Modelling the deactivation of Escherichia coli in Nigerian soils amended with differently treated manures.

AIM: This study aimed to simulate deactivation of Escherichia coli in soils amended with cattle manure after burning, anaerobic digestion, composting, or without treatment. METHOD AND RESULTS: The Weibull survival function was used to describe deactivation of E. coli. Parameters for each treatment were determined using E. coli measurements from manure-amended soils and evaluated against measurements at different application rates. A statistically significant correlation and high coincidence between the simulated and measured values were obtained. The simulations revealed that although anaerobic digestion or burning of cattle manure effectively reduced the E. coli loads to background levels, burning retained very little nitrogen, so the ash residue was ineffective as an organic fertilizer. Anaerobic digestion was most effective at reducing E. coli levels while retaining a high proportion of N in the bioslurry residue, but the persistence of E. coli was higher than in compost. CONCLUSION: The results from this study suggest that the safest method for production of organic fertilizer would involve anaerobic digestion to reduce E. coli, followed by composting to reduce its persistence.

Identifying the sources of human campylobacteriosis in Nigeria.

Campylobacter spp. have been shown to be the most common cause of bacterial gastroenteritis worldwide. Cases of human campylobacteriosis are usually reported as sporadic and not part of an outbreak which makes the identification of the source of infection difficult. A study of the relationships within isolate populations in Nigeria and source attribution analysis of Nigerian human Campylobacter spp. to other animal isolates was carried out to determine the possible sources for human Campylobacter infection in Nigeria. The results showed nine sequence types (STs) common to both humans and livestock isolated from abattoirs, farms and live bird markets with similar STs clustering together on a phylogenetic tree, confirming a degree of genetic similarity. Source attribution analysis suggests wild birds as the most important reservoir (38%) for human Campylobacter spp. infection in Nigeria followed by chicken (23%), pig (19%), cattle (11%) and sheep (8%). This might be an indication of the importance of this infection source to humans in Nigeria and probably other low-income countries due to farming practices and human habits.

The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni.

Campylobacter jejuni is a bacterial pathogen recognised as a major cause of foodborne illness worldwide. While Campylobacter jejuni generally does not grow outside its host, it can survive outside of the host long enough to pose a health concern. This review presents an up-to-date description and evaluation of biological, mathematical, and statistical approaches used to understand the behaviour of this foodborne pathogen and suggests future avenues which can be explored. Specifically, the incorporation of mathematical modelling may aid the understanding of C. jejuni biofilm formation both outside and inside the host. Predictive studies may be improved by the introduction of more standardised protocols for assessments of disinfection methods and by assessment of novel physical disinfection strategies as well as assessment of the efficiency of plant extracts on C. jejuni eradication. A full description of the metabolic pathways of C. jejuni, which is needed for the successful application of metabolic models, is yet to be achieved. Finally, a shift from animal models (except for those that are a source of human campylobacteriosis) to human-specific data may be made possible due to recent technological advancements, and this may lead to more accurate predictions of human infections.

Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing. RESULTS: Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI's pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters. CONCLUSIONS: In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.

Impacts of different treatment methods for cattle manure on the spread of faecal indicator organisms from soil to lettuce in Nigeria.

AIM: This study investigated impacts of different organic waste treatment methods on reduction and spread of faecal indicator organisms to food crops in a developing country. METHODS AND RESULTS: Fresh cattle manure was subjected to three different treatments; anaerobic digestion, burning and composting. Escherichia coli, coliforms and nitrogen content of cattle manure were measured before and after treatment in the amended soil and harvested lettuce. All treatments significantly reduced E. coli and coliform counts but differed in the ratio of E. coli or coliforms to nitrogen. Application of the recommended nitrogen dose of 120 kg ha-1 as bioslurry resulted in significantly lower E. coli and coliform contamination of soil than the same nitrogen rate applied as compost or ash. The E. coli content of lettuces grown on soil amended with treated wastes at recommended rates did not differ between treatments but was significantly lower than in lettuces grown on soil amended with untreated manure. CONCLUSIONS: Treatment of manure before use as an organic fertilizer significantly reduces potential contamination of both soil and food crops with E. coli and coliforms. To best reduce the spread of E. coli from organic fertilizers, manures should be treated by anaerobic digestion. SIGNIFICANCE AND IMPACT OF THE STUDY: Information from this study quantifies potential risks associated with use of manures in growing food crops by determining the ratio between pathogen content and required nitrogen application rate.

Importance of untested infectious individuals for interventions to suppress COVID-19.

The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 60-80% of all infected individuals during the early stages of the outbreaks. We propose that reducing the underlying transmission from untested cases is crucial to suppress the virus. This can be achieved through enhanced testing in combination with social distancing and other interventions that reduce transmission such as wearing face masks. Once transmission from silent carriers is kept under control by these means, the virus could have been fully suppressed through fast isolation and contact tracing of tested cases.

Estimated Dissemination Ratio-A Practical Alternative to the Reproduction Number for Infectious Diseases.

Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust measure of the trajectory of an outbreak that has been used for many years in the control of infectious disease in livestock. It is simple to calculate and explain. Its calculation and use are discussed below together with examples from the current COVID-19 outbreak in the UK. These applications illustrate that EDR can demonstrate changes in transmission rate before they may be clear from the epidemic curve. Thus, EDR can provide an early warning that an epidemic is resuming growth, allowing earlier intervention. A conceptual comparison between EDR and the commonly used reproduction number is also provided.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 1: Background and model description.

A new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is developed that attempts to overcome limitations in existing faecal indicator organism (FIO) models arising from coarse spatial discretisations and poorly-constrained hydrological processes. MAFIO is a spatially-distributed, process-based model presently designed to simulate the fate and transport of agents representing FIOs shed by livestock at the sub-field scale in small (<10 km2) agricultural catchments. Specifically, FIO loading, die-off, detachment, surface routing, seepage and channel routing are modelled on a regular spatial grid. Central to MAFIO is that hydrological transfer mechanisms are simulated based on a hydrological environment generated by an external model for which it is possible to robustly determine the accuracy of simulated catchment hydrological functioning. The spatially-distributed, tracer-aided ecohydrological model EcH2O-iso is highlighted as a possible hydrological environment generator. The present paper provides a rationale for and description of MAFIO, whilst a companion paper applies the model in a small agricultural catchment in Scotland to provide a proof-of-concept.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 2: Application to a small agricultural catchment.

The new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is applied to a small (0.42 km2) Scottish agricultural catchment to simulate the dynamics of E. coli arising from sheep and cattle farming, in order to provide a proof-of-concept. The hydrological environment for MAFIO was simulated by the "best" ensemble run of the tracer-aided ecohydrological model EcH2O-iso, obtained through multi-criteria calibration to stream discharge (MAE: 1.37 L s-1) and spatially-distributed stable isotope data (MAE: 1.14-3.02‰) for the period April-December 2017. MAFIO was then applied for the period June-August for which twice-weekly E. coli loads were quantified at up to three sites along the stream. Performance in simulating these data suggested the model has skill in capturing the transfer of faecal indicator organisms (FIOs) from livestock to streams via the processes of direct deposition, transport in overland flow and seepage from areas of degraded soil. Furthermore, its agent-based structure allowed source areas, transfer mechanisms and host animals contributing FIOs to the stream to be quantified. Such information is likely to have substantial value in the context of designing and spatially-targeting mitigation measures against impaired microbial water quality. This study also revealed, however, that avenues exist for improving process conceptualisation in MAFIO (e.g. to include FIO contributions from wildlife) and highlighted the need to quantitatively assess how uncertainty in the spatial extent of surface flow paths in the simulated hydrological environment may affect FIO simulations. Despite the consequent status of MAFIO as a research-level model, its encouraging performance in this proof-of-concept study suggests the model has significant potential for eventual incorporation into decision support frameworks.

Mining whole genome sequence data to efficiently attribute individuals to source populations.

Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.

Variability in growth responses of non-O157 EHEC isolates in leafy vegetables, sprouted seeds and soil extracts occurs at the isolate level.

Foods of plant origin are recognised as a major source of foodborne pathogens, in particular for Shigatoxigenic Escherichia coli (STEC). Most work for STEC and plant-based fresh produce has focused on the most prevalent outbreak serogroup, O157. However, non-O157 STEC is an emerging hazard, and as such it is important to characterise aspects within this group that reflect their ability to colonise alternative hosts and habitats relevant to horticultural production. Growth kinetics were quantified for a diverse set of clinical enterohaemorrhagic E. coli isolates in extracts made from different tissues of spinach, lettuce or sprouted seeds, or from soil, to represent association with ready-to-eat fresh produce production. For leafy vegetables, spinach apoplast supported the fastest rates of growth and lettuce root extracts generated the slowest growth rates. Growth rates were similar for the majority of isolates in fenugreek or alfalfa sprouted seed extracts. Monosaccharides were the major driver of bacterial growth. No correlations were found for growth rates between different serotypes or for Shigatoxin gene carriage. Thus, growth rates varied in a plant-dependent and isolate-dependent manner, for all plant or soil extracts tested, indicative of isolate-specific differences in metabolic flexibility. These findings are relevant for risk assessment of non-O157 STEC.

Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom.

BACKGROUND: Campylobacter jejuni is the most common bacterial cause of human infectious intestinal disease. METHODS: We genome sequenced 601 human C. jejuni isolates, obtained from two large prospective studies of infectious intestinal disease (IID1 [isolates from 1993-1996; n = 293] and IID2 [isolates from 2008-2009; n = 93]), the INTEGRATE project [isolates from 2016-2017; n = 52] and the ENIGMA project [isolates from 2017; n = 163]. RESULTS: There was a significant increase in the prevalence of the T86I mutation conferring resistance to fluoroquinolone between each of the three later studies (IID2, INTEGRATE and ENIGMA) and IID1. Although the distribution of major multilocus sequence types (STs) was similar between the studies, there were changes in both the abundance of minority STs associated with the T86I mutation, and the abundance of clones within single STs associated with the T86I mutation. DISCUSSION: Four population-based studies of community diarrhoea over a 25 year period revealed an increase over time in the prevalence of the T86I amongst isolates of C. jejuni associated with human gastrointestinal disease in the UK. Although associated with many STs, much of the increase is due to the expansion of clones associated with the resistance mutation.

A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing.

BackgroundCampylobacter is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data.ObjectivesThis review aimed to summarise approaches and findings of these studies and identify best practice lessons for this form of genomic epidemiology.MethodsWe systematically reviewed publications using MLST data to attribute human disease isolates to source. Publications were from January 2001, when this type of approach began. Searched databases included Scopus, Web of Science and PubMed. Information on samples and isolate datasets used, as well as MLST schemes and attribution algorithms employed, was obtained. Main findings were extracted, as well as any results' validation with subsequent correction for identified biases. Meta-analysis is not reported given high levels of heterogeneity.ResultsOf 2,109 studies retrieved worldwide, 25 were included, and poultry, specifically chickens, were identified as principal source of human infection. Ruminants (cattle or sheep) were consistently implicated in a substantial proportion of cases. Data sampling and analytical approaches varied, with five different attribution algorithms used. Validation such as self-attribution of isolates from known sources was reported in five publications. No publication reported adjustment for biases identified by validation.ConclusionsCommon gaps in validation and adjustment highlight opportunities to generate improved estimates in future genomic attribution studies. The consistency of chicken as the main source of human infection, across high income countries, and despite methodological variations, highlights the public health importance of this source.

Domestication of Campylobacter jejuni NCTC 11168.

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom.

We examined whole-genome-sequenced Campylobacter jejuni and C. coli from 2012-2015 isolated from birds and human stool samples in North East Scotland for the presence of antimicrobial resistance genes. We found that sequence type (ST) 5136 (clonal complex 464) was the most prevalent multidrug-resistant strain of C. jejuni exclusively associated with poultry host reservoirs and recovered from human cases of campylobacteriosis. Tetracycline resistance in ST5136 isolates was due to a tet(O/32/O) mosaic gene, ampicillin resistance was conferred by G → T transversion in the -10 promoter region of blaOXA-193, fluoroquinolone resistance was due to C257T change in gyrA, and aminoglycoside resistance was conferred by aac. Whole-genome analysis showed that the strain ST5136 evolved from ST464. The nationwide emergence of ST5136 was probably due to stepwise acquisition of antimicrobial resistance genes selected by high use of ß-lactam, tetracycline, fluoroquinolone, and aminoglycoside classes of drugs in the poultry industry.

Challenges of biofilm control and utilization: lessons from mathematical modelling.

This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.

Influence of Plant Species, Tissue Type, and Temperature on the Capacity of Shiga-Toxigenic Escherichia coli To Colonize, Grow, and Be Internalized by Plants.

Contamination of fresh produce with pathogenic Escherichia coli, including Shiga-toxigenic E. coli (STEC), represents a serious risk to human health. Colonization is governed by multiple bacterial and plant factors that can impact the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species) is predictive of the colonization of living plants, as assessed from growth kinetics and biofilm formation in plant extracts. The fitness of STEC isolates was compared to that of environmental E. coli isolates at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the highest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified to be the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonization occurred on alfalfa sprouts, though internalization was 10 times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that the growth potential of STEC could be inferred only for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonization. Overall, the capacity of E. coli to colonize, grow, and be internalized within plants or plant-derived matrices was influenced by the isolate type, plant species, plant tissue type, and temperature, complicating any straightforward relationship between in vitro and in planta behaviors.IMPORTANCE Fresh produce is an important vehicle for STEC transmission, and experimental evidence shows that STEC can colonize plants as secondary hosts, but differences in the capacity to colonize occur between different plant species and tissues. Therefore, an understanding of the impact that these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plant extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonize living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) but not those for leafy vegetables (lettuce and spinach) exhibited a positive relationship between plant extracts and living plants. Therefore, the detailed variations at the level of the bacterial isolate, plant species, and tissue type all need to be considered in risk assessment.

LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe.

We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.