both permanent snow fields and glaciers. Essential to general ecosystem function, snow can also be considered a transporter of aerosolized material. Given the magnitude of microbiota deposited by snowfall, which we report, it is likely that biological material within snowfall, with its geochemical underpinning-- and the associated genetic banks--have significant downstream ecological effects.\n\nUnderstanding what is contained in snowfall becomes especially urgent in a warming climate where high-impact meteorological and ecological changes are imminent and likely. With climate-induced changes to snowfall patterns, surface ecosystems are likely to be impacted by ensuing changes in microbiota deposition. Thus, the ecosystem function of soils, rock and surface waters are also likely to be impacted; these changes, in turn, greatly influence agriculture, weathering and infrastructure.

microbiology↗

bioRxiv2016

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.\n\nDATA SUMMARYThe paper describes a new, freely available public resource and therefore no data has been generated. The resource can be accessed at http://www.climb.ac.uk. Source code for software developed for the project can be found at http://github.com/MRC-CLIMB/\n\nI/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.\n\nIMPACT STATEMENTTechnological advances mean that genome sequencing is now relatively simple, quick, and affordable. However, handling large genome datasets remains a significant challenge for many microbiologists, with substantial requirements for computational resources and expertise in data storage and analysis. This has led to fragmentary approaches to software development and data sharing that reduce the reproducibility of research and limits opportunities for bioinformatics training. Here, we describe a nationwide electronic infrastructure that has been designed to support the UK microbiology community, providing simple mechanisms for accessing large, shared, computational resources designed to meet the bioinformatic needs of microbiologists.

Bioinformatics↗

bioRxiv2018

Bigger and Better? Representativeness of the Influenza A surveillance using one consolidated clinical microbiology laboratory data set as compared to the Belgian Sentinel Network of Laboratories

Infectious diseases remain a serious public health concern globally, while the need for reliable and representative surveillance systems remains as acute as ever. The public health surveillance of infectious diseases uses reported positive results from sentinel clinical laboratories or laboratory networks, to survey the presence of specific microbial agents known to constitute a threat to public health in a given population. This monitoring activity is commonly based on a representative fraction of the microbiology laboratories nationally reporting to a single central reference point. However in recent years a number of clinical microbiology laboratories (CML) have undergone a process of consolidation involving a shift towards laboratory amalgamation and closer real-time informational linkage. This report aims to investigate whether such merging activities might have a potential impact on infectious diseases surveillance. Influenza data was used from Belgian public health surveillance 2014-2017, to evaluate whether national infection trends could be estimated equally as effectively from only just one centralised CML serving the wider Brussels area (LHUB-ULB). The overall comparison reveals that there is a close correlation and representativeness of the LHUB-ULB data to the national and international data for the same time periods, both on epidemiological and molecular grounds. Notably, the effectiveness of the LHUB-ULB surveillance remains partially subject to local regional variations. These results illustrate that centralised CML-derived data are not only credible but also advantageous to use for future surveillance and prediction purposes, especially for automatic detection systems that might include multiple layers of information and timely implementation of control strategies.

epidemiology↗

bioRxiv2017

Preprinting Microbiology

The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain the Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer-review. Although use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem.

microbiology↗

bioRxiv2017

Discovery-oriented teaching: The use of chimeric proteorhodopsins for the development of a lab curriculum in marine microbiology and for the discovery of natural red-shifted proteorhodopsins

Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4-5 days, that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions - green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.

microbiology↗

bioRxiv2018

Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements

AimIdentify basic requirements for a metagenomic nanopore sequencing protocol permitting frequent application in a clinical microbiology daily routine diagnostic setting.\n\nBackgroundNanopore sequencing with the Oxford Nanopore Technologies MinION device has a potential to markedly improve clinical diagnosis of infections. Reports have emerged recently that it may provide direct-from-clinical-sample information; for example, with urine samples, bronchial tuberculosis samples and orthopedic prostheses. However, the ideal protocol for clinical use remains to be determined, especially relating to detection of relevant pathogen quantities and to finding a reasonable level of economic costs.\n\nResultsMinION can provide qualitatively and quantitatively correct identification of multiple species in metagenomics samples. For detection of clinically relevant quantities of bacteria (on a nanogram DNA level) there is a need for carrier DNA. Importantly, high-purity DNA and a naive MinION flow cell seem to be critical parameters.\n\nConclusionsOur results suggest that high-purity clinical sample DNA, addition of carrier DNA and a naive flow cell are critical factors for clinical use of MinION. A relatively high error rate may limit detection of antimicrobial resistance genes, and a realistic level of costs will require availability of a price-reduced and single-use flowcell.

microbiology↗

bioRxiv2018

Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing: addressing the microbiological, epidemiological, and bioinformatic challenges

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) has not been routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group strains were obtained from human cases (n =7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (clade III) and B. cereus sensu stricto (clade IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely-related and formed a well-supported clade relative to publicly-available emetic clade III genomes with an identical sequence type (ST 26). When compared to publicly-available emetic clade III ST 26 B. cereus group genomes, the 30 emetic clade III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly-available genomes by a mean of 301.7 to 528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. Based on both WGS and epidemiological data, we hypothesize that the outbreak was a single source outbreak caused by emetic clade III B. cereus belonging to the B. paranthracis species. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.

microbiology↗

bioRxiv2018

Linking Fungal and Bacterial Proliferation to Microbiologically Influenced Corrosion in B20 Biodiesel Storage Tanks

Biodiesel is a renewable substitute, or extender, for petroleum diesel that is composed of a mixture of fatty acid methyl esters (FAME) derived from plant and animal fats. Ultra-low sulfur diesel (ULSD) blended with up to 20% FAME can be used interchangeably with ULSD, is compatible with existing infrastructure, but is also more susceptible to biodegradation. Microbial proliferation and fuel degradation in biodiesel blends has not been directly linked in situ to microbiologically influenced corrosion. We, therefore, conducted a yearlong study of B20 storage tanks in operation at two locations, identified the microorganisms responsible for observed fuel fouling and degradation, and measured in situ corrosion. The bacterial populations were more diverse than the fungal populations, and largely unique to each location. The bacterial populations included members of the Acetobacteraceae, Clostridiaceae, and Proteobacteria. The abundant Eukaryotes at both locations consisted of the same taxa, including a filamentous fungus within the family Trichocomaceae, and the Saccharomycetaceae family of yeasts. Increases in the absolute and relative abundances of the Trichocomaceae were correlated with significant, visible fouling and pitting corrosion. This study identified the relationship between recurrent fouling of B20 with increased rates of corrosion, largely at the bottom of the sampled storage tanks.

microbiology↗

bioRxiv2015

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

Integrated -omics approaches are quickly spreading across microbiology research labs, leading to i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organisation and ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from - omics experiments. In this work, we present opportunities and challenges of multi -omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.

Systems Biology↗

bioRxiv2018

A Cross-Platform Comparison of Student’s Perceptions of the Learning Environment in an Introductory Microbiology Course

AbstractStudents positive perceptions of the learning environment increase retention and persistence in STEM disciplines. This study presents results from a Learning Environment Questionnaire administered at the beginning and end of the semester in a redesigned general/introductory microbiology course offered in traditional lecture, flipped and online sections. Split-sample t-tests and chi-squared tests were used for cross-section and within section analyses, respectively. The findings support the study hypothesis that student perceptions of the learning environment will vary as a function of platform. This work demonstrates the additional effect of the time in the semester when students complete the questionnaire and this effect on students perceptions over the course of the semester relative to their initial perceptions. The results of this study offer insight on student perceptions of the learning environment as universities embrace online education in introductory and gateway courses as a response to rising student enrollments and diminishing resources.

scientific communication and education↗

bioRxiv2016

Alternative Growth Behavior of Mycobacterium Avium Subspecies and Staphylococci with Implications for Clinical Microbiology and Blood Culture

Rapid culture of Mycobacterium avium subspecies paratuberculosis (MAP) from patients remains a challenge. During the process of developing a rapid culture method for MAP, we found that there is an alternative growth behavior present in MAP, MAH (Mycobacterium avium subspecies hominissuis) and other bacteria such as Staphylococcus aureus, and Staphylococcus pseudintermedius. The bacterial DNA, RNA and proteins are present in the supernatants of the liquid culture media after routine microcentrifugation. When cultured in the solid media plate, there are a limited number of colonies developed for MAP and MAH disproportionate to the growth. We believe there is an alternative growth behavior for MAP, MAH and other bacteria similar to \"phenoptosis\". Based on the alternative bacterial growth behavior, we tested 62 blood culture specimens that have been reported negative by routine automated blood culture method after 5 days of incubation. We used alternative culture media and molecular diagnostic techniques to test these negative culture bottles, and we found a large percentage of bacterial growth by alternative culture media (32%) and by molecular PCR amplification using 16s rDNA primer set and DNA sequencing (69%). The sensitivity of detection by the molecular PCR/sequencing method is significantly higher than by routine automated blood culture. Given the challenge of early diagnosis of sepsis in the hospital setting, it is necessary to develop more sensitive and faster diagnostic tools to guide clinical practice and improve the outcome of sepsis management.

Microbiology↗

bioRxiv2018

Epidemiology, Microbiology and Therapeutic Consequences of Chronic Osteomyelitis in Northern China: A Retrospective Analysis of 255 Patients

The study aimed to explore the epidemiology and clinical characteristics of chronic osteomyelitis observed in a northern China hospital. Clinical data of 255 patients with chronic osteomyelitis from January 2007 to January 2014 were collected and analyzed, including general information, disease data, treatment and follow-up data. Chronic osteomyelitis is more common in males and in the age group from 41-50 years of age. Common infection sites are the femur, tibiofibular, and hip joint. More g+ than g- bacterial infections were observed, with S. aureus the most commonly observed pathogenic organism. The positive detection rate from debridement bacterial culture is 75.6%. The detection rate when five samples are sent for bacterial culture is 90.6%, with pathogenic bacteria identified in 82.8% of cases. The two-stage debridement method (87.0%) has higher first curative rate than the one-stage debridement method (71.2%). To improve detection rate using bacterial culture, at least five samples are recommended. Treatment of chronic osteomyelitis with two-stage debridement, plus antibiotic-loaded polymethylmethacrylate (PMMA) beads provided good clinical results in this study and is therefore recommended.

microbiology↗

bioRxiv2014

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. Here we have demonstrated the use of SRST2 for microbial genome surveillance in a variety of public health and hospital settings. In the face of rising threats of antimicrobial resistance and emerging virulence amongst bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/.

Genomics↗

bioRxiv2017

Evidence-Based Design and Evaluation of a Whole Genome Sequencing Clinical Report for the Reference Microbiology Laboratory

BackgroundMicrobial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics - including clinicians, laboratorians, epidemiologists, and researchers - is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results.\n\nMethodsWe used Design Study Methodology - a human centered multi-stage approach drawn from the information visualization domain - to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report.\n\nResultsWe recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the alternative prototype designs over the existing version, and that both clinicians and non-clinicians expressed similar design preferences. Participants articulated clearer design preferences when asked to compare individual design elements versus entire reports. Both the quantitative and qualitative data informed the design of a revised report, which is available online as a LaTeX template.\n\nConclusionsWe show how a human-centered design approach integrating quantitative and qualitative feedback can be used to design an alternative report for representing complex microbial genomic data. We suggest experimental and design guidelines to inform future design studies in the bioinformatics and microbial genomics domains, and suggest that this type of mixed-methods study is important to facilitate the successful translation of pathogen genomics in the clinic, not only for clinical reports but also more complex bioinformatics data visualization software.

genomics↗

bioRxiv2016

An ex vivo lung model to study bronchioles infected with Pseudomonas aeruginosa biofilms

A key aim in microbiology is to determine the genetic and phenotypic bases of bacterial virulence, persistence and antimicrobial resistance in chronic biofilm infections. This requires tractable, high-throughput models that reflect the physical and chemical environment encountered in specific infection contexts. Such models will increase the predictive power of microbiological experiments and provide platforms for enhanced testing of novel antibacterial or antivirulence therapies. We present an optimised ex vivo model of cystic fibrosis lung infection: ex vivo culture of pig bronchiolar tissue in artificial cystic fibrosis mucus. We focus on the formation of biofilms by Pseudomonas aeruginosa. We show highly repeatable and specific formation of biofilms that resemble clinical biofilms by a commonly-studied lab strain and ten cystic fibrosis isolates of this key opportunistic pathogen.

Microbiology↗

bioRxiv2016

Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge

High-throughput whole-genome sequencing (WGS) is a revolutionary tool in public health microbiology and is gradually substituting classical typing methods in surveillance of infectious diseases. In combination with epidemiological methods, WGS is able to identify both sources and transmission-pathways during disease outbreak investigations. This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union. We describe how WGS has improved surveillance and outbreak detection of C. jejuni infections and how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen. However, the full implementation of this methodology in real-time is still hampered by a few hurdles. The limited insight into the genetic diversity of different lineages of C. jejuni impedes the validity of assumed genetic relationships. Furthermore, efforts are needed to reach a consensus on which analytic pipeline to use and how to define the strains cut-off value for epidemiological association while taking the needs and realities of public health microbiology in consideration. Even so, we claim that ample evidence is available to support the benefit of integrating WGS in the monitoring of C. jejuni infections and outbreak investigations.

Microbiology↗