RESISTANT BACTERIA IN AUSTRALIAN MAMMALS

Environmental pollution with antibiotic-resistant bacteria presents concerns for wildlife medicine. Issues include selection of treatment regimens, veterinary hospital- acquired infections and zoonotic transmission.

The first study demonstrated low-level widespread resistance among isolates representing seven enteric bac­terial species from wildlife hosts across the continent (Sherley et al. 2000). Using the disc diffusion assay, 30 antibiotics with varying activity against Gram-negative and Gram-positive bacteria were tested. Resistance pro­files differed between wildlife host taxa, but certain host groups had similar resistance profiles. Bacterial isolates from species in the Families Vespertillionidae, Potoroi- dae, Macropodidae, Phalangeridae and Muridae had similar antibiotic-resistance profiles. Isolates from the Dasyuridae were distinct from other wildlife groups and resistance profiles varied by geographical source (Sherley et al. 2000). Although not measured, antibiotic exposure in different geographical regions was suggested as the

Table 17.1. Published reports of antibiotic-resistant bacteria in Australian native mammals

¹Chen etal.

intermediate resistance.

driver of variation in resistant profiles observed between hosts, source location and bacterial isolates from similar hosts (Sherley et al. 2000). More recent studies have applied genetic screening, both with and without pheno­typic analyses, and revealed the extent that antibiotic resistant bacteria have infiltrated wildlife microbiomes.

4.1 Detection of antibiotic resistance determinants in terrestrial wildlife

The prevalence of class 1 integrons was determined for zoo-housed and free-ranging brush-tailed rock-wallabies (Petrogale penicillata) (Power et al. 2013), grey-headed flying-foxes (Pteropus poliocephalus) (McDougall et al. 2019), and koalas (Phascolarctos cinereus) (McDougall et al. 2024). In all three species, the prevalence of class 1 integrons was higher in zoo-housed individuals com­pared to their free-range counterparts; brush-tailed rock­wallabies (free-range 0.0%, zoo-housed 48.3%) (Power et al. 2013), adult grey-headed flying-foxes (free-range 5.3%, zoo-housed 41.2%) (McDougall et al. 2019) and koalas (free-range 0.0%, zoo-housed 46.9%) (McDougall et al. 2024). These class 1 integrons contained diverse genes encoding resistance to narrow-spectrum beta-lactams, trimethoprim and aminoglycosides, and included gene cassette arrays commonly seen in human clinical settings (Power et al.

Resistance genes to chloramphenicol (cat genes) and tetracycline/doxycycline (tet genes) have been detected in the urogenital and faecal microbiomes of free-range and zoo-housed koalas (McDougall et al. 2023). Chloram­phenicol and doxycycline are critical for the treatment of chlamydial disease in koalas, and the presence of resist­ance bacteria may contribute to negative treatment out­comes for koalas receiving anti-chlamydial antibiotics (McDougall et al. 2023).

4.2 Case examples of antibiotic resistant bacteria in wildlife

Resistance to the extended spectrum β-lactams and methicillin has been identified in Gram-positive bacteria associated with the respiratory system of zoo-housed and free-ranging groups of black-footed rock-wallaby (P. lat­eralis), yellow-footed rock-wallaby (P. xanthopus) and the tammar wallaby (Notamacropus eugenii) in SA. Four Staphylococcus spp. showed phenotypic resistance to ampicillin, penicillin, oxacillin and cefoxitin and genetic analyses revealed the presence of resistance genes (bla and mecA genes) in the isolated staphylococcal species (Chen et al. 2015; Chen et al. 2016). MDR strains were also detected (Table 17.1).

In grey-headed flying-foxes antimicrobial resistant E. coli and Klebsiella pneumoniae were detected in free- range and zoo-housed/rehabilitation (Table 17.1). Kleb­siella species are intrinsically resistant to many antibiotics, including penicillin, amoxicillin and ticarcillin. Most Klebsiella species are susceptible to aminoglycosides, sul­fonamides, trimethoprim/sulphonamide, fluoroquinolo­nes, cephalosporins and carbapenems (Stock and Wiedemann 2001; Bouza and Cercenado 2002). In free- range habitats the prevalence of amoxicillin-resistant E. coli was lower (3.5%) in adult grey-headed flying-fox com­pared to zoo-housed bats or those undergoing rehabilita­tion (McDougall et al. 2021a; McDougall et al. 2022). In zoos, whether transient or long-term the prevalence was significantly higher in adults (6.5%) and pups (77.4%) (McDougall et al. 2021a; McDougall et al. 2022). A propor­tion of amoxicillin-resistant E. coli isolates (54.8%) exhib­ited multidrug resistance to key antimicrobials including cephalosporins, aminoglycosides, trimethoprim plus sul­phonamide, tetracyclines, carbapenems and fluoroqui­nolones. Fluoroquinolone- and trimethoprim-resistant K. pneumoniae were also detected in free-ranging adults (McDougall et al. 2021b). The majority of the amoxicillin­resistant E. coli isolates (56.5%) in the study were classified as extraintestinal pathogenic strains and phylogenies indi­cated that all resistant E. coli and K. pneumoniae were anthropogenic in origin. Resistant bacteria have also been detected in other flying-fox species. A case of Streptococcus group F isolated from a black flying-fox (P. alecto) tracheal swab was resistant to enrofloxacin, tetracycline and mar- bofloxacin was reported to the Wildlife Health Informa­tion System (eWHIS) (Grillo et al. 2015).

Reports of other cases of antibiotic resistant bacteria in eWHIS include (Grillo et al. 2015). Resistant Klebsiella isolates were detected in a koala blood sample and an eastern grey kangaroo (Macropus giganteus) faecal sample. The Klebsiella spp. isolated from the kangaroo and koala were MDR, with both resistant to chloram­phenicol, tetracycline, doxycycline, trimethoprim/ sulfonamide, marbofloxacin, enrofloxacin and ceftazi­dime and ceftiofur (3rd- and 4th-generation cephalo­sporins, respectively). The Klebsiella sp. isolated from a koala blood sample was also resistant to amikacin and neomycin. Additionally, resistant Enterobacter gergoviae and Staphylococcus sp. isolated have been reported to eWHIS from koalas (various samples) (Grillo et al. 2015).

Antibiotic-resistant bacteria have also been reported in marsupials held in zoos outside of Australia. Bacteria isolated from the conjunctiva of red kangaroos (Osphranter rufus) were resistant to multiple antibiotics among a panel of 23 compounds. Resistance to β-lactams and cephalosporins was most frequent and the prevalence of resistance was quite high for ophthalmic antibiotics; 70.8% of isolates were resistant to bacitracin and 41.7% to both ticarcillin and polymixin B (Takle et al. 2010). The most common bacteria among the resistant isolates were Staphylococcus epidermidis and Corynebacterium spp.

The dissemination of antibiotic resistant bacteria extends to Australia’s marine wildlife. Escherchia coli car­rying class 1 integrons have been identified in zoo-housed Australian sea-lions (Neophoca cinerea) (Delport et al. 2015) and in free-range Australian sea-lion and Austral­ian fur seal (Arctocephalus pusillus doriferus) pups (Fulham et al. 2018; Fulham et al. 2022) (Table 17.1). DNA sequencing of integron cassette arrays identified genes that confer resistance to aminoglycosides, trimethoprim and rifampin (Table 17.1). Trimethoprim resistant Staph. warner i has been detected in faecal samples from dugongs (Dugong dugon) (McGowan et al. 2023) (Table 17.1). Ente­rococcus faecium isolated from a male juvenile long-nosed fur seal (A. fosteri) in NSW displayed resistance to vanco­mycin in culture and was vanB positive by PCR (P Thompson, L Vogelnest, pers. comm.).

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