Sequence variation in the alpha-toxin encoding plc gene of Clostridium perfringens strains isolated from diseased and healthy chickens

Genomic analysis and mobile genetic elements carriage of Clostridium perfringens type A

OBJECTIVES

To explore a comprehensive genomic analysis of Clostridium perfringens type A strains from diverse regions in China, investigating their virulence genes, antibiotic resistance genes, and mobile genetic elements (MGEs) to inform strategies for infection control and resistance gene surveillance.

METHODS

We conducted whole-genome sequencing on 168 C. perfringens type A strains from nine provinces in China (2016-2021). Previously described alpha-toxin (PLC) sequence typing for C. perfringens was used for comparisons with core genome multilocus sequence typing. Virulence genes, antibiotic resistance genes, and MGEs, including CRISPR/Cas, prophages, and plasmids of C. perfringens type A were investigated by molecular and bioinformatic methods.

RESULTS

PLC type II contained the largest number of isolates (n=44). The same type strains were largely clustered in the same branches. Tetracycline resistance genes tetA(P) and tetB(P) had high prevalence in type A isolates. 395 prophages were predicted including 265 "incomplete," 55 "questionable," and 75 "intact" prophages. CRISPR/Cas systems were more common in isolates from humans (63%) than in those from animals and food (52% and 46%, respectively). Fifty-seven percent of strains likely had the tcp conjugation locus (tcpC to tcpH), and 12 isolates likely carried the conjugative pCW3 plasmid. Type A strains exhibited fewer plasmid-encoded toxins.

CONCLUSIONS

cgMLST analysis demonstrated some micro-evolution and regional transmission trends within type A, which exhibited partial correlated with PLC typing. This study highlights the need for enhanced surveillance of antimicrobial resistance and pathogenicity-associated MGEs in C. perfringens type A.

Clonal diversity of Clostridium perfringens human clinical isolates with various toxin gene profiles based on multilocus sequence typing and alpha-toxin (PLC) typing

OBJECTIVES

Clostridium perfringens is a common anaerobic pathogen causing enteritis/enterocolitis and wound infections in humans. We analyzed clonal diversity and toxin gene prevalence in C. perfringens clinical isolates from humans in northern Japan.

METHODS

Prevalence of nine toxin genes was analyzed for 585 C. perfringens isolates from patients collected for 20-month period between May 2019 and December 2020 by molecular methods. Sequence type (ST) based on multilocus sequence typing (Xiao's scheme) and alpha-toxin (PLC) sequence type were determined for a total of 124 isolates selected in the present study along with those in our previous study (2017-2018).

RESULTS

Toxinotypes A (68.2%) was the most frequent, followed by F (31.6%), and G (0.2%), while additional toxin genes encoding binary enterotoxin (BEC/CPILE) and beta2 toxin were identified in one and six isolates, respectively. Among the 124 isolates with various toxin gene profiles, 62 STs including 53 novel types were identified, revealing the presence of six clonal complexes (CCs) consisting of 27 STs. Most of enterotoxin gene (cpe)-positive isolates belonged to CC36, CC41, and CC117. Based on 22 key amino acids in alpha toxin sequence, four PLC types (I-IV) including 21 subtypes were classified, and their relation to individual STs/CCs was clarified. Two isolates harboring bec/cpile belonged to different STs (ST95, ST131) and PLC types (If, IVb), indicating distribution of this toxin gene to distinct lineages.

CONCLUSIONS

The present study revealed the diversity in C. perfringens clones of human origin with various toxin gene profiles represented by ST/CC and PLC type.

A Rapid and Simple Assay Correlates In Vitro NetB Activity with Clostridium perfringens Pathogenicity in Chickens

Necrotic enteritis is an important enteric disease in poultry, caused by NetB-producing Clostridium (C.) perfringens strains. As no straight-forward method to assess the NetB activity of C. perfringens was available, we aimed to develop an easy, high-throughput method to measure the NetB activity produced by C. perfringens. First, the appearance of C. perfringens on different avian blood agar plates was assessed. Based on the size of the haemolysis surrounding the C. perfringens colonies, NetB-positive strains could phenotypically be discriminated from NetB-negative strains on both chicken and duck blood agar. Additionally, strains producing the consensus NetB protein induced more pronounced haemolysis on chicken blood agar as compared to the weak outer haemolysis induced by A168T NetB-variant-producing C. perfringens strains. Next, a 96-well plate-based haemolysis assay to screen NetB activity in the C. perfringens culture supernatants was developed. Using this assay, a positive correlation between the in vitro NetB activity and virulence of the C. perfringens strains was shown. The developed activity assay allows us to screen novel C. perfringens isolates for their in vitro NetB activity, which could give valuable information on their disease-inducing potential, or identify molecules and (bacterial) metabolites that affect NetB expression and activity.

Isolation of Alpha-Toxin-Deficient Clostridium perfringens Type F from Sewage Influents and Effluents

Clostridium perfringens is classified into types A to G, and all types produce alpha-toxins; however, C. perfringens type F that is negative for phospholipase C (PLC) activity of alpha-toxin has been isolated from the environment and cases of humans afflicted by food poisoning. This study aimed to elucidate the distribution of PLC-negative C. perfringens type F in sewage influents and effluents. Influents and effluents of two wastewater treatment plants were collected monthly between July 2016 and January 2020 and between August 2018 and January 2020, respectively. Isolation rates of PLC-negative C. perfringens type F from sewage influents and effluents were 38% (33/86) and 22% (8/36), and the numbers of isolates were 43 and 13, respectively. The locus of the enterotoxin gene of all isolates was determined to be in a plasmid with an IS1151 sequence, and multilocus sequence typing revealed that all 17 representative isolates were assigned as sequence type 186. Sequencing of the plc gene of these representative isolates showed that nonsense mutation (p.W98*) causing alpha-toxin deficiency should be responsible for a loss of PLC enzymatic activity. These results suggest that alpha toxin-deficient C. perfringens type F is distributed in living and water environments since sewage influents contain community wastewater, and effluents contaminate the environment. Detection of C. perfringens type F, independent of PLC activity, should be carried out on human and environmental samples. IMPORTANCE Understanding the diversity of biochemical characteristics that may affect the identification of bacteria is essential. C. perfringens is a ubiquitous bacterium found in the environment, humans, and animals and is responsible for infectious disease in the intestine. Although the alpha-toxin of C. perfringens may be used for its detection, variants of the alpha-toxin lacking its activity have been isolated from soil and humans experiencing symptoms of diarrhea. It is valuable to disclose the prevalence of the alpha-toxin variant in the sewage of wastewater treatment plants, as it may reflect the hygienic condition of the community, as it would be a pollution source for the environment. This study shows the persistent existence and genetic characteristics of the alpha-toxin variant in sewage and reveals a lacking mechanism of the alpha-toxin activity and proposes the detection method of C. perfringens, independent of the alpha-toxin activity.

Prevalence and Genetic Diversity of Toxin Genes in Clinical Isolates of Clostridium perfringens: Coexistence of Alpha-Toxin Variant and Binary Enterotoxin Genes (bec/cpile)

Clostridium perfringens (C. perfringens) is responsible for food-borne gastroenteritis and other infectious diseases, and toxins produced by this bacterium play a key role in pathogenesis. Although various toxins have been described for C. perfringens isolates from humans and animals, prevalence of individual toxins among clinical isolates has not yet been well explored. In the present study, a total of 798 C. perfringens clinical isolates were investigated for prevalence of eight toxin genes and their genetic diversity by PCR, nucleotide sequencing, and phylogenetic analysis. Besides the alpha-toxin gene (plc) present in all the isolates, the most common toxin gene was cpe (enterotoxin) (34.2%), followed by cpb2 (beta2 toxin) (1.4%), netB (NetB) (0.3%), and bec/cpile (binary enterotoxin BEC/CPILE) (0.1%), while beta-, epsilon-, and iota-toxin genes were not detected. Genetic analysis of toxin genes indicated a high level of conservation of plc, cpe, and netB. In contrast, cpb2 was revealed to be considerably divergent, containing at least two lineages. Alpha-toxin among 46 isolates was classified into ten sequence types, among which common types were distinct from those reported for avian isolates. A single isolate with bec/cpile harbored a plc variant containing an insertion of 834-bp sequence, suggesting its putative origin from chickens.

Detection of Clostridium perfringens in tsunami deposits after the Great East Japan Earthquake

The Great East Japan Earthquake struck off the Tohoku and caused a tsunami in 2011. Most of the microbial characteristics of tsunami-affected soil remain unknown and no published study has shown how a tsunami affects the risk of infection by Clostridium perfringens living in soil. In 2011 and 2015, C. perfringens was assessed in deposits in soil from tsunami-damaged areas and undamaged areas of Miyagi. It was found that the number of C. perfringens was overwhelmingly greater in 2011 than in 2015 in the tsunami-damaged areas. According to real-time PCR, the prevalence C. perfringens organisms (%) was 10³ fold greater in the damaged than in the undamaged areas.

Genomic diversity of necrotic enteritis-associated strains of Clostridium perfringens: a review

The investigation of genomic variation between Clostridium perfringens isolates from poultry has been an important tool to enhance our understanding of the genetic basis of strain pathogenicity and the epidemiology of virulent and avirulent strains within the context of necrotic enteritis (NE). The earliest studies used whole genome profiling techniques such as pulsed-field gel electrophoresis to differentiate isolates and determine their relative levels of relatedness. DNA sequencing has been used to investigate genetic variation in (a) individual genes, such as those encoding the alpha and NetB toxins; (b) panels of housekeeping genes for multi-locus sequence typing and (c) most recently whole genome sequencing to build a more complete picture of genomic differences between isolates. Conclusions drawn from these studies include: differential carriage of large conjugative plasmids accounts for a large proportion of inter-strain differences; plasmid-encoded genes are more highly conserved than chromosomal genes, perhaps indicating a relatively recent origin for the plasmids; isolates from NE-affected birds fall into three distinct sequence-based clades while non-pathogenic isolates from healthy birds tend to be more genomically diverse. Overall, the NE causing strains are closely related to C. perfringens isolates from other birds and other diseases whereas the non-pathogenic poultry strains are generally more remotely related to either the pathogenic strains or the strains from other birds. Genomic analysis has indicated that genes in addition to netB are associated with NE pathogenic isolates. Collectively, this work has resulted in a deeper understanding of the pathogenesis of this important poultry disease.

Clostridial toxins

Clostridia produce the highest number of toxins of any type of bacteria and are involved in severe diseases in humans and other animals. Most of the clostridial toxins are pore-forming toxins responsible for gangrenes and gastrointestinal diseases. Among them, perfringolysin has been extensively studied and it is the paradigm of the cholesterol-dependent cytolysins, whereas Clostridium perfringens epsilon-toxin and Clostridium septicum alpha-toxin, which are related to aerolysin, are the prototypes of clostridial toxins that form small pores. Other toxins active on the cell surface possess an enzymatic activity, such as phospholipase C and collagenase, and are involved in the degradation of specific cell-membrane or extracellular-matrix components. Three groups of clostridial toxins have the ability to enter cells: large clostridial glucosylating toxins, binary toxins and neurotoxins. The binary and large clostridial glucosylating toxins alter the actin cytoskeleton by enzymatically modifying the actin monomers and the regulatory proteins from the Rho family, respectively. Clostridial neurotoxins proteolyse key components of neuroexocytosis. Botulinum neurotoxins inhibit neurotransmission at neuromuscular junctions, whereas tetanus toxin targets the inhibitory interneurons of the CNS. The high potency of clostridial toxins results from their specific targets, which have an essential cellular function, and from the type of modification that they induce. In addition, clostridial toxins are useful pharmacological and biological tools.

In vitro production of necrotic enteritis toxin B, NetB, by netB-positive and netB-negative Clostridium perfringens originating from healthy and diseased broiler chickens

The Clostridium perfringens necrotic enteritis toxin B, NetB, was recently proposed as a new key virulence factor for the development of necrotic enteritis (NE) in broilers. The aim of the present study was to investigate the presence of the netB gene and the in vitro production of the NetB toxin in a well characterized collection of 48 C. perfringens Type A isolates, obtained from Danish broiler flocks. The investigation revealed netB gene prevalences of approx. 50% and 60% among isolates from diseased (NE) and healthy flocks, respectively. Only minor nucleotide variations were observed between the isolates in the coding sequence (CDS) of the netB gene, and the promoter region was observed to be completely conserved. However, in vitro NetB production was only observed in 4 out of 14 netB-positive C. perfringens isolates recovered from healthy birds, whereas 12 out of 13 netB-positive isolates from NE birds were shown to produce the NetB toxin. It is therefore proposed that genotype, i.e. presence of the netB gene, in itself is inadequate for predicting virulence of C. perfringens, and future investigations should focus on the bacterial phenotypes; the regulatory mechanisms involved in the expression of NetB, and potentially also other toxins, and its implications for the virulence of individual C. perfringens strains.