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. However, there still exists a gap in whole genome sequencing data on Escherichia coli ( E.coli) harboring AMR genes in camels ( Camelus dromedaries), a key component of livestock farming in arid and semi-arid regions of Northern Kenya.

Here, we report three draft genome sequences of beta-lactamase-producing E.coli isolated from camel fecal samples in Laikipia county, Northern Kenya. 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 ^oC awaiting processing.

The samples were cultured on MacConkey agar plate (HiMedia Lab, Mumbai, India) and incubated at 37°C for 18 hours. A single colony per MacConkey agar plate that displayed E. coli traits morphologically was identified through Gram staining and the IMViC (indol, methyl red, Voges Proskauer, and citrate) biochemical method and subjected to antimicrobial susceptibility testing (AST) against the beta-lactam antibiotic spectrum. Briefly, antimicrobial susceptibility testing (AST) was performed on Mueller Hinton agar (HiMedia Lab, Mumbai, India) using Kirby Bauer disk diffusion method. Antibiotics tested included, Ampicillin-10 μg (AMP), Chloramphenicol-30 μg (CHL), Tetracycline-30 μg (TCY), Gentamycin-10 μg (GEN), Streptomycin-10 μg (STR1), Trimethoprim-sulfamethoxazole-25 μg (SXT), Norfloxacin-10 μg (NOR), Ciprofloxacin-5 μg (CIP), Cefaclor-30 μg (CEC), Ceftriaxone-30 μg (CRO), Cefotaxime-30 μg (CTX), Cefuroxime-30 μg (CMX), Cefepime-30 μg (FEP), Amoxicillin–Clavulanate-20/10 μg (AMC), and Ceftazidime-30 μg (CA).

Production of beta-lactamase genes was assessed by conducting PCR to confirm genes encoding for CTX-M, TEM, CMY, SHV and OXA for the resistant isolates ( Livermore et al., 2007). Briefly, a 20ul PCR reaction was prepared by adding 10ul of the Platinum II Hot-Start PCR Master Mix (Invitrogen, Carlsbad, CA, U.S), 0.4 ul of 10nmol of forward and reverse primers, 4ul of Platinum GC enhancer, 0.2ul nuclease free water and 5ul DNA. Cycling was performed on Veriti™ Dx 96-well Thermal Cycler (Thermofisher, Waltham, Massachusetts, U.S) using primers and PCR conditions as in Table 1. The respective gene fragment sizes were confirmed in 1% agarose gel (Invitrogen, Carlsbad, CA, U.S)

Genomic DNA of beta-lactamase producing E.coli was extracted using Isolate II Genomic DNA Kit (Bioline) and sequencing performed using Oxford Nanopore Technologies (ONT). Briefly, manufacturer’s sample barcodes (Native Barcoding Expansion 1-12) (EXP-NBD104) and sequencing adapters (Ligation Sequencing kit) (SQK-LSK109)) were added following kit instructions. Sequencing was performed on MinION device using R9.4.1 flow cell to generate 186, 38153, and 31152 raw reads for the E.coli strains IPR_LC17, IPR_LC19 and IPR_LC20, respectively. Basecalling and demultiplexing of raw reads were performed using Guppy v3.6.1 ( https://nanoporetech.com). Adaptors were trimmed using PORECHOP v0.2.4 ( Wick et al., 2017) and poor quality reads, less than 500 bp and with an average quality score of below 10 were removed using NANOFLIT v2.8.0 ( De Coster et al., 2018).

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 2.