The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements

Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.

Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa

Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia

Background

Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A–G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use comparative genomics to provide insights into the genetic diversity and evolutionary history of bacteria that produce the potent botulinum neurotoxin.

Results

Comparative genomic analyses of over 170 Clostridia genomes, including our draft genome assemblies for 59 newly sequenced Clostridia strains from six continents and publicly available genomic data, provided in-depth insights into the diversity and distribution of BoNT-producing bacteria. These newly sequenced strains included Group I and II strains that express BoNT/A,/B,/E, or/F as well as bivalent strains. BoNT-producing Clostridia and closely related Clostridia species were delineated with a variety of methods including 16S rRNA gene, concatenated marker genes, core genome and concatenated multi-locus sequencing typing (MLST) gene phylogenies that related whole genome sequenced strains to publicly available strains and sequence types. These analyses illustrated the phylogenetic diversity in each Group and the diversity of genomic backgrounds that express the same toxin type or subtype. Comparisons of the botulinum neurotoxin genes did not identify novel toxin types or variants.

Conclusions

This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria. Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2502-z) contains supplementary material, which is available to authorized users.

On the origin of calcium oxalate monohydrate papillary renal stones

Calcium oxalate monohydrate (COM) papillary calculi can be initiated by subepithelial calcification of the renal papillae. Hydroxyapatite disruption of the papillary epithelial layer can become the nidus of a COM papillary calculus. This study evaluated the causes of papillary tissue calcifications in 60 patients with calcium oxalate lithiasis, 30 with COM papillary and 30 with calcium oxalate dihydrate (COD) calculi. Urinary redox potential was higher in the COM than the COD group, suggesting that the former is more deficient in antioxidants due to increased oxidative stress. Urinary calcium was significantly higher in the COD group, whereas urinary oxalate was significantly higher in the COM group, suggesting a greater degree of oxidative injury of renal cells. Evaluations of their diets showed that both groups consumed low amounts of phytate-rich products. Of chronic diseases possibly associated with urolithiasis, only the prevalence of gastroduodenal ulcer differed significantly, being higher in the COM group and suggesting that epithelial lesions are common to gastroduodenal ulcers and COM papillary renal stones. Occupational exposure to cytotoxic products occurred in 47 % of the COM and 27 % of the COD group, but this difference was not statistically significant. These findings indicate that oxidative stress is associated with injury to papillary tissue and that this is the origin of intrapapillary calcifications. The continuation of this process is due to modulators and/or deficiencies in inhibitors of crystallization. Identifying and eliminating the causes of injury may prevent recurrent episodes in patients with papillary COM calculi.

Analysis of a unique Clostridium botulinum strain from the Southern hemisphere producing a novel type E botulinum neurotoxin subtype

Background

Clostridium botulinum strains that produce botulinum neurotoxin type E (BoNT/E) are most commonly isolated from botulism cases, marine environments, and animals in regions of high latitude in the Northern hemisphere. A strain of C. botulinum type E (CDC66177) was isolated from soil in Chubut, Argentina. Previous studies showed that the amino acid sequences of BoNT/E produced by various strains differ by < 6% and that the type E neurotoxin gene cluster inserts into the rarA operon.

Results

Genetic and mass spectral analysis demonstrated that the BoNT/E produced by CDC66177 is a novel toxin subtype (E9). Toxin gene sequencing indicated that BoNT/E9 differed by nearly 11% at the amino acid level compared to BoNT/E1. Mass spectrometric analysis of BoNT/E9 revealed that its endopeptidase substrate cleavage site was identical to other BoNT/E subtypes. Further analysis of this strain demonstrated that its 16S rRNA sequence clustered with other Group II C. botulinum (producing BoNT types B, E, and F) strains. Genomic DNA isolated from strain CDC66177 hybridized with fewer probes using a Group II C. botulinum subtyping microarray compared to other type E strains examined. Whole genome shotgun sequencing of strain CDC66177 revealed that while the toxin gene cluster inserted into the rarA operon similar to other type E strains, its overall genome content shared greater similarity with a Group II C. botulinum type B strain (17B).

Conclusions

These results expand our understanding of the global distribution of C. botulinum type E strains and suggest that the type E toxin gene cluster may be able to insert into C. botulinum strains with a more diverse genetic background than previously recognized.

Linden flower (Tilia spp.) as potential vehicle of Clostridium botulinum spores in the transmission of infant botulism

Infant botulism is an intestinal toxemia caused principally by Clostridium botulinum. Since the infection occurs in the intestinal tract, numerous food products have been investigated for the presence of C. botulinum and its neurotoxins. In many countries, people use linden flower (Tilia spp) tea as a household remedy and give it to infants as a sedative. Therefore, to help provide a clear picture of this disease transmission, we investigated the presence of botulinum spores in linden flowers. In this study, we analyzed 100 samples of unwrapped linden flowers and 100 samples of linden flowers in tea bags to determine the prevalence and spore-load of C. botulinum. Results were analyzed by the Fisher test. We detected a prevalence of 3% of botulinum spores in the unwrapped linden flowers analyzed and a spore load of 30 spores per 100 grams. None of the industrialized linden flowers analyzed were contaminated with botulinum spores. C. botulinum type A was identified in two samples and type B in one sample. Linden flowers must be considered a potential vehicle of C. botulinum, and the ingestion of linden flower tea can represent a risk factor for infant botulism.

Phenotypic characterization of Clostridium botulinum strains isolated from infant botulism cases in Argentina

Infant botulism is the most common form of human botulism; however, its transmission has not been completely explained yet. Some of the most recognized potential sources of Clostridium botulinum spores are the soil, dust, honey and medicinal herbs. In Argentina, 456 cases of infant botulism were reported between 1982 and 2007. C. botulinum type A was identified in 455 of these cases whereas type B was identified in just one case. However, in Argentina, types A, B, E, F, G, and Af have been isolated from environmental sources. It is not clearly known if strains isolated from infant botulism cases have different characteristics from strains isolated from other sources. During this study, 46 C. botulinum strains isolated from infant botulism cases and from environmental sources were typified according to phenotypic characteristics. Biochemical tests, antimicrobial activity, and haemagglutinin-negative botulinum neurotoxin production showed uniformity among all these strains. Despite the variability observed in the botulinum neurotoxin's binding to cellular receptors, no correlation was found between these patterns and the source of the botulinum neurotoxin. However, an apparent geographical clustering was observed, since strains isolated from Argentina had similar characteristics to those isolated from Italy and Japan, but different to those isolated from the United States.

Presence of Clostridium botulinum spores in Matricaria chamomilla (chamomile) and its relationship with infant botulism

Nowadays, infant botulism is the most important form of human botulism in some countries. This illness affects infants younger than 52 weeks of age. The infection occurs in the intestinal tract; therefore, ingestion of Clostridium botulinum spores with food is proposed. In some countries, people use chamomile tea as a household remedy for intestinal colics and given this tea to infants. Chamomile can be contaminated with C. botulinum and could be a vehicle of its spores. Our aim was to study the prevalence and spore-load of C. botulinum in chamomile. We analysed 200 samples; the 7.5% of them were contaminated with botulinum spores. However, prevalence of these spores was significantly higher in chamomile sold by weight in herbal stores (unwrapped chamomile) than prevalence in chamomile sold in tea bags (p=0.0055). The spore-load detected in all positive samples was 0.3-0.4 spores per gram of chamomile. We identified C. botulinum types A, B, and F in the 53.3%, 6.7%, and 13.3%, respectively. Chamomile (principally, unwrapped chamomile) is a potencial vehicle of C. botulinum spores, and ingestion of chamomile tea could represent a risk for infant botulism.

Distribution of botulinum toxin-producing clostridia in soils of Argentina

We studied the presence of botulinum toxin-producing clostridia in 2,009 soil samples from five geographical regions of Argentina. The prevalence was 23.5%, and the distribution was not homogeneous among the regions. We observed a great multiplicity of serological types and a higher prevalence in nonvirgin soils than in virgin soils.

[Presence of botulinum-producing clostridia in the soils of Entre Ríos]

Botulism, well known for centuries, continues to preoccupy the Public Health authorities, food and agricultural industries. In its oldest form it results from ingestion of food containing botulinum toxin. To correctly evaluate the incidence of botulism it is fundamental to know the distribution of botulinum toxin-producing clostridia (Clostridium botulinum, C. baratii, C. butyricum and C. argentinense) in nature, specially in the soil, its main reservoir. In our country, this study has been carried out in a partial way. With the aim to contribute to such knowledge, 240 soil samples from Entre Ríos province were examined for C. botulinum and 35 (14.6%) samples resulted positive.

[Helical computerized tomography of the thorax in the diagnosis of unresolved chronic pulmonary thromboembolism]

We assessed the diagnostic usefulness of helical CT scan of the thorax in the setting of chronic thromboembolic pulmonary hypertension by prospectively comparing the results of helical CT scan to those of the pulmonary angiogram (gold standard). We studied 40 patients with diagnosis of pulmonary hypertension of diverse etiology (mean age: 40.7 +/- 12 y.o.; mean systolic pulmonary artery pressure: 91 +/- 33 mmHg)). Thirty of these patients fulfilled the diagnostic criteria of chronic thromboembolic pulmonary hypertension and the other ten were used as controls. Diagnosis in control patients included: primary pulmonary hypertension (4); patent ductus arteriosus (2); atrial septal defect (1); rheumatic valve disease (1); ischemic heart disease (1); and acute pulmonary embolism (1). Both helical CT scan and pulmonary angiogram were part of the routine diagnostic work up of these patients, and were, performed and interpreted almost simultaneously (within one week) by a different group of investigators in a blind manner. Only the diagnostic accuracy of the method regarding central (major arteries) vascular lesions was evaluated. Helical CT scan had an overall sensitivity of 100% (29/29), and a specificity of 91% (10/11). Positive predictive and negative predictive values were 96.6% (29/30) and 100% (10/10), respectively. Overall diagnostic accuracy was 97.5% (39/40). We conclude that helical CT scan of the thorax is an excellent alternative approach for the diagnosis of major arteries lesions in the setting of chronic thromboembolic pulmonary hypertension.

[Type D and A Clostridium botulinum in necropsy samples from bovines with "mal de Aguapey"]

Bacteriological studies were carried out on several necropsy samples from five animals whose deaths had been attributed to bovine botulism. This disease, regionally called Mal de Aguapey, enzootically affects animals from a wide area of the north-east of Argentina (Province of Corrientes) with a bovine population estimated at near to 2,500,000. Either C. botulinum type D, its toxin or both were identified in all animal samples, alternatively in contents of rumen, jejunum, ileum, caecum and in samples of spleen, liver and kidney (Table 1). C. botulinum type A was isolated respectively from the liver and the kidney of two animals. Cultures of 100 soil samples taken in the enzootic area were positive only for C. botulinum type A (3%). These results enlarge and confirm previous findings and lend support to the botulinic etiology of the Mal de Aguapey.

[Infections due to several species of Salmonella in Mendoza, Argentina]

Fifty nine sporadic cases and forty five cases from six outbreaks of salmonellosis occurring in Mendoza, Argentina between 1972-76 are reported. All 104 patients were studied epidemiologically searching for the etiologic agent, implicated food and contacts. Stools of patients and contacts were examined. Other clinical specimens and the implicated foods were examined bacteriologically. The Salmonella isolates were classified in eleven serotypes with the following order of frequency: a) Outbreaks: S. typhimurium (50,0%), S. derby (16,7%), S. newport (16,7%), S. bredeney (16,7%), S. enteritidis (16,7%), S. cholerae-suis (16,7%) and S. oranienburg (16,7%). b) Sporadic cases; S. typhimurium (35,9%), S. newport (15,6%), S. anatum (7,8%), S. oranienburg (6,2%), S. derby (4,7%), S. java (3,1%), S. cholerae-suis (3,1%), S. bredeney (1,6%), S. enteritidis (1,6%), S. minnesota (1,6%), S. urbana (1,6%), and Salmonella spp (17,2%). These results are compared with those obtained in the same areas between 1962-71 and with the serotype frequencies from different sources of infection found in Mendoza and other regions.