Biology subjects

Rakib, T. M.

Publications and source records attributed to Rakib, T. M..

7 recordsLinked to original sources

bioRxiv2026

Integron-Mediated Convergence of Carbapenemase and Disinfectant Resistance in Acinetobacter spp. from Critical Care Units

Acinetobacter spp. represents critical opportunistic pathogens driving severe bloodstream infections (BSIs) in intensive care unit (ICU) and neonatal intensive care unit (NICU) settings. The convergence of carbapenem resistance and emerging biocide tolerance, often mediated by mobile genetic elements, has intensified concerns regarding co-selection and persistence in clinical environments. A total of 90 molecularly confirmed Acinetobacter isolates (ICU = 44; NICU = 46) from bloodstream infections were analyzed. Antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method in accordance with CLSI M100 (2024) guidelines and extended-spectrum {beta}-lactamase production was assessed by combined disc diffusion. Polymerase chain reaction (PCR) was employed to detect carbapenemase genes (blaVIM, blaNDM, blaIMP, blaOXA-23, blaOXA-58), biocide resistance determinants (qacE, qac{Delta}E1), and the class 1 integron-integrase gene (intI1). Multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes were identified in 71.1% (64/90) and 22.2% (20/90) of isolates, respectively. High resistance (>71%) was observed against meropenem and cephalosporins, whereas colistin (58.8%, 53/90) and amikacin (47.8%, 43/90) showed moderate susceptibility. The most prevalent genotypes were qac{Delta}E1 (76.6%, 69/90) and blaVIM (56.6%, 51/90). Statistical and network analyses revealed significant correlations between biocide and carbapenemase genes, identifying IntI1 as a primary driver of co-resistance. The findings indicate a significant co-occurrence of carbapenemase genes, biocide resistance determinants, and class 1 integrons among Acinobacter spp. isolates. These associations suggest that mobile genetic elements may contribute to the dissemination of resistance traits.

microbiology↗

bioRxiv2026

Evolutionary analysis of V protein pseudogenization in an RNA editing-deficient paramyxovirus

In most paramyxoviruses, RNA editing in the P gene enables expression of the V protein. Human parainfluenza virus type 1 (HPIV-1) differs from most paramyxoviruses in that it lacks RNA editing and does not produce a functional V protein, although its genome retains sequences corresponding to the ancestral V reading frame. Here, we analyzed all HPIV-1 genome sequences available in the NCBI GenBank database to assess the evolutionary state of this V protein-specific region. Using Sendai virus (SeV) as a closely related reference with an identical P gene length, we defined a pseudo-V reading frame by virtually inserting a single nucleotide at the conserved RNA editing site. In this pseudo-V frame, HPIV-1 showed a marked excess of stop codons within the 253-amino-acid region corresponding to the post-editing sequence, far exceeding expectations under random codon usage. This pattern was not observed in other viral genes analyzed under the same definition, nor in SeV, nor was it reproduced by in silico evolutionary simulations under constraints preserving the primary open reading frame. These results are consistent with a virus-specific evolutionary trajectory following the loss of RNA editing, rather than with generic coding constraints acting on overlapping reading frames.

evolutionary biology↗

bioRxiv2026

Distinct virus-specific regulation of RNA synthesis across genome segments by thogotovirus polymerases: insights from Oz virus and Dhori virus

Thogotoviruses are a group of tick-borne, six-segmented, negative-sense single-stranded RNA viruses. These viruses encode an RNA-dependent RNA polymerase that recognizes promoter sequences located at the genomic termini to initiate RNA synthesis. The 5' and 3' ends of the genome bind to the polymerase and function as a promoter. Outside the catalytic center, they base-pair with each other to form a double-stranded RNA structure. This structure is referred to as the distal duplex and plays an important role in RNA synthesis. In this study, we investigated how the RNA sequence of the distal duplex influences polymerase activity using minigenome systems of two thogotoviruses, Oz virus (OZV) and Dhori virus (DHOV). Each virus exhibits distinct activities among its six segments. In OZV, one determinant of these differences is the base pair at positions 5'12 and 3'11 within the distal duplex, where promoter activity varies depending on whether the base pair is G:C or A:U. In contrast, the DHOV polymerase is not affected by this difference. These results indicate that, even within the genus Thogotovirus, viruses differ in whether they possess a mechanism that modulates promoter activity based on subtle sequence differences within the distal duplex. Furthermore, phylogenetic analysis and comparison of promoter sequences suggest that thogotoviruses can be divided into groups that do or do not regulate intersegment promoter activity via the base pair at positions 5'12 and 3'11. HighlightsO_LIMinigenome systems of Oz virus and Dhori virus reveal segment-specific differences in promoter activity C_LIO_LIThe distal duplex sequence modulates RNA synthesis in a virus-dependent manner C_LIO_LIThe base pair at positions 5'12/3'11 determines promoter activity in Oz virus but not in Dhori virus C_LIO_LIThogotoviruses can be divided into groups that do or do not regulate promoter activity via distal duplex sequence variation at positions 5'12/3'11 C_LI

microbiology↗

bioRxiv2025

Recovery of infectious Oz virus from cloned cDNA

Oz virus (OZV) is a tick-borne, six-segmented, negative-strand RNA virus in the genus Thogotovirus, family Orthomyxoviridae. A fatal human infection was reported in Japan in 2023. In this study, we established a reverse genetics system to generate infectious recombinant OZV. Six plasmids encoding the full-length OZV genome segments under a murine RNA polymerase I promoter, together with four plasmids expressing viral proteins essential for polymerase activity, were co-transfected into murine cells. This approach enabled efficient recovery of infectious OZV. The recovered recombinant virus exhibited replication kinetics comparable to wild-type OZV. This system provides a platform for molecular studies of OZV.

microbiology↗

bioRxiv2025

Nanopore sequencing-based measurement of paramyxovirus RNA editing reveals virus-specific differences in editing efficiency of mRNA, antigenome and genome

Paramyxovirus polymerase recognizes an RNA editing signal on the viral genome and transcribes mRNA in which guanine nucleotides are inserted in a template-independent manner. This enables the synthesis of multiple proteins from a single gene, which is important for viral growth. We developed a method to quantify RNA editing efficiency using Oxford Nanopore Technologies MinION platform. We performed sequence analysis of reverse transcription (RT)-PCR amplicons with the RNA editing sites in cells infected with Sendai virus (SeV) and canine distemper virus (CDV). By modifying RT primers, we simultaneously assessed RNA editing efficiency in mRNA, antigenome and genome. We observed distinct differences in mRNA editing efficiency between SeV and CDV. Notably, while RNA editing in SeV is confined to mRNA, in CDV it is also observed in antigenome/genome. (Anti)genomes harboring extra nucleotides may deviate from a multiple-of-six sequence, suggesting that RNAs not following the "Rule of Six" are produced in CDV-infected cells. HighlightsO_LIA method was established to quantify RNA editing efficiency in RNAs from paramyxovirus-infected cells using the MinION platform. C_LIO_LIRNA editing efficiency in mRNA differs between Sendai virus and canine distemper virus. C_LIO_LIAlthough RNA editing is confined to mRNA during Sendai virus infection, it is also observed in the antigenome and genome during canine distemper virus infection. C_LI

microbiology↗

bioRxiv2025

Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds

Lactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains, isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the genera Pediococcus and Lactiplantibacillus.

genomics↗

bioRxiv2025

Functional analysis of promoter element 2 within the viral polymerase gene of an emerging paramyxovirus, Sosuga virus

Paramyxovirus genomes carry bipartite promoters at the 3 ends of both their genome and antigenome, thereby initiating RNA synthesis, which requires the viral polymerase to recognize two elements: the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2). We have previously shown that the antigenomic PE2 (agPE2) in many viruses in the Rubulavirinae subfamily is located within the coding region of the viral RNA polymerase L gene. Sosuga virus (SOSV), belonging to the Rubulavirinae subfamily, is highly pathogenic to humans, thus necessitating high-level containment facilities for infectious virus research. The use of a minigenome system permits studies of viral RNA synthesis at lower biosafety levels. Because minigenomes of negative-strand RNA viruses generally comprise only the untranslated regions, agPE2 within the L coding region--such as those found in Rubulavirinae like SOSV--are typically omitted. However, generating an SOSV minigenome that retains agPE2 led to a pronounced increase in activity, enabling a detailed examination of the role of agPE2 in SOSV replication. In many Rubulavirinae, the agPE2 not only acts as a promoter but also encodes part of the L protein, resulting in a distinct motif at the C-terminus of the L protein. We have further shown that this motif is preserved even in Rubulavirinae that no longer contain the agPE2 within the L gene. ImportanceParamyxoviruses are classified into three major subfamilies: Orthoparamyxovirinae, Avulavirinae and Rubulavirinae. All paramyxovirus genomes and antigenomes possess bipartite promoters, comprising two elements: promoter element 1 (PE1) at the 3 end and promoter element 2 (PE2) located internally. We previously revealed that, in many Rubulavirinae, the antigenomic PE2 lies within the coding region of the viral RNA polymerase L gene. In this study, we used Sosuga virus, a member of the Rubulavirinae subfamily, to elucidate the role of antigenomic PE2 in viral replication. Because the PE2 region encodes part of the L protein, its presence leads to a distinctive motif at the C-terminus of L protein. Notably, this motif is conserved in all Rubulavirinae, including those that do not harbor the antigenomic PE2 within their L gene, indicating its importance in viral propagation.

microbiology↗