1.A Report of Vancomycin-susceptible, Teicoplanin-resistant Enterococcus faecalis ST6 in Malaysia
Loong, S.K. ; Che Mat Seri, N.A.A. ; Mahfodz, N.H. ; Akbar, S.Z. ; AbuBakar, S.
Tropical Biomedicine 2016;33(3):577-582
The ability to acquire antibiotic resistance and virulence has propelled Enterococcus
faecalis to become a major nosocomial pathogen. In Malaysia, data on the antibiotic resistance
determinants and virulence of Enterococcus circulating strains are still scarce. This study
aimed to assess the genotype of an E. faecalis isolate initially identified as Streptococcus
uberis, examine the antibiotic resistance genotypes, analyze the genetic variations within
Tn1546 and investigate the presence of virulence genes. The E. faecalis isolate was genetically
characterized using multilocus sequence typing (MLST). Minimum inhibitory concentrations
to vancomycin and teicoplanin were determined. Antibiotic resistance and other virulence
genes were amplified using nucleic acid polymerase chain reaction. Mapping of the Tn1546
transposon was performed and compared to the prototype sequences. The E. faecalis isolate
was found to have a MLST profile corresponding to sequence type 6. The isolate was resistant
to teicoplanin but susceptible to vancomycin. Its genome consisted the vanA and vanC1
genes. Novel genetic variations in the vanS, vanS-vanH intergenic region and vanY genes
were present and six virulence genes were detected. The detection of the vanC1 gene,
thought to be non-transferable, suggests the potential emergence of inter-species enterococcal
vanC1 gene transfer. The peculiar antibiotics resistance phenotype of this E. faecalis isolate
could be associated to the novel genetic variations found. This study highlights the presence
of E. faecalis belonging to the high-risk clonal complex with multiple virulence factors in
Malaysia.
2.Emergence of Enterococcus gallinarum carrying vanA gene cluster displaying atypical phenotypes
Loong, S.K. ; Che Mat Seri, N.A.A. ; Mahfodz, N.H. ; Teoh, B.T. ; AbuBakar, S.
Tropical Biomedicine 2016;33(4):837-841
Motile enterococci such as Enterococcus gallinarum has the ability to acquire
and transfer antibiotic resistance genes to other enterococci. Even though infections caused
by E. gallinarum are rare, the discovery of this bacteria in food sources and in clinical
environments is disturbing. Here, we report the isolation and identification of E. gallinarum
from the wound of a hospital in-patient. The isolate was identified using 16S rDNA sequencing.
Isolate 146 harboured the vanA and vanC1 gene clusters, was vancomycin-susceptible, and
displayed resistance to ampicillin, penicillin, erythromycin and teicoplanin. This isolate also
showed intermediate resistance to linezolid and sequencing of the 23S rRNA peptidyl
transferase region did not unveil any known mutations associated to the conferment of
linezolid resistance. The presence of vanA did not confer resistance to vancomycin. Structural
analyses into the Tn1546 transposon carrying the vanA gene revealed distinct genetic variations
in the vanS, vanY and vanS-vanH intergenic region that could be associated to the atypical
antibiotic resistance phenotypes of isolate 146. Finding from this study are suggestive of the
occurrence of interspecies horizontal gene transfer and that similarities in genotypic
characteristic may not necessarily correlate with actual antibiotic resistance pattern of E.
gallinarum.
3.Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM)
Tan, K.K. ; Tiong, V. ; Tan, J.Y. ; Wong, J.E. ; Teoh, B.T. ; Abd-Jamil, J. ; Johari, J. ; Nor&rsquo ; e, S.S. ; Khor, C.S. ; Yaacob, C.N. ; Zulkifli, M.M.S. ; CheMatSeri, A. ; Mahfodz, N.H. ; Azizan, N.S. ; AbuBakar, S.
Tropical Biomedicine 2021;38(No.3):283-288
Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.