Molecular characterization of Corynebacterium pseudotuberculosis isolated from goats using ERIC-PCR

Phenotypical and molecular characterization of Rhodococcus equi isolated from foals in the Agreste region of Pernambuco - Brazil

Equine rhodococcosis is caused by Rhodococcus equi, an intracellular coccobacillus whose main virulence factor is a plasmid that harbors genes encoding proteins from the Vap family, with the vapA gene being the most important in equine isolates. Furthermore, other factors observed in R. equi strains, such as antimicrobial resistance and biofilm production, may represent significant challenges in the treatment of affected animals. The objective of this study was to characterize four isolates of R. equi from foals in the state of Pernambuco, Brazil. All isolates were identified as R. equi through biochemical tests, amplification of the choE gene, and sequencing of 16 S rRNA. PCR analysis revealed that three isolates were positive for the plasmid virulence genes (vapA, -C, -D, -E, -F, -H and traA), although vapD was absent in one of the three isolates. One isolate did not present any virulence genes, possibly due to the loss of the plasmid after repeated passages at 37ºC. In the antimicrobial susceptibility test, all isolates were susceptible to erythromycin, clarithromycin, azithromycin, rifampicin, gentamicin, and doxycycline. However, all isolates were capable of forming biofilms, with moderate biofilm formation in isolates Rhodo1 and Rhodo2, and weak biofilm formation in isolates Rhodo3 and Rhodo4, which may be associated with increased antimicrobial tolerance. This molecular characterization demonstrated, for the first time, the presence of the virulence plasmid in R. equi isolates from foals in Northeast Brazil, as well as their capacity for biofilm formation.

Genotyping of Corynebacterium pseudotuberculosis isolates using PCR-based DNA fingerprinting methods

Phenotypic typing methods are often time consuming and do not adequately discriminate among the strains involved. Innovative molecular techniques can perform direct typing by analyzing DNA and are becoming widespread as important tools for bacterial typing, molecular epidemiology and molecular systematization. The aim of this study was to genotype Corynebacterium pseudotuberculosis strains using PCR-based DNA fingerprinting methods and to evaluate the methods comparatively. Within the scope of the study, 17 C. pseudotuberculosis strains were analyzed. The strains were genotyped by enterobacterial repetitive intergenic consensus (ERIC)-PCR using ERIC2 primer; by random amplified polymorphic (RAPD) DNA-PCR using primers P5, P6, P11, P14, P16, P21 and M13; and by (GTG)5-PCR using (GTG)5 primer. The discrimination power and confidence intervals of the methods were calculated based on the genotyping results using each primer. All strains produced amplification products with the primers used for genotyping. As a result of genotyping with ERIC2, P14, P11, (GTG)5, P21, P5, M13, P6 and P16 primers, the discrimination powers (confidence intervals) were calculated as 0.8603(0.858-0.862), 0.7132(0.709-0.716), 0.6838(0.668-0.699), 0.6397(0.623-0.656), 0.5809(0.560-0.601), 0.3235(0.293-0.353), 0.1176(0.081-0.153), 0.1176(0.081-0.153) and 0.1176(0.081-0.153), respectively. As a result of the comparative evaluation of the results, it was observed that ERIC2 and P14 primers had high discrimination power and confidence interval in genotyping C. pseudotuberculosis strains, while M13, P6 and P16 primers were insufficient in genotyping of strains. It was concluded that genotyping with ERIC2 and P14 primers can be used reliably in investigating the molecular epidemiology of infections and/or outbreaks caused by C. pseudotuberculosis.

Molecular Characterization and Antimicrobial Susceptibilities of Corynebacterium pseudotuberculosis Isolated from Caseous Lymphadenitis of Smallholder Sheep and Goats

Caseous lymphadenitis (CLA) is a bacterial infection caused by Corynebacterium pseudotuberculosis (C. pseudotuberculosis) that affects sheep and goats, leading to abscess formation in their lymph nodes. The present study aimed to isolate and identify C. pseudotuberculosis from CLA in smallholder sheep and goats, and determine the resistance patterns, virulence, and resistance genes of the isolates. Additionally, genotypic and phylogenetic analysis of the isolates was conducted using ERIC-PCR and DNA sequencing techniques. A cross-sectional study examined 220 animals (130 sheep and 90 goats) from 39 smallholder flocks for clinical signs of CLA. Fifty-four (24.54%) animals showed CLA-compatible lesions, confirmed by C. pseudotuberculosis isolation and PCR identification. Sheep had a lower infection rate of CLA (18.46%) compared with goats (33.3%). Antimicrobial susceptibility testing of 54 C. pseudotuberculosis isolates to 24 antimicrobial drugs revealed that they were 100% resistant to bacitracin and florfenicol, while none of the isolates were resistant to norfloxacin. A high resistance rate was observed for penicillin and erythromycin (92.6% each). Interestingly, 16.7% of C. pseudotuberculosis isolates recovered from sheep showed vancomycin resistance. Molecular characterization of C. pseudotuberculosis isolates revealed that PLD, PIP, and FagA virulence genes were present in all examined isolates. However, the FagB, FagC, and FagD genes were detected in 24 (100%), 20 (83%), and 18 (75%) of the sheep isolates, and 26 (87%), 26 (87%), and 18 (60%) of the goat isolates, respectively. The β-lactam resistance gene was present in all isolates. Furthermore, 83% of the sheep isolates carried the aminoglycoside (aph(3″)-lb), chloramphenicol (cat1), and bacitracin (bcrA) resistance genes. Among the isolates recovered from goats, 73% were found to contain macrolides (ermX), sulfonamide (sul1), and bacitracin (bcrA) resistance genes. It is worrisome that the glycopeptide (vanA) resistance gene was detected in 8% of the sheep isolates as a first report. ERIC-PCR genotyping of 10 multi-drug-resistant C. pseudotuberculosis isolates showed a high similarity index of 83.6% between isolates from sheep and goats. Nucleotide sequence analysis of partial 16S rRNA sequences of C. pseudotuberculosis revealed 98.83% similarity with biovar Ovis of globally available reference sequences on the Genbank database. Overall, our findings might indicate that C. pseudotuberculosis infection in smallholders in Egypt might be underestimated despite the significant financial impact on animal husbandry and potential health hazards it poses. Moreover, this study highlights the importance of implementing a sustainable control strategy and increasing knowledge and awareness among smallholder breeders to mitigate the economic impact of CLA.

Prevalence and antimicrobial-resistant characterization of Bacillus cereus isolated from ready-to-eat rice products in Eastern China

Bacillus cereus is a major food-borne bacterial pathogen in the world, which can cause diarrhea and emetic syndrome. This study aimed to reveal the quantitative prevalence of B. cereus in ready-to-eat (RTE) rice products in Eastern China and to gain essential information on the characteristics of B. cereus isolates. A total of 91 out of the 1071 samples were positive for B. cereus. The contamination level of B. cereus in 0.5 % of RTE rice product samples outnumbered 10³ CFU/g. The number of B. cereus attained 10⁵−10⁶ CFU/g in one sample. The distribution patterns of virulence genes in B. cereus isolates were identified. 84.6% of the B. cereus isolates had at least one enterotoxin or emetic toxin gene. The predominant pattern was XXV. 9.9% of isolates belonged to it and possessed one enterotoxin gene entFM. The occurrence rate of hblACD and nheABC was 36.3% and 47.3%, respectively. Antimicrobial susceptibility tests revealed a high resistance rate toward penicillin, and 23.1% of the isolates were multi-drug resistant. B. cereus isolates were genotyped by using ERIC-PCR. 89 genotypes were determined. The Hunter Gaston Discriminatory Index (HGDI) attained 0.9995. Relationships analysis revealed that Group A B. cereus isolates tended to carry hblA, hblC, hblD, nheA, nheB, and show resistance to penicillin/trimethoprim/sulfamethoxazole. This study was useful for updating the knowledge of the contamination status of B. cereus in RTE rice products in China.

Molecular Characterization of Corynebacterium pseudotuberculosis Isolated over a 15-Year Period in Switzerland

Corynebacterium pseudotuberculosis biovar Ovis is the etiological agent of the contagious and chronic disease caseous lymphadenitis (CLA) in sheep and goats. The economic impact of CLA in Switzerland remains largely unknown, and the transmission modalities, as well as the genetic diversity of circulating strains, are poorly understood. This work presents further characterization data for 215 C. pseudotuberculosis isolates from sheep, goats and a dromedary originating from Switzerland and the Principality of Liechtenstein, collected over a 15-year period. The isolates were classified into the two biovars Ovis and Equi, analyzed for the presence of the diphtheria-like toxin gene and characterized using MLSA. All sheep and goat isolates were classified as C. pseudotuberculosis biovar Ovis. The isolate from a dromedary was classified as biovar Equi. No isolates harboring the diphtheria-like toxin gene were detected. Phylogenetic analysis of the concatenated sequences of four genes revealed the existence of 24 clusters. There was no correlation between MLSA sequence types, year of isolation and the geographical origin of the isolates. These findings confirm the presence of several MLSA sequence types in the study area and over a 15-year period. Moreover, no sheep- and goat-specific MLSA sequence types were found.

Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi

BACKGROUND

Corynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis.

METHODS

In the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level.

RESULTS

A novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T, were compared to the results of nitrate reductase identification by biochemical test. The McNemar's Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16-6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90-0.98)].

CONCLUSIONS

The ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory.

Molecular epidemiology of Corynebacterium pseudotuberculosis isolated from horses in California

Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative lymphangitis. The host/pathogen factors dictating the form or severity of infection are currently unknown. Our recent investigations have shown that genotyping C. pseudotuberculosis isolates using enterobacterial repetitive intergenic consensus (ERIC)-PCR is useful for understanding the evolutionary genetics of the species as well for molecular epidemiology studies. The aims of the present study were to assess (i) the genetic diversity of C. pseudotuberculosis strains isolated from horses in California, United States and (ii) the epidemiologic relationships among isolates. One hundred and seven C. pseudotuberculosis biovar Equi isolates from ninety-five horses, and two C. pseudotuberculosis biovar Ovis strains, C. pseudotuberculosis ATCC 19410^T type strain and C. pseudotuberculosis 1002 vaccine strain, were fingerprinted using the ERIC 1+2-PCR. C. pseudotuberculosis isolated from horses showed a high genetic diversity, clustering in twenty-seven genotypes with a diversity index of 0.91. Minimal spanning tree showed four major clonal complexes with a pattern of temporal clustering. Strains isolated from the same horse showed identical ERIC 1+2-PCR genotype, with the exception of two strains isolated from the same animal that showed distinct genotypes, suggesting a co-infection. We found no strong genetic signals related to clinical form (including internal versus external infections). However, temporal clustering of genotypes was observed.

Corynebacterium pseudotuberculosis may be under anagenesis and biovar Equi forms biovar Ovis: a phylogenic inference from sequence and structural analysis

BACKGROUND

Corynebacterium pseudotuberculosis can be classified into two biovars or biovars based on their nitrate-reducing ability. Strains isolated from sheep and goats show negative nitrate reduction and are termed biovar Ovis, while strains from horse and cattle exhibit positive nitrate reduction and are called biovar Equi. However, molecular evidence has not been established so far to understand this difference, specifically if these C. pseudotuberculosis strains are under an evolutionary process.

RESULTS

The ERIC 1 + 2 Minimum-spanning tree from 367 strains of C. pseudotuberculosis showed that the great majority of biovar Ovis strains clustered together, but separately from biovar Equi strains that also clustered amongst themselves. Using evolutionarily conserved genes (rpoB, gapA, fusA, and rsmE) and their corresponding amino acid sequences, we analyzed the phylogenetic relationship among eighteen strains of C. pseudotuberculosis belonging to both biovars Ovis and Equi. Additionally, conserved point mutation based on structural variation analysis was also carried out to elucidate the genotype-phenotype correlations and speciation. We observed that the biovars are different at the molecular phylogenetic level and a probable anagenesis is occurring slowly within the species C. pseudotuberculosis.

CONCLUSIONS

Taken together the results suggest that biovar Equi is forming the biovar Ovis. However, additional analyses using other genes and other bacterial strains are required to further support our anagenesis hypothesis in C. pseudotuberculosis.

Evaluation of ERIC-PCR as genotyping method for Corynebacterium pseudotuberculosis isolates

The aim of this study was to evaluate the Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) as a tool for molecular typing of C. pseudotuberculosis isolates from eight different hosts in twelve countries. Ninety-nine C. pseudotuberculosis field strains, one type strain (ATCC 19410^T) and one vaccine strain (1002) were fingerprinted using the ERIC-1R and ERIC-2 primers, and the ERIC-1R+ERIC-2 primer pair. Twenty-nine different genotypes were generated by ERIC 1-PCR, 28 by ERIC 2-PCR and 35 by ERIC 1+2-PCR. The discriminatory index calculated for ERIC 1, ERIC 2, and ERIC 1+2-PCR was 0.89, 0.86, and 0.92, respectively. Epidemiological concordance was established for all ERIC-PCR assays. ERIC 1+2-PCR was defined as the best method based on suitability of the amplification patterns and discriminatory index. Minimal spanning tree for ERIC 1+2-PCR revealed three major clonal complexes and clustering around nitrate-positive (biovar Equi) and nitrate-negative (biovar Ovis) strains. Therefore, ERIC 1+2-PCR proved to be the best technique evaluated in this study for genotyping C. pseudotuberculosis strains, due to its usefulness for molecular epidemiology investigations.

The relationship between Corynebacterium pseudotuberculosis biovar equi phenotype with location and extent of lesions in horses

Equine infection with Corynebacterium pseudotuberculosis can manifest in several forms, including external or internal abscesses. The objective of this study was to phenotype clinical isolates of C. pseudotuberculosis and to investigate the relationship between lesion location and extent of lesions in the animals from which they were collected. One hundred and seventy-one C. pseudotuberculosis biovar equi isolates were collected from horses presenting to the University of California Veterinary Medical Teaching Hospital and two other sources in the period between September 1996 and December 2011. Bacterial isolates were grouped on the bases of biochemical characteristics and growth on brain heart infusion agar. Six phenotypes were identified: (1) large colonies that metabolized sucrose (n = 81); (2) large sucrose-negative colonies (n = 47); (3) medium sucrose-positive (n = 20); (4) medium sucrose-negative (n = 11); (5) small sucrose-positive (n = 7), and (6) small sucrose-negative (n = 5). Medical records corresponding to each isolate were accessed from the University's administrative computer system or from the submitting source in order to determine the anatomical site from which the isolate was collected (n = 171), as well as the extent of lesions (n = 164) in the patient. The relationship between phenotype, lesion location and extent of lesions was then investigated statistically. No significant relationship between strain and lesion location or extent of lesions was found. This suggests that phenotypic differences during in vitro culture does not account for external versus internal disease in horses. Further work to characterize strains genotypically and to identify determinants for bacterial virulence should be performed. Importantly, host and environmental factors should also be further investigated.