Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia

Abstract

dInfant botulism is a potentially life-threatening paralytic disease that can be associated with prolonged morbidity if not rapidly diagnosed and treated. Four infants were diagnosed and treated for infant botulism in NSW, Australia, between May 2011 and August 2013. Despite the temporal relationship between the cases, there was no close geographical clustering or other epidemiological links. Clostridium botulinum isolates, three of which produced botulism neurotoxin serotype A (BoNT/A) and one BoNT serotype B (BoNT/B), were characterized using whole-genome sequencing (WGS). In silico multilocus sequence typing (MLST) found that two of the BoNT/A-producing isolates shared an identical novel sequence type, ST84. The other two isolates were single-locus variants of this sequence type (ST85 and ST86). All BoNT/A-producing isolates contained the same chromosomally integrated BoNT/A2 neurotoxin gene cluster. The BoNT/B-producing isolate carried a single plasmid-borne bont/B gene cluster, encoding BoNT subtype B6. Single nucleotide polymorphism (SNP)-based typing results corresponded well with MLST; however, the extra resolution provided by the whole-genome SNP comparisons showed that the isolates differed from each other by >3,500 SNPs. WGS analyses indicated that the four infant botulism cases were caused by genomically distinct strains of C. botulinum that were unlikely to have originated from a common environmental source. The isolates did, however, cluster together, compared with international isolates, suggesting that C. botulinum from environmental reservoirs throughout NSW have descended from a common ancestor. Analyses showed that the high resolution of WGS provided important phylogenetic information that would not be captured by standard seven-loci MLST. Genomic epidemiology has provided novel insights into the genetic characteristics and phylogenetic diversity of botulinum neurotoxin (BoNT)-producing Clostridium species (1-8).BoNT subtypes are responsible for causing the serious paralytic disease botulism and their potent neuroparalytic activities make them one of the top (tier 1) agents considered to pose a significant threat to public health if used for bioterrorism (Electronic Code of Federal Regulations-Title 42: Part 73; http://www.ecfr.gov/cgi -bin/retrieveECFR?rϭPART&nϭ42y1.0.1.6.61) (9, 10). The same properties also make them powerful tools for both medical therapeutic and cosmetic applications (11).Botulism is a very rare disease in Australia (National Notifiable Diseases Surveillance System [NNDSS]; http://www9.health.gov .au/cda/source/cda-index.cfm), with only 20 cases reported since 1991. However, a global survey found that Australia had one of the highest numbers of notified cases of infant botulism in the world (12, 13). Infant botulism results from the ingestion of Clostridium botulinum spores which germinate and temporarily colonize the infant's colon, followed by growth of vegetative cells that produce . This form of the disease only occurs in infants, generally under 1 year old, as they h...

Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes

“…Local evolution of strains and commercial exchanges of food products with other countries might account for the diversity of French C. botulinum strains. Recent investigations also show similar C. botulinum diversity in other countries such as in Italy ( Giordani et al 2015 ), Japan ( Kenri et al 2014 ), Australia ( McCallum et al 2015 ) and other parts in the world (reviewed in Carter and Peck 2015 ; Hill et al 2015 ; Smith, Hill, Raphael 2015 ; Smith, Hill, Xie, et al 2015 ). Thereby, the BoNT-producing clostridia share a high genetic plasticity the mechanisms of which including acquisition or loss of genetic materials by mobile genetic elements (plasmids, phages) and genetic rearrangements by insertion, recombination, mutation events are not yet fully understood.…”

Impact of Clostridium botulinum genomic diversity on food safety

“…Isolates from the patient and their home environment were frequently present in the same clade, indicating the probable source of infective spores [62]. A study of four time-coincident infant botulism cases in Australia revealed that the four Group I strains involved were related but not identical, suggesting that they had not come from a single source, but had diverged from a common ancestor many hundreds of years ago [63]. It is likely that whole genome sequencing and other molecular techniques will be of great value in future microbial forensic studies [64, 65].…”

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

“…Botulinum neurotoxin-producing Clostridia have been identified from all continents except Antarctica. These microbes are often isolated from samples associated with human botulism cases (food poisonings or intestinal or wound infections), and researchers have also isolated BoNT-producing Clostridia from environmental samples including soils, honey, aquatic sediments and plants [ 17 , 23 – 34 ]. The distribution of serotypes A–G can be obtained from publications based upon characterization of strains within different culture collections, environmental sampling and reported botulism cases.…”