Lynn A. Joens

Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

Background The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni. Methodology/Principal Findings Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families. Conclusion/Significance This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

Characterization of Campylobacter jejuni Biofilms under Defined Growth Conditions

ABSTRACT Campylobacter jejuni is a major cause of human diarrheal disease in many industrialized countries and is a source of public health and economic burden. C. jejuni, present as normal flora in the intestinal tract of commercial broiler chickens and other livestock, is probably the main source of human infections. The presence of C. jejuni in biofilms found in animal production watering systems may play a role in the colonization of these animals. We have determined that C. jejuni can form biofilms on a variety of abiotic surfaces commonly used in watering systems, such as acrylonitrile butadiene styrene and polyvinyl chloride plastics. Furthermore, C. jejuni biofilm formation was inhibited by growth in nutrient-rich media or high osmolarity, and thermophilic and microaerophilic conditions enhanced biofilm formation. Thus, nutritional and environmental conditions affect the formation of C. jejuni biofilms. Both flagella and quorum sensing appear to be required for maximal biofilm formation, as C. jejuni flaAB and luxS mutants were significantly reduced in their ability to form biofilms compared to the wild-type strain.

Role of Catalase in Campylobacter jejuni Intracellular Survival

ABSTRACT The ability of Campylobacter jejuni to penetrate normally nonphagocytic host cells is believed to be a key virulence determinant. Recently, kinetics of C. jejuni intracellular survival have been described and indicate that the bacterium can persist and multiply within epithelial cells and macrophages in vitro. Studies conducted by Pesci et al. indicate that superoxide dismutase contributes to intraepithelial cell survival, as isogenicsod mutants are 12-fold more sensitive to intracellular killing than wild-type strains. These findings suggest that bacterial factors that combat reactive oxygen species enable the organism to persist inside host cells. Experiments were conducted to determine the contribution of catalase to C. jejuni intracellular survival. Zymographic analysis indicated that C. jejuniexpresses a single catalase enzyme. The gene encoding catalase (katA) was cloned via functional complementation, and an isogenic katA mutant strain was constructed. Kinetic studies indicate that catalase provides resistance to hydrogen peroxide in vitro but does not play a role in intraepithelial cell survival. Catalase does however contribute to intramacrophage survival. Kinetic studies of C. jejuni growth in murine and porcine peritoneal macrophages demonstrated extensive killing of both wild-type and katA mutant strains shortly following internalization. Long-term cultures (72 h postinfection) of infected phagocytes permitted recovery of viable wild-typeC. jejuni; in contrast, no viable katA mutant bacteria were recovered. Accordingly, inhibition of macrophage nitric oxide synthase or NADPH oxidase permitted recovery of katAmutant C. jejuni. These observations indicate that catalase is essential for C. jejuni intramacrophage persistence and growth and suggest a novel mechanism of intracellular survival.

Prevalence of Salmonella spp. in Oysters in the United States

ABSTRACT Food-borne diseases such as salmonellosis can be attributed, in part, to the consumption of raw oysters. To determine the prevalence of Salmonella spp. in oysters, oysters harvested from 36 U.S. bays (12 each from the West, East, and Gulf coasts in the summer of 2002, and 12 bays, four per coast, in the winter of 2002-2003) were tested. Salmonella was isolated from oysters from each coast of the United States, and 7.4% of all oysters tested contained Salmonella. Isolation tended to be bay specific, with some bays having a high prevalence of Salmonella, while other bays had none. Differences in the percentage of oysters from which Salmonella was isolated were observed between the summer and winter months, with winter numbers much lower probably due to a variety of weather-related events. The vast majority (78/101) of Salmonella isolates from oysters were Salmonella enterica serovar Newport, a major human pathogen, confirming the human health hazard of raw oyster consumption. Contrary to previous findings, no relationship was found between the isolation of fecal coliforms and Salmonella from oysters, indicating a necessity for specific monitoring for Salmonella and other pathogens rather than the current reliance on fecal coliform testing.

Human and animal enteric caliciviruses in oysters from different coastal regions of the United States.

ABSTRACT Food-borne diseases are a major cause of morbidity and hospitalization worldwide. Enteric caliciviruses are capable of persisting in the environment and in the tissues of shellfish. Human noroviruses (HuNoVs) have been implicated in outbreaks linked to shellfish consumption. The genetic and antigenic relatedness between human and animal enteric caliciviruses suggests that interspecies transmission may occur. To determine the occurrence of human and animal enteric caliciviruses in United States market oysters, we surveyed regional markets. Oysters were collected from 45 bays along the United States coast during the summer and winter of 2002 and 2003. Samples were analyzed by reverse transcription-PCR, and results were confirmed by hybridization and sequence analysis. Nine samples (20%) were positive for HuNoV genogroup II after hybridization. Animal enteric caliciviruses were detected in 10 samples (22%). Seven of these samples were positive for porcine norovirus genogroup II, and one sample was positive for porcine sapovirus after hybridization and confirmation by sequencing. Bovine noroviruses were detected in two samples, and these results were confirmed by sequencing. Five HuNoV samples sequenced in the polymerase region were similar to the norovirus genogroup II US 95/96 subset (genogroup II-4) previously implicated in diarrhea outbreaks. Different seasonal and state distributions were detected. The presence of animal enteric caliciviruses was associated with states with high livestock production. Although the presence of human caliciviruses in raw oysters represents a potential risk for gastroenteritis, disease confirmation by investigation of outbreaks is required. The simultaneous detection of human and animal enteric caliciviruses raises concerns about human infection or coinfection with human and animal strains that could result in genomic recombination and the emergence of new strains.

Characteristics of the internalization and intracellular survival of Campylobacter jejuni in human epithelial cell cultures

The characteristics associated with the internalization and intracellular behavior of Campylobacter jejuni during short-term and long-term cultivation with INT 407 cells were examined. The internalization of C. jejuni by INT 407 cells was inhibited by cytochalasin dansylcadaverine, chemicals that disrupt microfilament formation and inhibit receptor cycling, respectively. Ammonium chloride and methylamine, two chemicals that inhibit endosomal acidification, did not affect C. jejuni internalization. Once internalized, C. jejuni were found exclusively with membrane-bound vacuoles. With regard to intracellular survival, a decline in the number of viable intracellular bacteria, as determined by protection from gentamicin, occurred during the initial phase of infection and when a low level of the antibiotic was maintained in the culture medium. However, the number of intracellular C. jejuni increased markedly after the removal of the antibiotic. In the absence of antibiotic, the infection led to the deterioration of the cell monolayers, indicating that C. jejuni is able to survive within epithelial cells and elicit a cytotoxic effect. The ability of C. jejuni to enter and exert deleterious effects on cells may reflect a pathogenic mechanism associated with enteritis caused by this organism.

Carvacrol and cinnamaldehyde inactivate antibiotic-resistant salmonella entérica in buffer and on celery and oysters

The emergence of antibiotic-resistant Salmonella is of concern to food processors. The objective of this research was to identify antimicrobial activities of cinnamaldehyde and carvacrol against antibiotic-resistant Salmonella enterica in phosphate-buffered saline (PBS) and on celery and oysters. Twenty-three isolates were screened for resistance to seven antibiotics. Two resistant and two susceptible strains were chosen for the study. S. enterica cultures (10(5) CFU/ml) were added to different concentrations of cinnamaldehyde and carvacrol (0.1, 0.2, 0.3, and 0.4% [vol/vol]) in PBS, mixed, and incubated at 37 degrees C. Samples were taken at 0, 1, 5, and 24 h for enumeration. Celery and oysters were inoculated with S. enterica (10(6-7) CFU/ml), treated with 1% cinnamaldehyde or 1% carvacrol, incubated at 4 degrees C, and then sampled for enumeration on days 0 and 3. Both antimicrobials induced complete inactivation of S. enterica in PBS at 0.3 and 0.4% on exposure, and on 0.2% in 1 h. Exposure to cinnamaldehyde at 0.1% inactivated all pathogens at 1 h, and survivors were observed only for Salmonella Newport with 0.1% carvacrol at 1 h. In celery, 1% carvacrol reduced S. enterica populations to below detection on day 0, while 1% cinnamaldehyde reduced populations by 1 and 2.3 log on day 0 and day 3, respectively. In oysters, both antimicrobials caused about 5-log reductions on day 3. These results show the potential antimicrobial effects of carvacrol and cinnamaldehyde against antibiotic-resistant S. enterica in vitro and in foods.

Characterization of Genetically Matched Isolates of Campylobacter jejuni Reveals that Mutations in Genes Involved in Flagellar Biosynthesis Alter the Organism's Virulence Potential

ABSTRACT Phenotypic and genotypic evidence suggests that not all Campylobacter jejuni isolates are pathogenic for humans. We hypothesized that differences in gene content or gene expression alter the degree of pathogenicity of C. jejuni isolates. A C. jejuni isolate (Turkey) recovered from a turkey and a second C. jejuni isolate (CS) recovered from a chicken differed in their degrees of in vitro and in vivo virulence. The C. jejuni Turkey isolate invaded INT 407 human epithelial cells and secreted the Cia (Campylobacter invasion antigen) proteins, while the C. jejuni CS isolate was noninvasive for human epithelial cells and did not secrete the Cia proteins. Newborn piglets inoculated with the C. jejuni Turkey isolate developed more severe clinical signs of campylobacteriosis than piglets inoculated with the C. jejuni CS isolate. Additional work revealed that flagellin was not expressed in the C. jejuni CS isolate. Microarray and real-time reverse transcription-PCR analyses revealed that all flagellar class II genes were significantly downregulated in the C. jejuni CS isolate compared to the C. jejuni Turkey isolate. Finally, nucleotide sequencing of the flgR gene revealed the presence of a single residue that was different in the FlgR proteins of the C. jejuni Turkey and CS isolates. Complementation of the C. jejuni CS isolate with a wild-type copy of the flgR gene restored the isolates motility. Collectively, these findings support the hypothesis that critical differences in gene content or gene expression can alter the pathogenic potential of C. jejuni isolates.

Antimicrobial Edible Apple Films Inactivate Antibiotic Resistant and Susceptible Campylobacter jejuni Strains on Chicken Breast

UNLABELLED Campylobacter jejuni is the leading cause of bacterial diarrheal illness worldwide. Many strains are now becoming multidrug resistant. Apple-based edible films containing carvacrol and cinnamaldehyde were evaluated for bactericidal activity against antibiotic resistant and susceptible C. jejuni strains on chicken. Retail chicken breast samples inoculated with D28a and H2a (resistant strains) and A24a (a sensitive strain) were wrapped in apple films containing cinnamaldehyde or carvacrol at 0.5%, 1.5%, and 3% concentrations, and then incubated at 4 or 23 °C for 72 h. Immediately after wrapping and at 72 h, samples were plated for enumeration of viable C. jejuni. The antimicrobial films exhibited dose- and temperature-dependent bactericidal activity against all strains. Films with ≥1.5% cinnamaldehyde reduced populations of all strains to below detection at 23 °C at 72 h. At 4 °C with cinnamaldehyde, reductions were variable for all strains, ranging from 0.2 to 2.5 logs and 1.8 to 6.0 logs at 1.5% and 3.0%, respectively. Films with 3% carvacrol reduced populations of A24a and H2a to below detection, and D28a by 2.4 logs at 23 °C and 72 h. A 0.5-log reduction was observed for both A24a and D28a, and 0.9 logs for H2a at 4 °C at 3% carvacrol. Reductions ranged from 1.1 to 1.9 logs and 0.4 to 1.2 logs with 1.5% and 0.5% carvacrol at 23 °C, respectively. The films with cinnamaldehyde were more effective than carvacrol films. Reductions at 23 °C were greater than those at 4 °C. Our results showed that antimicrobial apple films have the potential to reduce C. jejuni on chicken and therefore, the risk of campylobacteriosis. Possible mechanisms of antimicrobial effects are discussed. PRACTICAL APPLICATION   Apple antimicrobial films could potentially be used in retail food packaging to reduce C. jejuni commonly present on food.

Plant-Derived Compounds Inactivate Antibiotic-Resistant Campylobacter jejuni Strains

Sixty-three Campylobacter jejuni isolates were screened for their resistance to the antibiotics ampicillin, cefaclor, ciprofloxacin, erythromycin, gentamycin, tetracycline, and trimethoprim-sulfamethoxazole. Based on this screen, the resistant strains D28a and H2a and the nonresistant strain A24a were selected for evaluation of their resistance and susceptibility to inactivation by cinnamaldehyde and carvacrol, the main constituents of plant-derived cinnamon and oregano oils, respectively. Different concentrations (0.05, 0.1, and 0.2% [vol/vol] in sterile phosphate-buffered saline) of cinnamaldehyde and carvacrol were added to C. jejuni cultures with initial populations of 10(4) CFU/ml. The samples were then mixed thoroughly and incubated at 37 degrees C. Viable bacterial populations were enumerated at incubation periods of 0, 30, 60, and 120 min. The results indicate that the extent of inhibition of microbial survival was related to both the nature and concentration of antimicrobials and the incubation time. Both cinnamaldehyde and carvacrol exhibited rapid antimicrobial activity against both antibiotic-resistant and non-resistant C. jejuni strains, at concentrations of approximately 0.1% and higher. The antimicrobial efficacy of cinnamaldehyde was greater than that of carvacrol. The possible significance of the results for microbiological food safety is discussed.