Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal

Baron, Sophie Alexandra; Mediannikov, Oleg; Abdallah, R. Ben; Yimagou, Edmond Kuete; Medkour, Hacène; Dubourg, Grégory; Elamire, Youssouf; Afouda, Pamela; Ngom, Issa Isaac; Angelakis, Emmanouil; Davoust, Bernard; Diatta, Georges; Barciela, Amanda; Hernández‐Aguilar, R. Adriana; Sokhna, Cheikh; Caputo, Aurélia; Levasseur, Anthony; Rolain, Jean‐Marc; Raoult, Didier

doi:10.1128/aac.02557-20

Cited by 15 publications

(12 citation statements)

References 38 publications

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“…Between 2010 and 2014, CG147 (mainly ST147) was described worldwide in association with several carbapenemases [17]. Most reported CG147 isolates are from clinical samples, although some were found in companion animals, chimpanzees, poultry and poultry environments, and river waters [18–24]. The above studies were locally restricted and, so far, no study of the global spread and genome dynamics of this clone has been performed.…”

Section: Introductionmentioning

confidence: 99%

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

et al. 2022

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The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: bla NDM-5 and two copies of bla OXA-181 in the chromosome, and a second copy of bla NDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured bla CTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal bla NDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.

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Section: Introductionmentioning

confidence: 99%

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

et al. 2022

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“…In addition, a K. pneumoniae ST307 clinical isolate harboring the bla OXA-48 gene on an IncL-type plasmid was reported in Tunisia in the same period [ 23 ]. Of note, genome sequencing identified ST307 among chimpanzees and termites in protected areas in Senegal, suggesting the circulation of strains between the two species [ 24 ].…”

Section: Resultsmentioning

confidence: 99%

Screening and Characterization of Multidrug-Resistant Enterobacterales among Hospitalized Patients in the African Archipelago of Cape Verde

et al. 2022

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This study aimed to investigate, for the first time, the occurrence and characteristics of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales in Cape Verde. A total of 98 inpatients hospitalized at Hospital Universitário Agostinho Neto were screened for rectal colonization. All ESBL- and carbapenemase-producing isolates were tested for antimicrobial susceptibility and characterized by multilocus sequence typing. Mating-out assay followed by PCR-based replicon typing were performed to characterize the plasmids harboring carbapenemase encoding genes. A large proportion of patients carried ESBL- or carbapenemase-producing Enterobacterales (56% and 6%, respectively). Among 93 ESBL-producing isolates, there were mainly Klebsiella pneumoniae (58%) and Escherichia coli (37%). Five different ESBLs were detected, with CTX-M-15 being highly predominant (92%). Six carbapenemase-producing isolates (five E. coli and one K. pneumoniae) were recovered, and all of the OXA-48-like type (four OXA-181, one OXA-48, and one OXA-244). The blaOXA-48 gene was located on an IncFI-type plasmid, the blaOXA-181 gene on IncFI or IncX3 plasmids, and the blaOXA-244 gene was found to be chromosomally located. The five carbapenemase-producing E. coli isolates belonged to five distinct sequence types. This study overall showed a very high prevalence of ESBL-producing Enterobacterales, as well as the emergence of carbapenemase producers in this hospital.

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“…Indeed, wild animals, including gorillas in MDNP, can acquire antimicrobial resistant bacteria and AMR genes through improperly disposed antimicrobial chemicals and through environments contaminated with animal faeces and remains [ 78 , 79 , 80 , 81 ]. This result could also be explained to a lesser extent by other mechanisms for resistance acquisition, such as horizontal gene exchange among bacteria or naturally acquired resistance [ 46 ], or even through the adaptation and evolution of these pathogenic enterobacterial isolates in their environment [ 82 ] or the consumption of various foods [ 46 , 83 ]. The results obtained in a very recent study tend to correlate with our observations on the prevalence of antimicrobial resistance in wildlife.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Groups, Pathotypes and Antimicrobial Resistance of Escherichia coli Isolated from Western Lowland Gorilla Faeces (Gorilla gorilla gorilla) of Moukalaba-Doudou National Park (MDNP)

Yinda

Onanga

Nguema³

et al. 2022

Pathogens

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(1) Background: Terrestrial mammals in protected areas have been identified as a potential source of antimicrobial-resistant bacteria. Studies on antimicrobial resistance in gorillas have already been conducted. Thus, this study aimed to describe the phylogroups, pathotypes and prevalence of antimicrobial resistance of Escherichia coli isolated from western lowland gorilla’s faeces living in MDNP. (2) Materials and Methods: Ninety-six faecal samples were collected from western lowland gorillas (Gorilla gorilla gorilla) during daily monitoring in the MDNP. Sixty-four E. coli isolates were obtained and screened for phylogenetic and pathotype group genes by polymerase chain reaction (PCR) after DNA extraction. In addition, antimicrobial susceptibility was determined by the disk diffusion method on Mueller Hinton agar. (3) Results: Sixty-four (64%) isolates of E. coli were obtained from samples. A high level of resistance to the beta-lactam family, a moderate rate for fluoroquinolone and a low rate for aminoglycoside was obtained. All E. coli isolates were positive in phylogroup PCR with a predominance of A (69% ± 11.36%), followed by B2 (20% ± 19.89%) and B1 (10% ± 8.90%) and low prevalence for D (1% ± 3.04%). In addition, twenty E. coli isolates (31%) were positive for pathotype PCR, such as EPEC (85% ± 10.82%) and EPEC/EHEC (15% ± 5.18%) that were obtained in this study. The majority of these MDR E. coli (DECs) belonged to phylogenetic group A, followed by MDR E. coli (DECs) belonging to group B2. (4) Conclusion: This study is the first description of MDR E. coli (DECs) assigned to phylogroup A in western lowland gorillas from the MDNP in Gabon. Thus, wild gorillas in MDNP could be considered as asymptomatic carriers of potential pathogenic MDR E. coli (DECs) that may present a potential risk to human health.

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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal

Cited by 15 publications

References 38 publications

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

Screening and Characterization of Multidrug-Resistant Enterobacterales among Hospitalized Patients in the African Archipelago of Cape Verde

Phylogenetic Groups, Pathotypes and Antimicrobial Resistance of Escherichia coli Isolated from Western Lowland Gorilla Faeces (Gorilla gorilla gorilla) of Moukalaba-Doudou National Park (MDNP)

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