Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals

Insights into the genomic traits of Yersinia frederiksenii, Yersinia intermedia and Yersinia kristensenii isolated from diverse sources in Brazil

Yersinia is an important genus comprising foodborne, zoonotic and pathogenic bacteria. On the other hand, species of the so-called group Yersinia enterocolitica-like are understudied and mostly characterized as non-pathogenic, despite of some reports of human infections. The present study aimed to provide genomic insights of Yersinia frederiksenii (YF), Yersinia intermedia (YI) and Yersinia kristensenii (YK) isolated worldwide. A total of 22 YF, 20 YI and 14 YK genomes were searched for antimicrobial resistance genes, plasmids, prophages, and virulence factors. Their phylogenomic relatedness was analyzed by Gegenees and core-genome multi-locus sequence typing. Beta-lactam resistance gene blaTEM-116 and five plasmids replicons (pYE854, ColRNAI, ColE10, Col(pHAD28) and IncN3) were detected in less than five genomes. A total of 59 prophages, 106 virulence markers of the Yersinia genus, associated to adherence, antiphagocytosis, exoenzymes, invasion, iron uptake, proteases, secretion systems and the O-antigen, and virulence factors associated to other 20 bacterial genera were detected. Phylogenomic analysis revealed high inter-species distinction and four highly diverse YF clusters. In conclusion, the results obtained through the analyses of YF, YI and YK genomes suggest the virulence potential of these strains due to the broad diversity and high frequency of prophages and virulence factors found. Phylogenetic analyses were able to correctly distinguish these closely related species and show the presence of different genetic subgroups. These data contributed for a better understanding of YF, YI and YK virulence-associated features and global genetic diversity, and reinforced the need for better characterization of these Y. enterocolitica-like species considered non-pathogenic.

Fatal gastritis and enterocolitis due to concurrent Helicobacter pylori and Campylobacter jejuni infection in a captive cheetah (Acinonyxjubatus)

A 3.5-year-old female cheetah (Acinonyx jubatus) died after a 10-day history of anorexia, regurgitation and diarrhoea despite symptomatic therapy. At gross post-mortem examination, the stomach was blood-filled with mucosal thickening and multifocal ulcerations. The intestinal mucosa was thickened and reddened, and the intestinal lumen was filled with dark red to black pasty content. Gastric histological lesions were compatible with gastritis due to Helicobacter infection, which was confirmed by polymerase chain reaction. Histology of the intestines revealed a severe necrotizing neutrophilic enterocolitis with abundant intralesional curved to spiral bacteria, corresponding to Campylobacter jejuni, which were subsequently isolated from both small and large intestinal contents. No other intestinal pathogens were detected despite thorough investigations. These findings suggest that C. jejuni may have played an aetiological role in the enterocolitis. Such an association has not been previously reported in non-domestic felids.

Zoonotic bacteria in clinically healthy goats in petting zoo settings of zoological gardens in Germany

Goats and other small ruminants are frequently used as contact animals in petting zoo settings of zoological gardens. However, they are capable to carry a broad spectrum of zoonotic pathogens without clinical signs. In this study, we analysed the presence of different zoonotic pathogens in 300 clinically healthy goats from 14 zoological gardens in Germany. Rectal and nasal swabs were investigated with a series of cultural and molecular techniques. In addition, vaginal swabs of the 230 female goats were investigated for the presence of Coxiella burnetii by real-time PCR. Antibodies against C. burnetii were tested in milk and serum by ELISA. Campylobacter spp. were found in 22.7%, Shiga-toxigenic Escherichia coli in 20.0% and Arcobacter spp. were found in 1.7% of the tested 300 goats after culture from rectal swabs and subsequent PCR. One sample contained an Escherichia fergusonii isolate with a bla_CTX-M-1 -encoded extended-spectrum beta-lactamase phenotype. Neither Yersinia spp. nor Salmonella spp. were found. Nasal swabs of 20.7% of the goats yielded Staphylococcus aureus including one mecC-positive methicillin-resistant isolate. Neither Yersinia spp. nor Salmonella spp. were found, and none of the 230 vaginal swabs was positive for C. burnetii. Attempts to detect dermatophytes failed. In conclusion, a possible risk of transmission of zoonotic bacteria from goats in petting zoos to visitors should be considered. Appropriate information and facilities for hand washing and disinfection should be provided in all zoological gardens using goats as contact animals due to the regular presence of zoonotic bacteria in the collection.

Biodiversity and Phylogenetic Relationships of Novel Bacteriocinogenic Strains Isolated from Animal's Droppings at the Zoological Garden of Lille, France

This study aimed at exploring droppings of animals living in captivity in the zoological garden (Zoo) of Lille (France), as novel sources of bacteriocinogenic strains. A collection of 295 bacterial isolates was constituted from droppings of capybara, alpaca, muntjac, zebra, tapir, rhinoceros, binturong, armadillo, saki monkey and cockatoo. Of 295 isolates, 51 exhibited antagonism against a panel of pathogenic target bacteria like Escherichia coli MC4100, Clostridium perfringens DSM 756 and Salmonella enterica subsp. enterica Newport ATCC6962. Remarkably, within this collection, only 2 Gram-negative bacilli exhibited activity against E. coli MC4100 strain used as target organism. Then, the 16S rDNA sequencing revealed these thereafter cited species, Pediococcus pentosaceus, Weissella cibaria, E. coli, Lactobacillus reuteri, Enterococcus hirae and Enterococcus faecalis. Characterization of this antagonism has revealed 11 strains able producing extracellular protease-sensitive inhibitory compounds. These strains included E. coli ICVB442 and ICVB443, Ent. faecalis ICVB472, ICVB474, ICVB477 ICVB479, ICVB481, ICVB497 and ICVB501 and Ped. pentosaceus ICVB491 and ICVB492. The genomes of the 5 most promising bacteriocinogenic strains were sequenced and analysed with Bagel4 software. Afterwards, this bioinformatics analysis permitted to locate genes encoding bacteriocins like colicin Y (E. coli), enterocin 1071A, enterocin 107 B (Ent. faecalis) and penocin A (Ped. pentosaceus), associating the above-mentioned antibacterial activity of proteinaceous nature to possible production of bacteriocins. All these results enabled us to select different bacteriocinogenic strains for a further characterization in terms of beneficial traits.

Arcobacter butzleri: Up-to-date taxonomy, ecology, and pathogenicity of an emerging pathogen

Arcobacter butzleri, recently emended to the Aliarcobacter butzleri comb. nov., is an emerging pathogen causing enteritis, severe diarrhea, septicaemia, and bacteraemia in humans and enteritis, stillbirth, and abortion in animals. Since its recognition as emerging pathogen on 2002, advancements have been made in elucidating its pathogenicity and epidemiology, also thanks to advent of genomics, which, moreover, contributed in emending its taxonomy. In this review, we provide an overview of the up-to-date taxonomy, ecology, and pathogenicity of this emerging pathogen. Moreover, the implication of A. butzleri in the safety of foods is pinpointed, and culture-dependent and independent detection, identification, and typing methods as well as strategies to control and prevent the survival and growth of this pathogen are provided.

Marker genes of fecal indicator bacteria and potential pathogens in animal feces in subtropical catchments

We investigated the abundance of marker genes of two fecal indicator bacteria (FIB) and eight potential pathogens in fecal samples of humans (n = 14) and 10 domestic and native wild animals (n = 134). For each target animal, between 10 and 14 individual fecal samples were collected (n = 148 individual fecal samples in total). The abundance of FIB and potential pathogens within each sample was determined using quantitative PCR (qPCR) assays. All animals tested were positive for Escherichia coli (EC) and the concentrations ranged from 6.13 (flying fox) to 8.87 (chicken) log₁₀ GC/g of feces. These values for Enterococcus spp. (ENT) were 5.25 log₁₀ GC/g for flying fox and 8.12 log₁₀ GC/g of feces for chicken. Moderate correlations were observed between EC with P. aeruginosa, EC O157 and Cryptosporidium parvum, whereas weak correlations were observed between EC and Salmonella spp. and Giardia lamblia, Mycobacterium avium complex (MAC) and Campylobacter spp. The prevalence of MAC and P. aeruginosa were low in dog (14.3% each) and moderate (57.2%, MAC; 42.9% P. aeruginosa) in Eastern grey kangaroo fecal samples. Cryptosporidium parvum was detected in one cattle and one human fecal sample, while G. lamblia was detected in one dog, one flying fox, and one pig fecal samples. Among the eight potential pathogens tested, five pathogens were detected in chicken and dog fecal samples. The remaining animal species contained up to three potential pathogens in their feces. The data generated in this study may aid in the calculation of pathogen loads in the environment, and hence to assess the risks from human and animal fecal contamination of source waters.

Molecular characterization of fluoroquinolone and/or cephalosporin resistance in Shigella sonnei isolates from yaks

Background

Members of the genus Shigella are intestinal pathogens and a major cause of seasonal outbreaks of bacterial diarrhea worldwide. Although humans are the conventional hosts of Shigella species, expansion of the Shigella host range to certain animals was recently reported. To investigate the prevalence of Shigella sonnei (S. sonnei) in yaks and perform molecular characterization, we analyzed 1132 fresh yak diarrheal stool samples and collected a total of 44 S. sonnei isolates.

Results

We performed multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with XbaI-digested DNA to study genetic relatedness among the 44 isolates, which were differentiated into 4 sequence types (STs) and 32 PFGE types (PTs). All isolates harbored virulence genes, and 87.36% tested positive for invasion plasmid antigen H (ipaH), invasion associated locus (ial) and the Shigella enterotoxin gene sen. According to the results of antimicrobial susceptibility tests, 45.45% (20/44) were resistant to fluoroquinolones and/or cephalosporin. By sequencing the quinolone resistance determining region (QRDR) genes, we identified double mutations in gyrA (Ser83-Leu and Asp87-Asn) and a single mutation in parC (Ser80-Ile). All 12 fluoroquinolone-resistant S. sonnei isolates tested positive for the aac(6′)-Ib-cr gene but negative for qepA. Three isolates harbored qnr genes, including two with qnrS and one with qnrB. In addition, three types of β-lactamase genes, bla_TEM-1, bla_OXA-1 and bla_CTX-M-14/79, were detected in cephalosporin-resistant isolates.

Conclusions

The findings of this study have enriched our knowledge of fluoroquinolone- and/or cephalosporin-resistant S. sonnei isolates from yaks, which has important public health significance.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1500-6) contains supplementary material, which is available to authorized users.

Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review

Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries. Arcobacters are implicated as causative agents of diarrhea, mastitis and abortion in animals, while causing bacteremia, endocarditis, peritonitis, gastroenteritis and diarrhea in humans. Three species including A. butzleri, A. cryaerophilus and A. skirrowii are predominantly associated with clinical conditions. Arcobacters are primarily transmitted through contaminated food and water sources. Identification of Arcobacter by biochemical tests is difficult and isolation remains the gold standard method. Current diagnostic advances have provided various molecular methods for efficient detection and differentiation of the Arcobacters at genus and species level. To overcome the emerging antibiotic resistance problem there is an essential need to explore the potential of novel and alternative therapies. Strengthening of the diagnostic aspects is also suggested as in most cases Arcobacters goes unnoticed and hence the exact epidemiological status remains uncertain. This review updates the current knowledge and many aspects of this important food-borne pathogen, namely etiology, evolution and emergence, genetic diversity, epidemiology, the disease in animals and humans, public health concerns, and advances in its diagnosis, prevention and control.

A Systematic Review and Meta-Analysis of the Campylobacter spp. Prevalence and Concentration in Household Pets and Petting Zoo Animals for Use in Exposure Assessments

Animal contact is a potential transmission route for campylobacteriosis, and both domestic household pet and petting zoo exposures have been identified as potential sources of exposure. Research has typically focussed on the prevalence, concentration, and transmission of zoonoses from farm animals to humans, yet there are gaps in our understanding of these factors among animals in contact with the public who don't live on or visit farms. This study aims to quantify, through a systematic review and meta-analysis, the prevalence and concentration of Campylobacter carriage in household pets and petting zoo animals. Four databases were accessed for the systematic review (PubMed, CAB direct, ProQuest, and Web of Science) for papers published in English from 1992-2012, and studies were included if they examined the animal population of interest, assessed prevalence or concentration with fecal, hair coat, oral, or urine exposure routes (although only articles that examined fecal routes were found), and if the research was based in Canada, USA, Europe, Australia, and New Zealand. Studies were reviewed for qualitative synthesis and meta-analysis by two reviewers, compiled into a database, and relevant studies were used to create a weighted mean prevalence value. There were insufficient data to run a meta-analysis of concentration values, a noted study limitation. The mean prevalence of Campylobacter in petting zoo animals is 6.5% based on 7 studies, and in household pets the mean is 24.7% based on 34 studies. Our estimated concentration values were: 7.65x103cfu/g for petting zoo animals, and 2.9x105cfu/g for household pets. These results indicate that Campylobacter prevalence and concentration are lower in petting zoo animals compared with household pets and that both of these animal sources have a lower prevalence compared with farm animals that do not come into contact with the public. There is a lack of studies on Campylobacter in petting zoos and/or fair animals in Canada and abroad. Within this literature, knowledge gaps were identified, and include: a lack of concentration data reported in the literature for Campylobacter spp. in animal feces, a distinction between ill and diarrheic pets in the reported studies, noted differences in shedding and concentrations for various subtypes of Campylobacter, and consistent reporting between studies.

Global Distribution and Prevalence of Arcobacter in Food and Water

The emerging foodborne and waterborne pathogen, Arcobacter, has been linked to various gastrointestinal diseases. Currently, 19 species are established or proposed; consequently, there has been an increase in the number of publications regarding Arcobacter since it was first introduced in 1991. To better understand the potential public health risks posed by Arcobacter, this review summarizes the current knowledge concerning the global distribution and the prevalence of Arcobacter in food and water. Arcobacter spp. were identified in food animals, food-processing environments and a variety of foods, including vegetables, poultry, beef, dairy products, seafood, pork, lamb and rabbit. A wide range of waterbodies has been reported to be contaminated with Arcobacter spp., such as wastewater, seawater, lake and river water, drinking water, groundwater and recreational water. In addition, Arcobacter has also been isolated from pets, domestic birds, wildlife, zoo and farm animals. It is expected that advancements in molecular techniques will facilitate better detection worldwide and aid in understanding the pathogenicity of Arcobacter. However, more extensive and rigorous surveillance systems are needed to better understand the occurrence of Arcobacter in food and water in various regions of the world, as well as uncover other potential public health risks, that is antibiotic resistance and disinfection efficiency, to reduce the possibility of foodborne and waterborne infections.

Carriage of Shiga-toxigenic Escherichia coli by native marsupials in Australia

Shiga-toxigenic strains of Escherichia coli (STEC) are zoonotic pathogens with human health, meat processing and trade impacts. Cattle are the principal reservoirs of STEC, although other animals can be carriers. The STEC status of Australian native marsupials has not been formatively described to date. The aim of the current study was to investigate carriage of STEC by native Australian marsupials in Southeast Queensland. Faeces from a variety of marsupial species, stratified by gastrointestinal morphology and dietary type, were screened for stx(1), stx(2) and other STEC virulence genes by PCR. Positive samples were cultured to isolate STEC for characterisation. A number of macropods from both captive and wild habitats had evidence of STEC in their faeces. Rates of stx carriage by macropods (8.6%) were comparable, though generally low, compared to cattle. Eastern grey kangaroos had the highest rate of stx presence in faeces (10.3%). Hindgut-fermenting and monogastric marsupials had no evidence of STEC shedding. Based on virulence marker possession and serotype, the human pathogenic potential of isolates was low. This is the first report of Australian marsupials carrying STEC. Australian native macropods may act as reservoirs for STEC strains, but the potential significance to public health and/or livestock epidemiology remains questionable.

Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter

The genus Arcobacter, defined almost 20 years ago from members of the genus Campylobacter, has become increasingly important because its members are being considered emergent enteropathogens and/or potential zoonotic agents. Over recent years information that is relevant for microbiologists, especially those working in the medical and veterinary fields and in the food safety sector, has accumulated. Recently, the genus has been enlarged with several new species. The complete genomes of Arcobacter butzleri and Arcobacter nitrofigilis are available, with the former revealing diverse pathways characteristic of free-living microbes and virulence genes homologous to those of Campylobacter. The first multilocus sequence typing analysis showed a great diversity of sequence types, with no association with specific hosts or geographical regions. Advances in detection and identification techniques, mostly based on molecular methods, have been made. These microbes have been associated with water outbreaks and with indicators of fecal pollution, with food products and water as the suspected routes of transmission. This review updates this knowledge and provides the most recent data on the taxonomy, species diversity, methods of detection, and identification of these microbes as well as on their virulence potential and implication in human and animal diseases.

Molecular identification of airborne bacteria associated with aerial spraying of bovine slurry waste employing 16S rRNA gene PCR and gene sequencing techniques

Polymerase chain reaction amplification of the universal 16S ribosomal RNA (rRNA) gene was performed on a collection of 38 bacterial isolates, originating from air sampled immediately adjacent to the agricultural spreading of bovine slurry. A total of 16 bacterial genera were identified including both Gram-positive and Gram-negative genera. Gram-positive organisms accounted for 34/38 (89.5%) of total bacterial numbers consisting of 12 genera and included Staphylococcus (most common genus isolated), Arthrobacter (2nd most common genus isolated), Brachybacterium, Exiguobacterium, Lactococcus, Microbacterium and Sporosarcina (next most common genera isolated) and finally, Bacillus, Brevibacterium, Frigoribacterium, Mycoplana and Pseudoclavibacter. Gram-negative organisms accounted for only 4/38 (10.5%) bacterial isolates and included the following genera, Brevundimonas, Lysobacter, Psychrobacter and Rhizobium. No gastrointestinal pathogens were detected. Although this study demonstrated a high diversity of the microorganisms present, only a few have been shown to be opportunistically pathogenic to humans and none of these organisms described have been described previously as having an inhalational route of infection and therefore we do not believe that the species of organisms identified pose a significant health and safety threat for immunocompetant individuals.

Structural analysis of the full-length gene encoding a fibronectin-binding-like protein (CadF) and its adjacent genetic loci within Campylobacter lari

Background

The combined sequences encoding a partial and putative rpsI open reading frame (ORF), non-coding (NC) region, a putative ORF for the Campylobacter adhesin to fibronectin-like protein (cadF), a putative Cla_0387 ORF, NC region and a partial and putative Cla_0388 ORF, were identified in 16 Campylobacter lari isolates, using two novel degenerate primer pairs. Probable consensus sequence at the -35 and -10 regions were identified in all C. lari isolates, as a promoter.

Results

Thus, cadF (-like) gene is highly conserved among C. lari organisms. Transcription of the cadF (-like) gene in C. lari cells in vivo was also confirmed and the transcription initiation site was determined. A peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins was completely conserved amongst the putative cadF (-like) ORFs from the C. lari isolates.

Conclusion

The putative cadF (-like) ORFs from all C. lari isolates were nine amino acid larger than those from C. jejuni, and showed amino acid residues 137 -140 of FALG (50% identity), instead of the FRLS residues of the maximal fibronectin-binding activity site demonstrated within C. jejuni CadF. A neighbor joining tree constructed based on cadF (-like) gene sequence information formed a major cluster consisting of C. lari isolates, separating from the other three thermophilic campylobacters.