Pathogenic anaerobic bacteria and the environment

Time-dependent microbial shifts during crayfish decomposition in freshwater and sediment under different environmental conditions

Fossilization processes and especially the role of bacterial activity during the preservation of organic material has not yet been well understood. Here, we report the results of controlled taphonomic experiments with crayfish in freshwater and sediment. 16S rRNA amplicon analyzes showed that the development of the bacterial community composition over time was correlated with different stages of decay and preservation. Three dominating genera, Aeromonas, Clostridium and Acetobacteroides were identified as the main drivers in the decomposition of crayfish in freshwater. Using micro-computed tomography (µ-CT), scanning electron microscopy (SEM) and confocal Raman spectroscopy (CRS), calcite clusters were detected after 3-4 days inside crayfish carcasses during their decomposition in freshwater at 24 °C. The precipitation of calcite clusters during the decomposition process was increased in the presence of the bacterial genus Proteocatella. Consequently, Proteocatella might be one of the bacterial genera responsible for fossilization.

Clostridium botulinum type C, D, C/D, and D/C: An update

Clostridium botulinum is the main causative agent of botulism, a neurological disease encountered in humans as well as animals. Nine types of botulinum neurotoxins (BoNTs) have been described so far. Amongst these "toxinotypes," the A, the B and E are the most frequently encountered in humans while the C, D, C/D and D/C are mostly affecting domestic and wild birds as well as cattle. In France for instance, many cases and outbreaks are reported in these animal species every year. However, underestimation is very likely at least for avifauna species where the detection of dead animals can be challenging. Knowledge about BoNTs C, D, C/D, and D/C and the diseases they cause in animals and humans is still scarce and unclear. Specifically, the potential role of animal botulism outbreaks in cattle and poultry as a source of human illness needs to be further assessed. In this narrative review, we present the current knowledge about toxinotypes C, D, C/D, and D/C in cattle and poultry with, amongst various other aspects, their epidemiological cycles. We also discuss the zoonotic potential of these toxinotypes and some possible ways of risk mitigation. An adapted and effective management of botulism outbreaks in livestock also requires a better understanding of these less common and known toxinotypes.

Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields

Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach and 6/60 (10%) of soil samples using culture-based techniques. Whole genome sequencing (WGS) analysis identified the spinach isolates as belonging to the hypervirulent clade 5, sequence type (ST) 11, ribotypes (RT) 078 and 126 and carried the genes encoding toxins A, B and CDT. The soil isolates belonged to clade 1 with different toxigenic ST/RT (ST19/RT614, ST12/RT003, ST46/RT087, ST16/RT050, ST49/RT014/0) strains and one non-toxigenic ST79/RT511 strain. Antimicrobial resistance to erythromycin (one spinach isolate), rifampicin (two soil isolates), clindamycin (one soil isolate), both moxifloxacin and rifampicin (one soil isolate), and multi-drug resistance to erythromycin, vancomycin and rifampicin (two soil isolates) were observed using the E test, although a broader range of resistance genes were detected using WGS. Although the sample size was limited, our results demonstrate the presence of C. difficile in horticulture and provide further evidence that there are multiple sources and dissemination routes for these bacteria.

Systematic mapping on the importance of vultures in the Indian public health discourse

Vultures are of immense ecological significance to forest and urban ecosystems. These birds play a major role in curbing environmental contamination through scavenging on carcasses. Prevention of spread of diseases is pivotal for public health and is an inexorable economic burden for any country. We present the crucial role vultures can play in disease mitigation and public health by regulating or decreasing the spread of zoonotic diseases. We elaborate examples from three zoonotic diseases; rabies, brucellosis and tuberculosis, which spread among dogs and cattle as well as human population. We establish the viable links in the transmission of these diseases from the infected dead and alive animals to humans and their possible exacerbation in the absence of vultures. These indirect links help formulate the case for increased interventions for disease spread and control along with conservation of these scavengers. Their role as natural and effective cleaners of the environment in the Indian health discourse is of importance because they can reduce the expenses of the government in waste management and maintenance of public health.

Spoilage Investigation of Chill Stored Meagre (Argyrosomus regius) Using Modern Microbiological and Analytical Techniques

Spoilage status of whole and filleted chill-stored meagre caught in January and July was evaluated using sensory, microbiological, 16S metabarcoding and Volatile Organic Compounds (VOCs) analysis. Based on the sensory analysis, shelf-life was 15 and 12 days for the whole fish taken in January and July, respectively, while 7 days for fish fillets of both months. For the whole fish, Total Viable Counts (TVC) at the beginning of storage was 2.90 and 4.73 log cfu/g for fish caught in January and July respectively, while it was found about 3 log cfu/g in fish fillets of both months. The 16S metabarcoding analysis showed different profiles between the two seasons throughout the storage. Pseudomonas (47%) and Psychrobacter (42.5%) dominated in whole meagre of January, while Pseudomonas (66.6%) and Shewanella (10.5%) dominated in fish of July, at the end of shelf-life. Regarding the fillets, Pseudomonas clearly dominated at the end of shelf-life for both months. The volatile profile of meagre was predominated by alcohols and carbonyl compounds. After univariate and multivariate testing, we observed one group of compounds (trimethylamine, 3-methylbutanoic acid, 3-methyl-1-butanol) positively correlating with time of storage and another group with a declining trend (such as heptanal and octanal). Furthermore, the volatile profile seemed to be affected by the fish culturing season. Our findings provide insights into the spoilage mechanism and give information that helps stakeholders to supply meagre products of a high-quality level in national and international commerce.

The impact of rainfall on drinking water quality in Antananarivo, Madagascar

Low-income cities that are subject to high population pressure and vulnerable to climate events often have a low capacity to continuously deliver safe drinking water. Here we reported the results of a 32-year survey on the temporal dynamics of drinking water quality indicators in the city of Antananarivo. We analyzed the long-term evolution of the quality of the water supplied and characterized the interactions between climatic conditions and the full-scale water supply system. A total of 25,467 water samples were collected every week at different points in the supplied drinking water system. Samples were analyzed for total coliforms (TC), Escherichia coli (EC), intestinal Enterococci (IE), and Spores of Sulphite-Reducing Clostridia (SSRC). Nine-hundred-eighty-one samples that were identified as positive for one or more indicators were unevenly distributed over time. The breakpoint method identified four periods when the time series displayed changes in the level and profile of contamination (i) and the monthly pattern of contamination (ii), with more direct effects of rainfall on the quality of supplied drinking water. The modeling showed significantly different lags among indicators of bacteria occurrence after cumulative rainfall, which range from 4 to 8 weeks. Among the effects of low-income urbanization, a rapid demographic transition and the degradation of urban watersheds have gradually affected the quality of the water supplied and resulted in the more direct effects of rainfall events. We focused on the need to adopt an alternative perspective of drinking water and urban watersheds management.

Seasonality of Clostridium difficile in the natural environment

Clostridium difficile is considered the leading cause of antibiotic-associated disease worldwide. In the past decade, a large number of studies have focused on identifying the main sources of contamination in order to elucidate the complete life cycle of the infection. Hospitals, animals and retail foods have been considered as potential vectors. However, the prevalence of C. difficile in these types of samples was found to be rather low, suggesting that other contamination routes must exist. This study explores the presence of C. difficile in the natural environment and the seasonal dynamics of the bacterium. C. difficile was isolated from a total of 45 samples out of 112 collected (40.2%) on 56 sampling points. A total of 17 points were positive only during the winter sampling (30.4%), 10 were positive only during the summer sampling (17.9%) and 9 sampling points (16.1%) were positive in both summer sampling and winter sampling. Spore counts in soil samples ranged between 50 and 250 cfu/g for 24.4% of the positive samples, with the highest concentrations detected in samples collected in the forest during winter campaign (200-250 cfu/g). A total of 17 different PCR ribotypes were identified, and 15 of them had the genes coding for toxins A and B. Most of those ribotypes had not previously been found or had been isolated only sporadically (<1% of samples) from hospitals in Belgium. Regarding antimicrobial susceptibility, most of the resistant strains were found during the summer campaign. These findings bear out that C. difficile is present in the natural environment, where the bacterium undergoes seasonal variations.

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus

Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.

A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

Background

Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system.

Material and methods

The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system.

Results and discussion

A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.

Impact of cemeteries on groundwater contamination by bacteria and viruses - a review

In the process of decomposition of a human body, 0.4-0.6 litres of leachate is produced per 1 kg of body weight. The leachate contains pathogenic bacteria and viruses that may contaminate the groundwater and cause disease when it is used for drinking. So far, this topic has been investigated in several regions of the world (mainly Brazil, Australia, the Republic of South Africa, Portugal, the United Kingdom and Poland). However, recently more and more attention has been focused on this issue. This study reviews the results of investigations related to the impact of cemeteries on groundwater bacteriology and virology. This topic was mainly discussed in the context of the quantities and qualities of changes in types of microorganisms causing groundwater contamination. In some cases, these changes were related to the environmental setting of a place, where a cemetery was located. The review is completed by a list of recommendations. Their implementation aims to protect the local environment, employees of funeral homes and the residents living in the vicinity of cemeteries. In this form, this review aims to familiarize the reader with the results of this topic, and provide practical guidance for decision-makers in the context of expansion and management of cemeteries, as well as the location of new ones.

Environmental factors influencing the prevalence of a Clostridium botulinum type C/D mosaic strain in nonpermanent Mediterranean wetlands

Between 1978 and 2008, 13 avian botulism outbreaks were recorded in the wetlands of Mancha Húmeda (central Spain). These outbreaks caused the deaths of around 20,000 birds from over 50 species, including globally endangered white-headed ducks (Oxyura leucoceophala). Here, a significant association was found between the number of dead birds recorded in each botulism outbreak and the mean temperature in July (always >26°C). The presence of Clostridium botulinum type C/D in wetland sediments was detected by real-time PCR (quantitative PCR [qPCR]) in 5.8% of 207 samples collected between 2005 and 2008. Low concentrations of Cl(-) and high organic matter content in sediments were significantly associated with the presence of C. botulinum. Seventy-five digestive tracts of birds found dead during botulism outbreaks were analyzed; C. botulinum was present in 38.7% of them. The prevalence of C. botulinum was 18.2% (n = 22 pools) in aquatic invertebrates (Chironomidae and Corixidae families) and 33.3% (n = 18 pools) in necrophagous invertebrates (Sarcophagidae and Calliphoridae families), including two pools of adult necrophagous flies collected around bird carcasses. The presence of the bacteria in the adult fly form opens up new perspectives in the epidemiology of avian botulism, since these flies may be transporting C. botulinum from one carcass to another.

Post-mortem volatiles of vertebrate tissue

Volatile emission during vertebrate decay is a complex process that is understood incompletely. It depends on many factors. The main factor is the metabolism of the microbial species present inside and on the vertebrate. In this review, we combine the results from studies on volatile organic compounds (VOCs) detected during this decay process and those on the biochemical formation of VOCs in order to improve our understanding of the decay process. Micro-organisms are the main producers of VOCs, which are by- or end-products of microbial metabolism. Many microbes are already present inside and on a vertebrate, and these can initiate microbial decay. In addition, micro-organisms from the environment colonize the cadaver. The composition of microbial communities is complex, and communities of different species interact with each other in succession. In comparison to the complexity of the decay process, the resulting volatile pattern does show some consistency. Therefore, the possibility of an existence of a time-dependent core volatile pattern, which could be used for applications in areas such as forensics or food science, is discussed. Possible microbial interactions that might alter the process of decay are highlighted.

Genetic diversity among toxigenic clostridia isolated from soil, water, meat and associated polluted sites in South India

PURPOSE

To investigate the genetic diversity of toxigenic Clostridium strains isolated from soil, water, meat and its associated polluted sites of Southern India.

MATERIALS AND METHODS

A total of 27 identified isolates of six different toxigenic clostridial species including C. bifermentans , C. botulinum , C. chauvoei , C. ramosum , C. tetani and C. novyi were isolated and characterized by conventional DNA restriction digestion analysis (REA) and by whole-cell and excretory protein patterns on SDS-PAGE.

RESULTS

The DNA fragment size ranged from 35-160 kilobases and the protein bands 30-200 KDa, followed by numerical analyses and phylogenetic analyses. Whole-cell protein banding pattern were unique with strains of C. chauvoei , C. novyi and C. ramosum . All the strains were heterogeneous and distinct in restriction digestion pattern and excretory protein patterns.

CONCLUSION

These analyses contribute to the understanding of prevalence of toxigenic clostridial species and phylogeny within the species and assist in development of improved diagnostics and therapeutics for the treatment of clostridial infections.

Clostridium perfringens toxin types from wild-caught Atlantic cod (Gadus morhua L.), determined by PCR and ELISA

Ninety-five fecal samples from Atlantic cod (Gadus morhua L.), caught along the northern Norwegian coast, were examined bacteriologically for occurrence of C. perfringens. Isolates were examined by polymerase chain reaction (PCR) for genes encoding the four lethal toxins (alpha, beta, epsilon, and iota) for classification into toxin types and for genes encoding enterotoxin and the novel beta2 toxin for further subclassification. In addition, a commercial enzyme-linked immunosorbent assay (ELISA) kit for detection of C. perfringens alpha, beta, and epsilon toxin was used. Clostridium perfringens could be isolated in 37 fecal samples (38.9%) from cod. All isolates were C. perfringens toxin type A (alpha toxin positive) as determined by PCR and also ELISA. In addition, in isolates from two cod (2.1%) the gene encoding for beta2 toxin was found (A, beta2) by PCR. Genes encoding for beta, epsilon, and iota toxins and enterotoxin were not found. This is the first detection of C. perfringens alpha and beta2 toxin in cod and of beta2 toxin in fish in general. The origin of this bacterium in cod is discussed.

Clostridium perfringens toxin types in hooded seals in the Greenland Sea, determined by PCR and ELISA

Very little is known about the occurrence of Clostridium perfringens and of diseases caused by this anaerobic bacterium in marine mammals, especially those that are free-living. During a scientific expedition to the Greenland Sea (West Ice) in spring 1999, faeces samples from 70 hooded seals (Cystophora cristata) were taken to isolate C. perfiringens. Subsequently, PCR analysis of the isolates was performed with oligonucleotide primers of the genes encoding the four major lethal toxins (alpha, beta, epsilon and iota) for classification of toxin type and of the genes encoding C. perfringens beta2-toxin and enterotoxin for further subclassification. In addition, a commercial ELISA kit for detection of C. perfringens alpha, beta- and epsilon-toxin was used. C. perfingens was isolated in samples from 38 (54.3%) hooded seals. All isolates were C. perfringens toxin type A (alpha-toxin positive). This is the first report on the occurrence of C. perfringens in this arctic marine mammal species. Myositis and enterotoxemia caused by C. perfrigens were described in other marine mammals and it may be assumed that the pathogenesis of an outbreak of disease is similar to that encountered in terrestrial animals. Although there is some controversy surrounding the enteropathogenicity and virulence of alpha-toxin (concerning enterotoxemia), this study suggests that a possible outbreak of enterotoxemia caused by C. perfringens type A in hooded seals may, however, not be excluded.

Localization of symbiotic clostridia in the mixed segment of the termite Nasutitermes takasagoensis (Shiraki)

Phylogeny and the distribution of symbiotic bacteria in the mixed segment of the wood-eating termite Nasutitermes takasagoensis (Shiraki) were studied. Bacterial 16S rRNA genes (rDNA) were amplified from the mixed segment of the gut by PCR, and two kinds of sequences were identified. The phylogenetic tree was constructed by neighbor-joining and maximum parsimony methods to identify symbionts harbored in the mixed segment. They are classified as low-G+C-content gram-positive bacteria and are most closely related to the genus Clostridium. The distribution of these bacteria throughout the whole gut was examined by PCR using specific primers, which suggested that they are confined to the mixed segment despite the presence of bacteria throughout the gut. In situ hybridization indicated that the symbiotic bacteria were localized to the ectoperitrophic space between the midgut wall and the peritrophic membrane in the mixed segment. Electron microscopy revealed the close association between these bacteria and the mesenteric epithelium, suggesting that they have some interactions with the gut tissue of termites.

Frequency of Clostridium perfringens types in Jordanian sheep

778 fecal samples from 29 Jordanian sheep flocks were examined for the presence of Clostridium perfringens. 252 field strains were isolated and typed by the enzyme immunosorbent assay. The presence of C. perfringens types B, C and D in Jordanian sheep was confirmed. Type D was found in 55% of the flocks examined. Types B and C were each isolated from 7% of the flocks examined. The proteinase activity of isolated type B field strains was similar to that of type B reference strains. According to the results, it does not seem to be necessary to include locally isolated C. perfringens strains in the Jordanian vaccine production.