Biology subjects

Hasan, Z.

Publications and source records attributed to Hasan, Z..

8 recordsLinked to original sources

bioRxiv2026

Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors

Objectives: Klebsiella pneumoniae is a significant global health concern due to its ability to cause diverse infections and its increasing multidrug resistance. This study analyzed the whole-genome sequence of multidrug-resistant K. pneumoniae strain CP4, isolated from a vaginal swab of an infertile woman, to characterize its virulence factors, antibiotic resistance mechanisms, and epidemiological features. Methods: The Kirby-Bauer disk diffusion assay was used to screen antibiotic resistance. Whole genome sequencing was conducted using the Illumina MiSeq platform and followed by comprehensive bioinformatic analysis. Results: Antibiotic susceptibility testing revealed that the K. pneumoniae strain CP4 exhibited resistance to 11 of 18 tested antibiotics, including carbapenems, and displayed a Multiple Antibiotic Resistance (MAR) index of 0.611. Whole-genome sequencing identified an array of putative virulence and metal-resistant genes, classifying it as a human pathogen with a probability score of 0.887. The strain was characterized as sequence type 327 with K16 capsular and O1/O2v1 somatic antigens. The antibiotic resistome included 38 putative genes conferring resistance to a spectrum of antibiotics. Moreover, point mutations were identified in several genes that ResFinder predicted to be associated with resistance to fluoroquinolones, cephalosporins, and carbapenems. Additionally, K. pneumoniae strain CP4 harbored six putative plasmid-replicon types and 454 putative mobile genetic element-associated protein hits among predicted ORFs. Several putative antibiotic resistance genes, including tet(A), floR, mph(A), and aph(6)-Id, were associated with insertion sequences, transposons, and integrons, indicating a potential for horizontal gene transfer. Conclusions: The genomic features of multidrug-resistant K. pneumoniae CP4 highlight its potential for antimicrobial resistance and virulence, emphasizing the need for continued genomic surveillance and targeted interventions. Keywords: Klebsiella pneumoniae, Whole Genome Sequencing, Antimicrobial Resistance, Pangenome analysis

microbiology↗

bioRxiv2025

LAP Drives Monocyte-Mediated and Extracellular Translocation of Listeria monocytogenes Across the Placental Barrier

Listeria monocytogenes (Lm) is a major cause of fetal infection, yet the mechanisms by which it traverses the placental barrier remain incompletely defined. We established and validated a physiologically relevant in vitro human placental co-culture barrier model using BeWo trophoblasts and primary human placental vascular endothelial cells (HPVECs), which exhibited robust barrier integrity and organized tight junctions. Using this model, we demonstrate that Lm exploits a Trojan-horse transmigration mechanism via infected monocytes. Lm-infected THP-1 monocytes displayed a [~]4.8-fold higher monocyte transmigration and [~]8.12-fold greater intracellular bacterial delivery across the placental barrier compared with non-pathogenic Listeria innocua (Li). Monocyte transmigration was associated with claudin-1 and occludin disruption, increased paracellular permeability, and localization of infected monocytes at junctional breach sites. Monocyte-mediated placental traversal required the Lm virulence factors Listeria adhesion protein (LAP) and internalin B (InlB), as lap- and{Delta} inlB mutants exhibited Li-like transmigration and an [~]90% reduction in intracellular bacterial delivery, despite normal monocyte uptake. Lm-infected monocytes induced a [~]1.86-fold increase in sVCAM-1 secretion, which was LAP- and InlB-dependent, consistent with pro-transmigration endothelial phenotype. In contrast, extracellular traversal required LAP and internalin A (InlA), as lap- and{Delta} inlA mutants exhibited severe defects comparable to Li, whereas{Delta} inlB and{Delta} hly were minimally impaired. Exposure of monocytes to extracellular Lm further amplified transmigration and barrier permeability. Together, these data define two distinct placental invasion routes: a monocyte-associated LAP/InlB-dependent pathway and an extracellular LAP/InlA-dependent pathway, identifying LAP as a critical noncanonical virulence factor in placental infection and mechanisms of vertical transmission.

microbiology↗

bioRxiv2025

Pairing extinction training with vagus nerve stimulation (VNS) reduces drug-seeking by altering activity in afferents to the medial prefrontal cortex

Relapse triggered by drug-associated cues or stress remains a major challenge in treating substance use disorders (SUDs), as re-exposure reliably provokes craving and reinstatement of drug seeking. Extinction-based interventions can reduce cue reactivity, yet extinction learning is often weak or context-dependent, limiting its clinical impact. Vagus nerve stimulation (VNS) enhances learning-related plasticity via widespread engagement of neuromodulatory systems and cortical circuits. Recent preclinical work shows that pairing extinction with VNS facilitates extinction learning and reduces cue-induced reinstatement of cocaine seeking, suggesting translational potential as an adjunct to exposure-based therapies. However, the circuit-level mechanisms underlying these effects remain unclear. To address this gap, we examined how VNS paired with extinction alters activity in medial prefrontal cortex (mPFC) networks that regulate drug seeking, focusing specifically on afferent projections from the basolateral amygdala (BLA) and ventral hippocampus (vHPC). Male rats received retrograde AAV-eGFP infusions into either the prelimbic (PL) or infralimbic (IL) cortex to label upstream projections, followed by cocaine self-administration, extinction training with VNS or sham stimulation, and cue-induced reinstatement. cFos immunolabeling in the BLA and vHPC revealed pathwayspecific modulation: VNS decreased overall BLA activity and reduced activation of BLA to IL projections, but increased activation of BLA to PL projections. In the vHPC, VNS selectively decreased activation of vHPC to IL projections without affecting PL-projecting neurons. Because these pathways synapse onto parvalbumin interneurons (PVIs) in the mPFC, we quantified PVI activation and found that VNS decreased overall prefrontal cFos expression, but increased PVI activity in the PL, and decreased PVI activity in the IL. Together, these results demonstrate that VNS paired with extinction reshapes prefrontal-amygdala-hippocampal circuits in a pathway-specific manner, potentially modulating feed-forward inhibition to reduce relapse-like behavior. These findings support VNS as a promising strategy to strengthen extinction learning and improve treatment outcomes in SUD.

neuroscience↗

bioRxiv2025

Structural and Conformational Impact of Deleterious Spike Protein Mutations in SARS-CoV-2 Omicron Lineages

BackgroundA large number of mutations in the Spike (S) protein of the SARS-CoV-2 omicron variant have been noted to alter the receptor binding domain (RBD) and increase the binding surface and enhance the opening of the binding pocket. The cumulative effect of S1 and S2 subunit mutations can influence the conformational dynamics of the binding surface, facilitating the release of viral genome into host cells. AimThis study investigates the deleterious mutations across all Omicron lineages identified in our analysis and their effect on the conformational stability of RBD opening. MethodsWhole Genome Sequencing of 231 SARS-CoV-2 positive patients in Karachi, Pakistan, were performed using Illumina Miseq instrument and raw reads were analyzed using viralrecon pipeline. The mutational effects of omicron variant on the stability of S protein, including wild-type (7FG7), close (6VXX) and open (6VYB) states, were assessed through MD simulations. ResultsFour deleterious missense mutations (Tyr505His, Asn764Lys, Asp950Asn, Asn969Lys) were identified in the S1 and S2 subunit of the S protein of omicron variant. In the wildtype and open state mutant models, Tyr505His, Asp950Asn and Asn969Lys caused destabilizing effects, higher RMSDs vs. wild-type, and fluctuations in the RBD (438-510) region and S2 subunit (946-1010), compared to the native structure. These mutations increased the binding pocket propensity to open in mutant model compared to the native open conformation (6VYB). This structural change promoted trimer opening in the open state through -helix movement in the S2 subunit away from the RBD region. In the closed state, only S2 subunit mutations (Asp950Asn and Asn969Lys) lead to predicted destabilization through the movement of protomer C towards protomer B (RBD region). These S2 subunit mutations are predicted to stabilize the RBD "down" conformation potentially enhancing spike antigenic heterogeneity. ConclusionThis study highlighted the cumulative effect of S1 (Tyr505His) and S2 (Asp950Asn and Asn969Lys) subunits mutations on different S protein states, potentially controlling its conformational dynamics and presentation to host receptors. Future experimental studies are needed to elucidate the biological significance of these alterations, particularly by establishing a link between the identified mutations and their impact on viral biology.

bioinformatics↗

bioRxiv2023

A Versatile Tool for Precise Variant Calling in Mycobacterium tuberculosis Genetic Polymorphisms

BackgroundWhole genome sequencing (WGS) facilitates the diagnosis of multidrug-resistant MDR-TB through the interpretation of sequence variations (SV) in Mycobacterium tuberculosis (MTB) genes. Information on phenotypic and genotypic resistance associations continues to evolve, it is important to identify SV within genes of interest. We developed an MTB-VCF variant calling pipeline that can compare against the reference genome for any gene of interest. We demonstrate its utility for calling SV in genes associated with Rifampicin (RIF), Isoniazid (INH), Ethambutol (EM), and Streptomycin (SM) resistance. MethodsMTB-VCF is a Python-based command line Variant Calling pipeline designed to streamline batch processing from raw reads (FastQ) files. SV called by MTB-VCF were compared with those identified by TBProfiler, KVARQ, CASTB, Mykrobe Predictor and Phy-ResSE pipelines. The sensitivity and Specificity of MTB-VCF SV calling were calculated against the drug susceptibility testing (DST) phenotype. ResultsMTB-VCF identified 868 SV present in 200 phenotypically resistant MDR-TB isolates. These were across rpsl, rrs, rpoB, inhA, katG, ahpC, gidB and embCAB genes. Of these, 684 SV were known to be associated with a resistance genotype, leading to a specificity of 97.75%. The SV called by the MTB-VCF was compared separately to resistance genotypes called by TB-Profiler, KvarQ, CASTB, Mykrobe Predictor, and PhyRes-SE pipelines, demonstrating a sensitivity of 99.5%. ConclusionThe MTB-VCF pipeline offers a rapid and accurate solution for identifying SV in target genes for interpretation later. It can be run in large batches, proving flexible computing that allows for the customization of core bioinformatic pipelines, enabling the analysis of WGS data from different technologies.

bioinformatics↗

bioRxiv2022

BBIBP-CorV (Sinopharm) vaccination- induced immunity is affected by age, gender and prior COVID-19 and activates responses to spike and other antigens

Long-term solutions against SARS-CoV-2 infections require understanding of immune protection induced by different vaccine COVID-19 formulations. We investigated humoral and cellular immunity induced by Sinopharm (BBIBP-CorV) in a region of high SARS-CoV-2 seroprevalence. Levels of IgG antibodies to SARS-CoV-2 spike protein and its receptor-binding domain (RBD) were determined 24-weeks. Cellular immunity was investigated using a commercially available IFN-{gamma} release assay to SARS-CoV-2 spike (Ag1 and 2) and extended genome antigens (Ag3). Increasing IgG seropositivity to Spike protein and RBD was observed post-vaccination. Seropositivity was reduced in those over 50 years and raised in females and those with prior COVID-19. After 20 weeks post-vaccination, only one third of participants had positive T cell responses to SARS-CoV-2 antigens. Prior COVID-19 impacted IFN{gamma} responses, with reactivity enhanced in those infected earlier. The frequency of IFN{gamma} responses was highest to extended genome antigen set. Overall, BBIBP-CorV- induced antibody responses were impacted by age, gender and prior COVID-19. Cellular immunity was present in a limited number of individuals after 20 weeks but was enhanced by prior infection. This suggests the need for booster vaccinations in older individuals. BBIBP-CorV-induced cellular activation is broader than to spike, requiring further study to understand how to monitor vaccine effectiveness.

immunology↗

bioRxiv2020

SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic

ObjectivesPakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country. MethodsWe performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May. ResultsStrains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions. ConclusionsThis data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.

genomics↗

bioRxiv2020

Phage recombination drives evolution of spore-forming Bacilli

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SP{beta} prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SP{beta} recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SP{beta} and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SP{beta}-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

microbiology↗