1.Isolation and Identification of an Emerging Pathogen, Kocuria marina, from Rattus rattus diardii
Loong, S.K. ; Johari, J. ; Che Mat Seri, N.A.A. ; AbuBakar, S.
Tropical Biomedicine 2016;33(3):589-593
Members of the genus Kocuria are commonly found in the environment and they
are also commensals of the mammalian skin and oropharynx mucosa. Human infections,
although rare, are increasingly being reported recently suggesting that this genus has mostly
been overlooked or misidentified. Its transmission route however, is still not known. We
report here the isolation and identification of a Kocuria marina isolate from the lung of a
wild urban rat (Rattus rattus diardii) caught at a wet market. The isolate was susceptible to
most of the commonly used antibiotics. The finding suggests a possibility that rats could be
a vector for K. marina.
2.Miracle Recovery After ASIA B Traumatic Cervical Cord Injury
Zarullail NH ; Johari J ; Yusof MI
Malaysian Orthopaedic Journal 2018;12(Supplement A):24-
3.Computed Tomographic Study of Occipital Thickness in Ethnic Malays
Yusof MI ; Sadagatullah AN ; Johari J ; Salim AA ; Govindasamy M
Malaysian Orthopaedic Journal 2022;16(No.2):15-22
Introduction: Occipitocervical fusion is performed to
address craniocervical and atlantoaxial instability. A screw of
at least 8mm is needed for biomechanical stability. Occipital
thickness of Malay ethnicity is unknown, and this study
presents the optimal screw placement positions for occiput
screw in this population. This was a retrospective crosssectional study of 100 Malays who underwent computed
tomography (CT) scan for brain assessment. To measure the
occipital bone thickness of Malay ethnicity at the area of
common screw placement for occipitocervical fusion. The
subject’s data was obtained from the institutional database
with consent from the administrations and the patients. None
of the patients had any head and neck pathology.
Materials and methods: The subject’s data was obtained
from the institutional database with consent from the
administrations and the patients. None of the patients had
any head and neck pathology. Computed tomography (CT)
of 100 Malay patients who underwent head and neck CT
were analysed, based on our inclusion and exclusion criteria.
Measurements were taken using a specialised viewer
software where 55 points were measured, followed a grid
with 10mm distance using external occipital protuberance
(EOP) as the reference point.
Results: There were 57 males and 43 females of Malay
ethnicity with a mean age of 36.7 years analysed in this
study. The EOP was the thickest bone of the occiput which
measured 16.15mm. There was an area of at least 8mm
thickness up to 20mm on either side of the EOP, and at level
10mm inferior to the EOP. There is thickness of at least
8mm, up to 30mm inferior to the EOP at the midline. The
males have significantly thicker bone especially along the
midline compared to females.
Conclusion: Screws of at least 8mm can be safely inserted
in the Malay population at 20mm on either side of the EOP
at the level 10mm inferior to the EOP and up to 30mm
inferior to the EOP at the midline.
4.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.