Summary Chlamydiae are globally widespread obligate intracellular bacteria, which several species are a well‐recognized threat to human and animal health. In Australia, the most successful chlamydial species are the infamous koala pathogen C. pecorum, and C. psittaci, an emerging pathogen associated with zoonotic events. Little is known about infections caused by other chlamydial organisms in Australian livestock or wildlife. Considering that these hosts can be encountered by humans at the animal/human interface, in this study, we investigated genetic diversity of chlamydial organisms infecting Australian domesticated and wild ungulates. A total of 185 samples from 129 domesticated (cattle, horses, sheep, and pigs) and 29 wild (deer) ungulate hosts were screened with C. pecorum and C. psittaci species‐specific assays, followed by a screen with pan‐Chlamydiales assay. Overall, chlamydial DNA was detected in 120/185 (65%) samples, including all ungulate hosts. Species‐specific assays further revealed that C. pecorum and C. psittaci DNA were detected in 27% (50/185) and 6% (11/185) of the samples, respectively, however from domesticated hosts only. A total of 46 “signature” 16S rRNA sequences were successfully resolved by sequencing and were used for phylogenetic analyses. Sequence analyses revealed that genetically diverse novel as well as traditional chlamydial organisms infect an expanded range of ungulate hosts in Australia. Detection of the C. psittaci and C. pecorum in livestock, and novel taxa infecting horses and deer raises questions about the genetic make‐up and pathogenic potential of these organisms, but also concerns about risks of spill‐over between livestock, humans, and native wildlife.

Uropathogenic Escherichia coli (UPEC) strains are found in high numbers in the gut of patients with urinary tract infections (UTIs). We hypothesised that in hospitalised patients, UPEC strains might translocate from the gut to the blood stream and that this could be due to the presence of virulence genes (VGs) that are not commonly found in UPEC strains that cause UTI only. To test this, E. coli strains representing 75 dominant clonal groups of UPEC isolated from the blood of hospitalised patients with UTI (urosepsis) (n = 22), hospital-acquired (HA) UTI without blood infection (n = 24) and strains isolated from patients with community-acquired (CA)-UTIs (n = 29) were tested for their adhesion to, invasion and translocation through Caco-2 cells, in addition to the presence of 34 VGs associated with UPEC. Although there were no differences in the rate and degree of translocation among the groups, urosepsis and HA-UTI strains showed significantly higher abilities to adhere (P = 0.0095 and P < 0.0001 respectively) and invade Caco-2 cells than CA-UTI isolates (P = 0.0044, P = 0.0048 respectively). Urosepsis strains also carried significantly more VGs than strains isolated from patients with only UTI and/or CA-UTI isolates. In contrast, the antigen 43 allele RS218 was found more commonly among CA-UTI strains than in the other two groups. These data indicate that UPEC strains, irrespective of their source, are capable of translocating through gut epithelium. However, urosepsis and HA-UTI strains have a much better ability to interact with gut epithelia and have a greater virulence potential than CA-UPEC, which allows them to cause blood infection.

No abstract

No abstract

No abstract

No abstract

Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups.

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.