Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian fruit bats (Pteropus poliocephalus)

McDougall, Fiona; Wyres, Kelly L.; Judd, Louise M.; Boardman, Wayne; Holt, Kathryn E.; Power, Michelle

doi:10.1016/j.resmic.2021.103879

Cited by 12 publications

(36 citation statements)

References 72 publications

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“…In recent years, K. michiganensis has been isolated from a diverse range of animals: farm animals (cows, poultry and pigs) [13,52], companion animals (cat, dog and horses) [12,52] and other animals including hedgehogs, guineapigs, mice, fruit bats, turtles and invertebrates [13,[52][53][54][55]. This is from using tools capable of discriminating between members of the KoC, but further work is needed to assess the true clinical and epidemiological significance of K. michiganensis in animals.…”

Section: Identification Of Members Of the Koc From Clinical And Veter...mentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

et al. 2022

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High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.

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Section: Identification Of Members Of the Koc From Clinical And Veter...mentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

et al. 2022

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“…These unhealthy individuals may have suffered increased susceptibility to opportunistic colonization and dissemination of KpSC isolates, e.g. from other wildlife or domestic animals that were housed in close proximity, which we speculate facilitated the broad-scale dissemination of K. pneumoniae ST5035 in the population [isolated from 15 of 20 sampled individuals (McDougall et al, 2021b)].…”

Section: Discussionmentioning

confidence: 99%

“…Over time, this approach should become more robust as databases become more complete (https://www.genome.jp/kegg/docs/upd_map.html) (Kanehisa and Goto, 2000). There may also be other genetic differences between flying fox and human strains of KpSC such as K/O loci, previously discussed within the context of flying fox isolates by McDougall et al (2021b); however, due to a paucity of grey-headed flying fox isolates, we lack the statistical power to discern this.…”

Section: Discussionmentioning

confidence: 99%

“…Thirty-nine KpSC isolates including 30 K. pneumoniae, one K. variicola subsp. variicola and eight K. africana were previously isolated from four different grey-headed flying fox colonies (McDougall et al, 2021b); Blackalls Park, sampled on 12/12/2017 and 10/4/2018; Camellia Gardens, 4/1/2018; Adelaide Botanic Park, 11/2/2018, Mylor (captive colony), 12/2/2018; Centennial Park, 9/3/2018. One isolate (K. pneumoniae FF996) was not utilized in this study due to DNA contamination issues identified during high-resolution analysis.…”

Section: Bacterial Isolate Collection and Whole-genome Sequencingmentioning

confidence: 99%

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Transmission of Klebsiella strains and plasmids within and between grey‐headed flying fox colonies

Vezina

Judd

McDougall

et al. 2022

Environmental Microbiology

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The grey-headed flying fox (Pteropus poliocephalus) is an endemic Australian fruit bat, known to carry zoonotic pathogens. We recently showed they harbour bacterial pathogen Klebsiella pneumoniae and closely related species in the K. pneumoniae species complex (KpSC); however, the dynamics of KpSC transmission and gene flow within flying fox colonies are poorly understood. High-resolution genome comparisons of 39 KpSC isolates from grey-headed flying foxes identified five putative strain transmission clusters (four intra-and one inter-colony). The instance of inter-colony strain transmission of K. africana was found between two flying fox populations within flying distance, indicating either direct or indirect transmission through a common food/water source. All 11 plasmids identified within the KpSC isolates showed 73% coverage (mean) and ≥95% identity to human-associated KpSC plasmids, indicating gene flow between human clinical and grey-headed flying fox isolates. Along with strain transmission, interspecies horizontal plasmid transmission between K. pneumoniae and Klebsiella africana was also identified within a flying fox colony. Finally, genome-scale metabolic models were generated to predict and compare substrate usage to previously published KpSC models, from human and environmental sources. These models indicated no distinction on the basis of metabolic capabilities. Instead, metabolic capabilities were consistent with population structure and ST/lineage.

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“…In recent years, K. michiganensis has been isolated from a diverse range of animals: farm animals (cows, poultry and pigs) (13,55), companion animals (cat, dog and horses) (12,55) and other animals including hedgehogs, guineapigs, mice, fruit bats, turtles and invertebrates (13,(55)(56)(57)(58). This is from using tools capable of discriminating between members of the KoC, but further work is needed to assess the true clinical and epidemiological significance of K. michiganensis in animals.…”

Section: Identification Of Members Of the Koc From Clinical And Veter...mentioning

confidence: 99%

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Smith-Zaitlik

Shibu

McCartney

et al. 2022

Preprint

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High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.

show abstract

Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian fruit bats (Pteropus poliocephalus)

Cited by 12 publications

References 72 publications

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Transmission of Klebsiella strains and plasmids within and between grey‐headed flying fox colonies

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

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