
==== Front
New Microbes New Infect
New Microbes New Infect
New Microbes and New Infections
2052-2975
Elsevier

S2052-2975(24)00256-7
10.1016/j.nmni.2024.101472
101472
Letter to the Editor
Staphylococcus nepalensis infecting a companion animal: Genomic insights from an emerging multidrug-resistant pathogen
Sartori Luciana
Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
Sacramento Andrey G.
Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
One Health Brazilian Resistance Project (OneBR), Brazil
Sellera Fábio P.
One Health Brazilian Resistance Project (OneBR), Brazil
Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
Furlan João Pedro Rueda
Paulista School of Medicine, Federal University of Sao Paulo, Sao Paulo, São Paulo, Brazil
Barbosa Fernanda B.
Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
Esposito Fernanda
Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
Lincopan Nilton lincopan@usp.br
⁎⁎
Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
One Health Brazilian Resistance Project (OneBR), Brazil
Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
Knöbl Terezinha tknobl@usp.br
⁎
Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
⁎⁎ Corresponding author. lincopan@usp.br
⁎ Corresponding author. tknobl@usp.br
27 8 2024
12 2024
27 8 2024
62 10147226 5 2024
26 8 2024
© 2024 The Authors. Published by Elsevier Ltd.
2024

https://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords

Staphylococci
Companion animals
One Health
MDR bacteria
Genomic surveillance
Handling Editor: Patricia Schlagenhauf
==== Body
pmcDear Editor,

The global dissemination of multidrug-resistant (MDR) Staphylococcus species has been categorized as a One Health concern, requiring immediate implementation of mitigation strategies and ongoing genomic epidemiology surveillance to track its prevalence in both human and non-human populations [1]. Although in human medicine the prevalence of staphylococcal infections is due to Staphylococcus aureus, in small animal practice coagulase-negative staphylococci (CoNS) species have been emerging [2]. Staphylococcus nepalensis is a CoNS species that was first identified among goats suffering from pneumonia in the Himalayas [3]. Recently, S. nepalensis has been identified as a commensal agent of the oral microbiota of healthy cats, with the potential to act as a reservoir of transferrable antimicrobial resistance genes (ARGs) [4]. We hereby report the first genome sequence of a S. nepalensis strain isolated from a feline urinary tract infection worldwide, as well as a comparative genomic analysis of S. nepalensis circulating at the One Health context.

Between May 2022 and May 2023, a local surveillance study was conducted in a private veterinary diagnostic laboratory in São Paulo, Brazil, to monitor the presence of clinically relevant small animal pathogens. Of the 6087 clinical samples screened, 2246 Staphylococcus species were recovered, with 291 isolated from urinary tract infections. In this regard, a urine sample collected via cystocentesis from a 3-year-old male mixed-breed cat presenting with urinary tract infection (UTI) was submitted for urine culture. A CoNS strain, named STACOHU, was recovered from the urine sample. The phenotypic identification and antimicrobial susceptibility testing were determined by BD Phoenix (BD Diagnostics, Sparks, MD, USA). The results of antimicrobial susceptibility were interpreted according to the Brazilian Committee on Antimicrobial Susceptibility Testing guidelines (v.13.0, 2023) and the Clinical and Laboratory Standards Institute guidelines (CLSI, VET 6th ed., 2023).

The genome of STACOHU strain was sequenced on an Illumina NextSeq 2000 platform with 2 × 76 bp run configuration (Illumina, San Diego, USA). The reads were trimmed, de novo assembled, and annotated using BBDuk v.38.84 (Geneious Prime® v.2024.0.5), SPAdes v.3.15.2 (https://github.com/ablab/spades), RAST v.2.0 (https://rast.nmpdr.org/), respectively. Species identification was determined by JSpeciesWS (https://jspecies.ribohost.com/jspeciesws/). Plasmid replicons and ARGs were identified using PlasmidFinderv.2.1 and ResFinder v.4.5.0, respectively, from the Center for Genomic Epidemiology (https://www.genomicepidemiology.org/). For comparative analysis, all S. nepalensis genomes, except metagenome-assembled genomes, were retrieved from GenBank database. A phylogenetic tree based on single nucleotide polymorphism (SNP) was built using CSI Phylogeny v.1.4 (https://cge.food.dtu.dk/services/CSIPhylogeny/) using default parameters with S. nepalensis JS11 strain (BioSample: SAMN05846264) as a reference. The tree visualization was performed on iTOL v.6 (https://itol.embl.de/).

Strain STACOHU was initially identified by BD Phoenix as Staphylococcus cohnii and was further ascertained as S. nepalensis (GenBank: JBCEYT010000000) by average nucleotide identity analysis. This strain displayed resistance to ampicillin, amoxicillin/clavulanic acid, cephalexin, cefovecin, doxicillin, ciprofloxacin (MIC > 4 μg/mL), enrofloxacin, levofloxacin (MIC > 4 μg/mL), marbofloxacin, norfloxacin, oxacillin (MIC 1 μg/mL), imipenem, meropenem, and trimethoprim/sulfamethoxazole (MIC >8/152 μg/mL). On the other hand, it remained susceptible to amikacin, gentamicin (MIC < 4 μg/mL), and nitrofurantoin (MIC < 32 μg/mL). In this context, STACOHU strain was classified as MDR.

Resistome analysis showed that STACOHU strain harbored resistance genes to β-lactams (blaZ), lincosamides [lnu(A)], tetracyclines [tet(K)], aminoglycosides (str), folate pathway antagonist (dfrG), and quaternary ammonium compounds (qacG). This strain also presented plasmid replicons belonged to different families as follows: Rep_Trans (rep7a), RepA_N (rep19c), and Rep1 (rep21). The blaZ gene was embedded on the Tn552 transposon located on a plasmid contig. In addition, the BlaZ β-lactamase sequence from STACOHU strain presented six amino acid substitutions associated with decreased susceptibility to oxacillin, as previously reported in a borderline oxacillin-resistant S. aureus strain [5], explaining the displayed phenotype.

SNP differences among all S. nepalensis genomes ranged from 0 to 15,623, with STACOHU strain being clustered (304 SNPs difference) with the 23-2-3-SC strain isolated from Livingstone's fruit bat in Jersey (Fig. 1; Supplementary Table S1). Overall, whole-genome sequenced S. nepalensis strains were obtained from 1960 onwards mainly from a broad diversity of animals in European localities, did not presented ARGs, and have distributed plasmid replicons. In fact, only eight strains presented more than one ARG, with STACOHU strain harboring the highest amount and being the only one encoding a biocide resistance gene (Fig. 1).Fig. 1 The SNP-based phylogenetic tree of S. nepalensis strains. Red, blue, and orange painted circles represent positive antimicrobial resistance genes, biocide resistance genes, and plasmid replicons, respectively. The tree was rooted at the midpoint. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1

Here, we report a MDR S. nepalensis isolated from a domestic cat suffering from UTI in Brazil. Although there are reports the occurrence of S. nepalensis carrying clinically relevant ARGs [4], genomic data on this species are scant. In this study, to the best of our knowledge, we present the first genomic analysis of a MDR S. nepalensis strain that could provide valuable genomic information and enhance our understanding of the landscape of antimicrobial resistance (AMR) in CoNS. Therefore, a better comprehension of the genomic traits, epidemiology, and evolution of AMR in non-aureus staphylococci is crucial, given the recognized interplay of mobile genetic elements within the Staphylococcus genus.

Funding statement

This study was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; 2019/15778-4, 2020/08224-9, and 2022/11917-1), and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; 422984/2021-3).

Ethical approval

Not required.

CRediT authorship contribution statement

Luciana Sartori: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing – original draft, Writing – review & editing. Andrey G. Sacramento: Conceptualization, Data curation, Investigation, Methodology, Writing – original draft, Writing – review & editing. Fábio P. Sellera: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing. João Pedro Rueda Furlan: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing. Fernanda B. Barbosa: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing – original draft, Writing – review & editing. Fernanda Esposito: Data curation, Formal analysis, Investigation, Methodology, Writing – review & editing. Nilton Lincopan: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Writing – original draft, Writing – review & editing. Terezinha Knöbl: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing.

Declaration of competing interest

The authors Luciana Sartori, Andrey G. Sacramento, Fábio P. Sellera, João Pedro Rueda Furlan, Fernanda B. Barbosa, Fernanda Esposito, Nilton Lincopan, and Terezinha Knöbl, declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper entitled “Staphylococcus nepalensis infecting a companion animal: genomic insights from an emerging multidrug-resistant pathogen”.

Appendix A Supplementary data

The following is the Supplementary data to this article:Multimedia component 1

Multimedia component 1

Acknowledgments

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), FAPESP, and CNPq research grants are gratefully acknowledged. FPS is a research fellow of Programa Nacional de Pós-Doutorado/CAPES (88887.463868/2019-00). JPRF is a research fellow of FAPESP (23/16216-4). NL is a research fellow of CNPq (314336/2021-4). TK is a research fellow of CNPq (306396/2020-3).

Appendix A Supplementary data to this article can be found online at https://doi.org/10.1016/j.nmni.2024.101472.
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References

1 Turner N.A. Sharma-Kuinkel B.K. Maskarinec S.A. Eichenberger E.M. Shah P.P. Carugati M. Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research Nat Rev Microbiol 17 2019 203 218 10.1038/s41579-018-0147-4 30737488
2 Loncaric I. Tichy A. Handler S. Szostak M.P. Tickert M. Diab-Elschahawi M. Prevalence of methicillin-resistant Staphylococcus sp. (MRS) in different companion animals and determination of risk factors for colonization with MRS Antibiotics 8 2019 36 10.3390/antibiotics8020036 30959767
3 Spergser J. Wieser M. Täubel M. Rosselló-Mora R.A. Rosengarten R. Busse H.J. Staphylococcus nepalensis sp. nov., isolated from goats of the Himalayan region Int J Syst Evol Microbiol 53 2003 2007 2011 10.1099/ijs.0.02646-0 14657137
4 Andrade-Oliveira A.L. Rossi C.C. Souza-Silva T. Giambiagi-de Marval M. Staphylococcus nepalensis, a commensal of the oral microbiota of domestic cats, is a reservoir of transferrable antimicrobial resistance Microbiology 166 2020 727 734 10.1099/mic.0.000940 32520697
5 Nomura R. Nakaminami H. Takasao K. Muramatsu S. Kato Y. Wajima T. A class A β-lactamase produced by borderline oxacillin-resistant Staphylococcus aureus hydrolyses oxacillin J Glob Antimicrob Resist 22 2020 244 247 10.1016/j.jgar.2020.03.002 32200127
