Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya

We report the draft genome sequences and annotation of three beta-lactamase-producing Escherichia coli ( E.coli) strains isolated from fecal samples of healthy camels in Laikipia county, Kenya. This data adds to the online genome resources to support the ongoing antimicrobial resistance surveillance in the livestock-wildlife interface.


Introduction
Antimicrobial resistance (AMR), especially on the readily available beta-lactam antibiotics continues to threaten effective healthcare management and global economic success in livestock farming (Fashae et al., 2021;Kiiru et al., 2012).Recently, concerted efforts have been employed to explore the AMR situation following a One Health Approach Previously, we and others have demonstrated an increased occurrence of broad-spectrum producing Enterobacteriaceae in livestock (Akunda et al., 2023;Nüesch-Inderbinen et al., 2020).Importantly, extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae have been implicated in the development of multi-drug resistance in both humans and animals.However, there still exists a gap in whole genome sequencing data on Enterobacteriaceae harboring AMR genes in camels (Camelus dromedaries), a key component of livestock farming in arid and semi-arid regions of Northern Kenya.We therefore aimed at sequencing the genomes of extended-spectrum beta lactamase Enterobacteriaceae using Escherichia coli (E.coli) as our model organism.

Methods
Here, we report three draft genome sequences of beta-lactamase-producing E. coli isolated from camel fecal samples in Laikipia county, Northern Kenya as previously described (Akunda et al., 2023).Fecal samples were collected from healthy camels reared under both ranching systems and pastoralism, transported in Cary Blair media (HiMedia Lab, Mumbai, India) and stored at 4°C awaiting processing.

REVISED Amendments from Version 1
This version highlights the rationale of sequencing E. coli in camels.This version contains a table showing antibiotics susceptibility and beta-lactamase genes profile of the isolates sequenced.
Any further responses from the reviewers can be found at the end of the article primers and PCR conditions as in Table 2.The respective gene fragment sizes were confirmed in 1% agarose gel (Invitrogen, Carlsbad, CA, U.S). ESBL producing E. coli isolates were phenotypically confirmed using double-disc synergy test (DDST) (Drieux et al., 2008).
E. coli PR_LC17 genome was assembled using Canu v2.2 (Koren et al., 2017) while E. coli (IPR_LC19) and E. coli (IPR_LC20) were assembled using Flye v2.9.1 (Kolmogorov et al., 2019).The taxonomy of the organism was confirmed using public databases for molecular typing and microbial genome diversity (PubMLST) (Jolley et al., 2018).Quality of the assembled genomes was assessed using QUAST v5.1.0(Gurevich et al., 2013) and annotated using NCBI's PGAP (Tatusova et al., 2016).The assembly metrics and annotation summaries are as shown in Table 3. interactions between human and camels in this part of Kenya, hence the likelihood of Animal to human transmission of beta lactamase producing E coli, It might help if the authors can write down a justification for why the study was conducted.
Why was there a focus on beta-lactamase producing E coli only?For example is it the most important isolate in this (human and camel) population?
In total how many camels are represented in the study or were these random fecal Is it possible to be more precise about the location, for example provide GPS co-ordinates of the sampling locations -A county is a very wide area.
Are the rationale for sequencing the genome and the species significance clearly described?Partly

Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genomic epidemiology, Microbiology I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
obvious and these sequences are of course a very useful resource for the community.However I have a request for minor revisions.I found that the paper needs to address a few more points: The authors need to provide more background on the need for sequencing E. coli samples from camel populations.There are some recent studies on beta-lactamase producing isolates from camle and other populations from Kenya.These studies (and more) can be referenced: Karegi I et al The results can be recorded in a separate section.Table 2 on genome annotation statistics can be moved to this section.

2.
The results for the antibiotic susceptibility testing for the three isolates can be provided as a separate table. 3.
The results of the PCR reactions for the 3 isolates describing which plasmids were detected from the samples need to be provided.These results can be corroborated with existing literature on the beta-lactamase encoding plasmid prevalence in Africa.

4.
In Table 2, the statistics for partial genes detected in each strain can be listed.Overall, the authors can comment on the draft nature of the genome in the results section (% completeness, number of contigs etc.).
5. Reviewer Expertise: Genomics, Transcriptomics, Anti-microbial resistance, Protein sequencestructure-funcion relationships, Database and algorithm development, Big-data analysis I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

References
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Are the rationale for sequencing the genome and the species significance clearly described? Partly Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests:
No competing interests were disclosed.