Detection of toxigenic Clostridium perfringens and Clostridium botulinum from food sold in Lagos, Nigeria

Chukwu, Emelda E.; Nwaokorie, Francisca O.; Coker, A. O.; Ávila-Campos, Mário Júlio; Solís, Rosa L.; Llanco, Luis; Ogunsola, Folasade

doi:10.1016/j.anaerobe.2016.10.009

Cited by 29 publications

(19 citation statements)

References 28 publications

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“…SYT1 (Figure 7B) is a cell surface receptor by which the type B botulinum neurotoxin enters human neurons [Connan et al, 2017]. Selection here may be a response to pervasive foodborne bacterial contamination by Clostridium botulinum , similar to what exists in modern times [Chukwu et al, 2016]. Pierron et al [2014] named HEMGN (which Pickrell et al [2009] also identified), involved in erythrocyte differentiation, as a selection signal common to Malagasy populations derived from common ancestry with YRI.…”

Section: Discussionmentioning

confidence: 99%

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

Harris

Garud

DeGiorgio

2018

Preprint

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Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity. These selective sweeps can be hard or soft. In the case of a hard selective sweep, a single adaptive haplotype rises to high population frequency, whereas multiple adaptive haplotypes sweep through the population simultaneously in a soft sweep, producing distinct patterns of genetic variation in the vicinity of the selected site. Measures of expected haplotype homozygosity have previously been used to detect sweeps in multiple study systems. However, these methods are formulated for phased haplotype data, typically unavailable for nonmodel organisms, and may have reduced power to detect soft sweeps due to their increased genetic diversity relative to hard sweeps. To address these limitations, we applied the H12 and H2/H1 statistics of Garud et al. [2015] to unphased multilocus genotypes, denoting them as G12 and G2/G1. G12 (and the more direct expected homozygosity analogue to H12, denoted G123) has comparable power to H12 for detecting both hard and soft sweeps. G2/G1 can be used to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 or G123 values. The reason for this power is that under random mating, the most frequent haplotypes will yield the most frequent multilocus genotypes. Simulations based on parameters compatible with our recent understanding of human demographic history suggest that expected homozygosity methods are best suited for detecting recent sweeps, and increase in power under recent population expansions. Finally, we find candidates for selective sweeps within the 1000 Genomes CEU, YRI, GIH, and CHB populations, which corroborate and complement existing studies.

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Section: Discussionmentioning

confidence: 99%

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

Harris

Garud

DeGiorgio

2018

Preprint

View full text Add to dashboard Cite

show abstract

“…SYT1 ( Figure 7B) is a cell surface receptor by which the type B botulinum neurotoxin enters human neurons (Connan et al 2017). Selection here may be a response to pervasive foodborne bacterial contamination by Clostridium botulinum, similar to what exists in modern times (Chukwu et al 2016). Pierron et al (2014) named HEMGN [which Pickrell et al (2009) also identified], involved in erythrocyte differentiation, as a selection signal common to Malagasy populations derived from common ancestry with YRI.…”

Section: Application Of G12 and G123 To Empirical Datamentioning

confidence: 98%

Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity

2018

View full text Add to dashboard Cite

Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity. These selective sweeps can be hard or soft. In the case of a hard selective sweep, a single adaptive haplotype rises to high population frequency, whereas multiple adaptive haplotypes sweep through the population simultaneously in a soft sweep, producing distinct patterns of genetic variation in the vicinity of the selected site. Measures of expected haplotype homozygosity have previously been used to detect sweeps in multiple study systems. However, these methods are formulated for phased haplotype data, typically unavailable for nonmodel organisms, and some may have reduced power to detect soft sweeps due to their increased genetic diversity relative to hard sweeps. To address these limitations, we applied the H12 and H2/H1 statistics proposed in 2015 by Garud et al., which have power to detect both hard and soft sweeps, to unphased multilocus genotypes, denoting them as G12 and G2/G1. G12 (and the more direct expected homozygosity analog to H12, denoted G123) has comparable power to H12 for detecting both hard and soft sweeps. G2/G1 can be used to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 or G123 values. The reason for this power is that, under random mating, the most frequent haplotypes will yield the most frequent multilocus genotypes. Simulations based on parameters compatible with our recent understanding of human demographic history suggest that expected homozygosity methods are best suited for detecting recent sweeps, and increase in power under recent population expansions. Finally, we find candidates for selective sweeps within the 1000 Genomes CEU, YRI, GIH, and CHB populations, which corroborate and complement existing studies.

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“…Genotyping of C. perfringens isolates, however, can overcome this problem and has become the standard for toxinotyping of C. perfringens . Polymerase chain reaction (PCR) protocols, especially multiplex PCR assay, have been established for simultaneous detection of these toxin genes ( cpa, cpb, etx, iap, cpe and cpb2 ) [ 24 , 25 , 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

Prevalence, Genotypic and Phenotypic Characterization and Antibiotic Resistance Profile of Clostridium perfringens Type A and D Isolated from Feces of Sheep (Ovis aries) and Goats (Capra hircus) in Punjab, Pakistan

Mohiuddin

Iqbal

Siddique

et al. 2020

Toxins

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Clostridium perfringens poses a serious threat to small ruminants by causing moderate to severe enterotoxaemia. Due to its ability to produce a wide arsenal of toxins, it is ranked among the most prevalent and important pathogens in livestock. This study focused on the molecular characterization of different Clostridium perfringens types along with their antimicrobial resistance profile. An overall higher prevalence of C. perfringens (46.1%) was detected based on mPCR among sheep and goats (healthy and diseased) in the Punjab province, Pakistan. The majority of the isolates were characterized as type A (82%), followed by type D (18%). Among the isolates from diseased sheep and goats, 27% were positive for cpa, 49% for cpa and cpb2, 9% for cpa and etx, 15% for cpa, cpb2 and etx. In the case of isolates from healthy sheep and goats, 59% were positive for cpa, 34% for cpb2 and cpa, 4% for cpa and etx, and 3% for cpa, cpb2 and etx. The prevalence of the beta2 toxin gene in the diseased sheep and goat population was 64% as compared to 37% in healthy animals. All 184 isolates (100%) were sensitive to rifampin and ceftiofur; the majority (57%) was sensitive to teicoplanin, chloramphenicol, amoxicillin, linezolid and enrofloxacin. A lower proportion of isolates (43%) were sensitive to ciprofloxacin and only 14% were susceptible to erythromycin. The findings of this study highlight the higher prevalence of C. perfringens in small ruminants and indicate that detailed pathogenesis studies are necessary to understand the explicit role of various toxins in causing enteric infections in sheep and goats including how they might be exploited to develop vaccines against these diseases.

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Detection of toxigenic Clostridium perfringens and Clostridium botulinum from food sold in Lagos, Nigeria

Cited by 29 publications

References 28 publications

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity

Prevalence, Genotypic and Phenotypic Characterization and Antibiotic Resistance Profile of Clostridium perfringens Type A and D Isolated from Feces of Sheep (Ovis aries) and Goats (Capra hircus) in Punjab, Pakistan

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