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Fulltext Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing

Ten KE, Md Zoqratt MZH, Ayub Q, Tan HS

BMC Res Notes, 2021 Mar 04;14(1):83.
PMID: 33663564 DOI: 10.1186/s13104-021-05493-z

OBJECTIVE: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen.
RESULTS: One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.
Fulltext Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

Md Zoqratt MZH, Eng WWH, Thai BT, Austin CM, Gan HM

PeerJ, 2018;6:e5826.
PMID: 30397546 DOI: 10.7717/peerj.5826

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
Impacts of morphological-controlled ZnO nanoarchitectures on aerobic microbial communities during real wastewater treatment in an aerobic-photocatalytic system

Chang JS, Chong MN, Poh PE, Ocon JD, Md Zoqratt MZH, Lee SM

Environ Pollut, 2020 Apr;259:113867.
PMID: 31896479 DOI: 10.1016/j.envpol.2019.113867

This study aimed to evaluate the impacts of morphological-controlled ZnO nanoarchitectures on aerobic microbial communities during real wastewater treatment in an aerobic-photocatalytic system. Results showed that the antibacterial properties of ZnO nanoarchitectures were significantly more overwhelming than their photocatalytic properties. The inhibition of microbial activities in activated sludge by ZnO nanoarchitectures entailed an adverse effect on wastewater treatment efficiency. Subsequently, the 16S sequencing analysis were conducted to examine the impacts of ZnO nanoarchitectures on aerobic microbial communities, and found the significantly lower microbial diversity and species richness in activated sludge treated with 1D-ZnO nanorods as compared to other ZnO nanoarchitectures. Additionally, 1D-ZnO nanorods reduced the highest proportion of Proteobacteria phylum in activated sludge due to its higher proportion of active polar surfaces that facilitates Zn2+ ions dissolution. Pearson correlation coefficients showed that the experimental data obtained from COD removal efficiency and bacterial log reduction were statistically significant (p-value
Fulltext Adaptation of a fluoroquinolone-sensitive Shigella sonnei to norfloxacin exposure

Wong BC, Law SKK, Md Zoqratt MZH, Ayub Q, Tan HS

R Soc Open Sci, 2024 Jun;11(6):232025.
PMID: 39100177 DOI: 10.1098/rsos.232025

Shigella causes shigellosis that requires antibiotic treatment in severe cases. Sublethal antibiotic concentrations can promote resistance, but their effect on antibiotic-sensitive bacteria before resistance development is unclear. This study investigated the effects of sublethal norfloxacin (NOR) challenges on a NOR-sensitive strain, Shigella sonnei UKMCC1015. Firstly, the whole genome of S. sonnei UKMCC1015 was assembled, and 45 antimicrobial resistance (AMR) genes were identified. Interestingly, transcriptomic analysis showed that low NOR levels do not change either the expression of the AMR genes or NOR targets such as gyrA. Instead, multiple ribosomal protein genes were downregulated, which could be attributed to decreased ribosomal protein promoter activity, modulated by elevated guanosine pentaphosphate and tetraphosphate (ppGpp) levels. This alarmone is involved in the bacterial stringent response during environmental stress, and it is mainly produced from the ppGpp synthetase (relA). Additionally, we observed that a relA overexpression (prolonged period of elevated ppGpp levels) may negatively affect the NOR tolerance of the bacteria. In conclusion, this study revealed that a NOR-sensitive strain responds differently to sublethal NOR than commonly reported in resistant strains.
Fulltext Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

Muzahid NH, Md Zoqratt MZH, Ten KE, Hussain MH, Su TT, Ayub Q, et al.

Sci Rep, 2023 Aug 03;13(1):12596.
PMID: 37537198 DOI: 10.1038/s41598-023-39642-0

Acinetobacter species are widely known opportunistic pathogens causing severe community and healthcare-associated infections. One such emerging pathogen, Acinetobacter colistiniresistens, is known to exhibit intrinsic resistance to colistin. We investigated the molecular characteristics of A. colistiniresistens strain C-214, isolated from the fecal sample of a healthy community member, as part of a cohort study being conducted in Segamat, Malaysia. Comparison of the whole genome sequence of C-214 with other A. colistiniresistens sequences retrieved from the NCBI database showed 95% sequence identity or more with many of the genome sequences representing that species. Use of the Galleria mellonella killing assay showed that C-214 was pathogenic in this model infection system. The strain C-214 had a colistin and polymyxin B MIC of 32 and 16 mg/L, respectively. Besides, it was resistant to cefotaxime, amikacin, and tetracycline and showed moderate biofilm-producing ability. Different genes associated with virulence or resistance to major classes of antibiotics were detected. We observed mutations in lpxA/C/D in C-214 and other A. colistiniresistens strains as probable causes of colistin resistance, but the biological effects of these mutations require further investigation. This study provides genomic insights into A. colistiniresistens, a potentially pathogenic bacterium isolated from a community member and notes the public health threat it may pose.
A survey on the occurrence of papaya ringspot virus-P (PRSV-P) in Malaysia and genetic diversity assessment of the coat protein region

Mohsin Mohsen N, Aziz MA, Thangaraja K, Mohammad Nasir MA, Md Zoqratt MZH, Bhassu S, et al.

Environ Monit Assess, 2024 Nov 04;196(12):1154.
PMID: 39495404 DOI: 10.1007/s10661-024-13321-7

Papaya ringspot virus (PRSV) is a plant virus transmitted by aphids that has spread throughout many countries, including Malaysia, causing yield losses and economic impacts to the papaya industry worldwide. PRSV infection in papaya-distinctive ring-shaped patterns on papaya leaves resulted in stunted growth and reduced fruit quality. Management strategies such as the use of resistant varieties, cultural practices, and vector control are employed to mitigate the spread of PRSV. However, the evolution of new virus strains and the uncertainties posed by climate change pose ongoing challenges for the management of PRSV worldwide. Therefore, in this present study, we aim to confirm the presence of PRSV in symptomatic papaya leaves, to depict the current status of PRSV in Malaysia. Using reverse-transcription PCR (RT-PCR) targeting PRSV partial nuclear inclusion b protein (NIb) and coat protein (CP), 13 out of 40 papaya leaves collected were found positive for the PRSV strain-P (PRSV-P). Nucleotide analysis revealed a high similarity with strains from Taiwan and India, showing 96.83%, 97.03%, and 97.03% identity with the Taiwan strains (DQ340771, AY027810) and the India strain (KJ755852), respectively. Compared to the CP gene of Malaysian isolates reported in 2016 (EU082207), several nonsynonymous mutations have been discovered suggesting genetic diversity within the PRSV population in Malaysia. Overall, this study confirms the current circulation of PRSV infection in Malaysia since it was first identified in Johore in 1991. The re-occurrence of PRSV-P in this study highlights the need for continuous monitoring and targeted management strategies to prevent the further spread of PRSV-P in Malaysia.
Fulltext Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Azzeri A, Mohamed NA, Wan Rosli SH, Abdul Samat MN, Rashid ZZ, Mohamad Jamali MA, et al.

PLoS One, 2024;19(3):e0291892.
PMID: 38483913 DOI: 10.1371/journal.pone.0291892

Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values-indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.