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Genome Sequences
bacteriologyBacteriologyDraft genome sequence of Acinetobacter haemolyticus strain MUWRP1017 isolated from the pus of a female inpatient at Bwera General Hospital in Uganda
https://orcid.org/0000-0001-8079-3474
Wokorach Godfrey 1 2 Data curation Formal analysis Investigation Validation Writing – original draft
Erima Bernard 1 Data curation Formal analysis Investigation Methodology Validation Writing – review and editing
Alafi Stephen 1 Data curation Formal analysis Investigation Methodology Validation Writing – review and editing
Kabatesi Hope O. 1 Data curation Formal analysis Investigation Validation Writing – review and editing
Muhindo Julius T. 3 Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Validation Writing – review and editing
Najjuka Florence 4 Conceptualization Data curation Formal analysis Funding acquisition Investigation Validation Writing – review and editing
Kiyengo James 5 Conceptualization Data curation Formal analysis Investigation Project administration Validation Writing – review and editing
Kibuuka Hannah 1 Conceptualization Data curation Formal analysis Investigation Project administration Validation Writing – review and editing
Musinguzi Ambrose K. 5 Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Validation Writing – review and editing
Wabwire-Mangen Fred 1 4 Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Project administration Resources Validation Writing – review and editing
https://orcid.org/0000-0002-4175-5659
Byarugaba Denis K. 1 4 Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Project administration Resources Validation Writing – review and editing denis.byarugaba@mak.ac.ug

1 Makerere University Walter Reed Project , Kampala, Uganda
2 Department of Biology, Faculty of Science, Muni University , Arua, Uganda
3 Bwera District Hospital , Kasese, Uganda
4 Makerere University , Kampala, Uganda
5 Uganda Peoples Defence Forces , Kampala, Uganda
Editor Klepac-Ceraj Vanja Department of Biological Sciences, Wellesley College , Wellesley, Massachusetts, USA

Address correspondence to Denis K. Byarugaba, denis.byarugaba@mak.ac.ug
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00566-2429 5 2024
18 7 2024
Copyright © 2024 Wokorach et al.
2024
Wokorach et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

The bacterium Acinetobacter haemolyticus, with a genome size of 3.4 Mb, was isolated from a pus swab of a wound on the left lower limb above the ankle joint of a female patient. This strain carries the antimicrobial resistance genes cephalosporinase blaADC-25, oxallinase blaOXA-264, floR, and sul2 and other resistance and virulence genes.

KEYWORDS

blaOXA-264
blaADC-25
Acinetobacter
bacteria
Gram-negative bacteria
Uganda
cover-dateSeptember 2024
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pmcANNOUNCEMENT

Acinetobacter is a group of Gram-negative coccobacillus bacteria with increasing prevalence in hospitals worldwide, causing various infections (1). Acinetobacter haemolyticus is an emerging species with serious multidrug resistance agents like A. baumanii. It belongs to the haemolytic clade and has been implicated in nosocomial infections, with some carrying carbapenem-resistance determinants, making treatment difficult (2). This study describes the genome of strain MUWRP1017 isolated from a wound on the lower left limb of a female patient from the Democratic Republic of Congo. She received healthcare service at Bwera General Hospital in Kasese district, Uganda.

A swab obtained from pus was immediately inoculated on blood agar, and the resulting single colony was transferred to nutrient agar. The bacterial colony was presumptively identified as Gram-negative coccobacillus by Gram staining and was later grown on Luria broth to obtain cell mass for DNA extraction. All culturing procedures were done at 37°C for 24 hours under aerobic conditions. DNA was extracted using the DNeasy UltraClean microbial kit (Qiagen, Germantown, Maryland, USA) without modification. Extracted DNA was used to create libraries with the Kapa HyperPlus library preparation kit (Roche Diagnostics, Indianapolis, IN, USA). Paired-end sequencing (2 × 151 bp) of the libraries produced 11,677,660 total reads on Illumina NextSeq (Illumina, Inc., San Diego, CA). Raw reads were evaluated using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with Btrim v0.2.0 (3). Assembly with Newbler v2.7 generated a genome with 523 x coverage (4). The assembled genome was evaluated for completeness using CheckM v1.2.2 (5). The annotation of the draft genome was done using PGAP version 6.7 (6). The taxonomy assignment was done using the Genome Taxonomy Database (GTDB Release 214.1) considering an average nucleotide identity (ANI) index of ≥95% (7). Antimicrobial resistant genes were predicted with ResFinder v4.3.2 (8). The virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) was used to predict the presence of virulence genes (9). All software utilized default settings, unless otherwise stated. Ethical approval was obtained from Makerere University School of Public Health Higher Degrees and Research Ethics Committee (HDREC 087) and Walter Reed Army Institute of Research IRB (WRAIR #1711).

CheckM v1.2.2 indicates the assembled genome was 99.99% complete. The assembly generated a genome of 3.4 Mb and 119 contigs with an N50 value of 70 kb. About 39.5% of the genome is made of GC bases. The genome was predicted to have 3,235 genes, of which 3,151 were protein-coding genes. The MUWRP1017 strain was identified as Acinetobacter haemolyticus, with the closest match to type strain (MTCC 9819), with an ANI value of 98.13% (Table 1). The MUWRP1017 strain carries aac(6')-Ig, aph (6)-Id, and aph(3'')-Ib aminoglycoside resistant genes. The cephalosporinase blaADC-25 and oxallinase blaOXA-264 were the detected beta-lactam-resistant genes. Amphenicol (floR) and folate pathway antagonist (sul2) resistant genes were also detected. Adherence genes (pilT, pilU, pilB, mshE, tapT, and htpB) and Type VI secretion system tip protein (vgrG/tssI) were the virulence genes detected. The finding of Acinetobacter-derived cephalosporinase blaADC-25, the oxallinase blaOXA-264, and other resistance determinants is an alert for potential resistance threats in future.

TABLE 1 Average nucleotide identity (ANI) index of type strains with strain MUWRP1017

Organism name	Type strain	Accession	Taxonomy ID	ANI (%)	
A. haemolyticus	MTCC 9819	GCA_000430205.1	29430	98.13	
A. haemolyticus	CIP 64.3	GCA_000369065.1	29430	98.25	
A. haemolyticus	FDAARGOS_1392	GCA_019355995.1	29430	98.30	
A. haemolyticus	NCTC10305	GCA_900444835.1	29430	98.30	

ACKNOWLEDGMENTS

Whole-genome sequencing was performed by Walter Reed Army Research Institute (WRAIR)’s Multi-Drug-Resistant Organism Repository and Surveillance Network (MRSN) and are greatly acknowledged.

This research was funded by the United States Armed Forces Health Surveillance Division (AFHSD), Global Emerging Infections Surveillance (GEIS) Branch under PROMIS ID: USAMRD-K 17_KY_1.1.7.

DATA AVAILABILITY

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JBDPJG000000000. The version described in this paper is version JBDPJG010000000. The GenBank assembly accession number is GCA_039839735.1. The raw sequences were deposited in the Sequence Read Archive (SRA) under the accession number SRR29081551.
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