Biology subjects

Yeo, C. C.

Publications and source records attributed to Yeo, C. C..

3 recordsLinked to original sources

bioRxiv2025

The road less travelled: Exploring the genomic characteristics and antimicrobial resistance potential of Acinetobacter baumannii from the indigenous Orang Asli community in Peninsular Malaysia

Acinetobacter baumannii is widely recognized as a multidrug-resistant pathogen, but with most public genome datasets biased toward hospital-derived isolates. Little is thus known about A. baumannii isolates from healthy individuals from the community. This study analysed genome sequences from nine A. baumannii isolates obtained from the upper respiratory tract of healthy individuals of the indigenous Orang Asli community in their rural settlements located in the east coast of Peninsular Malaysia. Genomic analysis revealed all nine A. baumannii isolates to be genetically distinct and included three new sequence types (STs) under the Pasteur scheme and six novel STs under the Oxford scheme. Notably, one isolate, A. baumannii 19064, belonged to Global Clone 8 (GC8), a lineage associated with clinical infections. Core genome phylogeny indicated that the Orang Asli community isolates were interleaved with several non-GC clinical isolates from the tertiary hospital within the same state. This is suggestive of the potential of these community isolates to cause infections under conducive conditions. This is also attested by the identification of several virulence factors in their genomes. All nine isolates carried various intrinsic blaOXA-51-like class D {beta}-lactamase genes and class C Acinetobacter-derived cephalosporinase (ADC) blaADC genes but remained susceptible to meropenem. Two isolates, A. baumannii 19053 and 19062, were tetracycline resistant but minocycline susceptible and harboured the tet(39)-tetR gene pair within mobile pdif modules located on distinct Rep_3 family plasmids. Only one isolate, A. baumannii 19055, is plasmid-free; the rest mainly harboured cryptic Rep_3-type plasmids, often containing identifiable pdif modules. These findings highlight the clinical relevance of A. baumannii strains residing in healthy individuals, particularly in isolated communities that are seldom accessible to public health. Despite their remote location, the Orang Asli A. baumannii isolates possess virulence factors and antibiotic resistance genes similar to those found in hospital settings. This underscores the importance of genomic surveillance of commensal pathogens, and taking this road which is less travelled can help inform broader epidemiological insights and guide future public health strategies.

microbiology↗

bioRxiv2024

Identification of novel prophages and variants of Integrative and Conjugative Elements in Elizabethkingia anophelis clinical isolates from Seremban, Malaysia

Elizabethkingia anophelis is an emerging multidrug-resistant pathogen that has been identified globally, including in Malaysia. In this study, we used the Oxford Nanopore Technologies (ONT) long-read platform to generate the complete genome sequences of seven clinical isolates of E. anophelis from a tertiary hospital in the city of Seremban, located in the state of Negeri Sembilan in Peninsular Malaysia. These sequences were analysed alongside over 400 publicly available E. anophelis genomes from other countries. Three of the seven E. anophelis isolates, Eli4, Eli5, and Eli6, were almost identical and their isolation over a period of six weeks from the same hospital was suggestive of nosocomial transmission. Besides these three isolates, the other E. anophelis isolates were genetically diverse and related to distinct isolates from other countries. No plasmids were identified in the genomes of all seven E. anophelis isolates. A novel 39,686 bp prophage was identified in the genome of E. anophelis Eli4 while a presumptive incomplete prophage was found in the genomes of Eli2, Eli4, Eli5 and Eli6. E. anophelis genomes are notable for possessing integrative and conjugative elements (ICEs), which enable the bacterium to acquire new genes, including those encoding antimicrobial resistance or virulence. Several novel ICE sequences were discovered in the Seremban E. anophelis genomes, and this includes an ICE found in Eli8, designated Eli8_ICE1, which encodes phage defence genes such as type I restriction-modification systems, a bacterial cyclic oligonucleotide-based anti-phage signalling system (CBASS) and prokaryotic argonaute systems. The latter two phage defence genes have so far not been reported in the E. anophelis genome. This study demonstrates the utility of long-read sequencing in assessing the diversity and plasticity of E. anophelis genomes and emphasises further research into the role of ICEs in phage defence systems and their potential impact on antimicrobial treatment and phage therapy. RepositoriesThe Elizabethkingia anophelis genomes in this study have been deposited in the NCBI database under BioProject PRJNA1175025.

microbiology↗

bioRxiv2020

Complete genome sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 unveils a large multidrug resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases

Carbapenem-resistant Acinetobacter spp. are considered priority drug-resistant human pathogenic bacteria. The genomes of two carbapenem-resistant Acinetobacter spp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namely A. baumannii AC1633 and A. nosocomialis AC1530, were sequenced. Both isolates were found to harbor the carbapenemase genes blaNDM-1 and blaOXA-58 in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11 and an IS4 family element in pAC1633-1, and ISAba11 along with relBE toxin-antitoxin genes flanked by inversely orientated pdif (XerC/XerD) recombination sites in pAC1530. The blaNDM-1 gene was encoded in a Tn125 composite transposon structure flanked by ISAba125 whereas blaOXA-58 was flanked by ISAba11 and ISAba3 downstream and a partial ISAba3 element upstream within a pdif module. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species of Acinetobacter from the same hospital are suggestive of conjugative transfer but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event. A. baumannii AC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3 and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids whereas pAC1633-2 is a 12,651 bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes the tetA(39) tetracycline resistance determinant in a pdif module.

microbiology↗