The genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria

Abstract

Introduction: The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets.

Methods: This descriptive integrated typing study included 252 human isolates, 53 dog isolates and 10 cat isolates collected from 2019 to 2022 at the Charité University Hospital in Berlin, Germany. CgMLST was performed to characterize methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant gram-negative bacteria. The genetic diversity of the MDROs of the different host populations was determined and compared based on sequence type and core genome complex type.

Results: Within this study the majority of samples from pets and humans was genetically distinct. However, for some isolates, the number of allelic differences identified by cgMLST was low. Two cases of putative household transmission or shared source of VR E. faecium and MDR E. coli between humans and pets were documented.

Conclusions: The interaction between humans and their pets appears to play a minor role in the spread of the MDROs studied. However, further research is needed. This study emphasizes the importance of comprehensive molecular surveillance and a multidisciplinary One Health approach to understand and contain the spread of MDROs in human and animal populations.

Trial registration: The study is registered with the German Clinical Trials Register (DRKS00030009).

Keywords: Molecular typing; Multidrug-resistance; One Health; cgMLST.

Fig. 1

Flow chart of the isolates included in the study. List of excluded bacterial species: *Citrobacter spp.: 9, Enterobacter aerogenes: 1, Klebsiella oxytoca: 1, Proteus mirabilis: 1, Enterococcus faecalis: 3; †Citrobacter spp.: 2, Enterococcus cloacae: 1, Proteus penneri: 1; ‡Citrobacter spp.: 2

Fig. 2

Absolute occurrence of sequence types (STs) and complex types (CTs) among all VR E. faecium isolates according to the cgMLST analysis. On the x-axis, the isolates are grouped according to their ST, and the individual bars correspond to the CTs. The number above the bars indicates the percentage of the respective CT among all VR E. faecium isolates. The patterned bar coloring indicates pet isolates. ND = CT could not be determined

Fig. 3

Neighbor joining tree based on 110 VR E. faecium core genomes of humans, dogs and cats. The phylogenetic tree and cluster analysis were initially performed using the software SeqSphere + and subsequently visualized and annotated in iTOL v6.8.1. The tree was rooted at the center. Combinations of sequence types (STs) and complex types (CTs) are indicated by colored circles at leaf nodes. The colors within the ranges indicate the different clusters. The outer ring represents the host populations (human, dog, cat). Cluster Threshold: ≤ 20 allelic differences

Fig. 4

Absolute occurrence of sequence types (STs) among all MDR E. coli isolates according to MLST analysis. The number above the bars indicates the percentage of the respective ST among all isolates. The patterned bars indicate pet isolates. All STs that occurred only once are summarized as “Others”

Fig. 5

Neighbor joining tree based on MDR E. coli core genomes of 64 humans, 38 dogs and four cats. The phylogenetic tree and cluster analysis were created using SeqSphere + software and annotated in iTOL v6.8.1. The tree was rooted in the center. Combinations of sequence types (STs) and complex types (CTs) are indicated by colored circles at the leaf nodes. The colored ranges indicate the different clusters. The outer ring represents the host population (human, dog, cat). *No STs could be detected for the isolates with the study IDs COLI23 and COLI56 using the Warwick scheme. Therefore, the ST based on the Pasteur scheme is given here. Cluster Threshold: ≤ 10 allelic differences

Fig. 6

Neighbor joining tree of 25 MDR E. cloacae complex core genomes of 18 humans, five dogs and two cats. The phylogenetic tree and cluster analysis were created using SeqSphere + software and annotated in iTOL v6.8.1. The tree was rooted in the center. Sequence types (STs) – if applicable – are indicated by colored circles at the leaf nodes. The outer ring represents the host population (human, dog, cat). Cluster Threshold: ≤ 10 allelic differences