Aamir Ali

• PhD, MPhil, DVM
• Principal Scientist and Faculty Member at National Institute for Biotechnology and Genetic Engineering

Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem particularly in developing countries. The available vaccines have certain limitations regarding their efficacy, and inability to induce an immune response especially in individuals under 2 years of age. Conjugate vaccines which consist of a bacteria-spe...

Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is a human restricted pathogen that can cause systemic infection (paratyphoid fever) with recently increased incidence particularly in developing countries. Currently there is no licensed vaccine for prevention of infection from S. Paratyphi A. In this study the O-specific polysaccharide (OSP...

Classically Salmonella enterica serovar Typhi (S. Typhi) is associated with typhoid, a major health problem in developing countries. However, in recent years S. Paratyphi A and Vi-negative variants of S. Typhi have emerged rapidly. We have developed a nested multiplex PCR targeting five different genes for differential diagnosis of typhoidal pathog...

Objective: Development of a rapid, reliable PCR - based method for molecular identification of Salmonella enterica serovar Paratyphi A directly from blood samples. Methodology: S. Paratyphi A isolates were used for regular PCR targeting specific region of fliC-a gene. New primers were designed and conditions were optimized for a nested PCR that cou...

Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study...

Salmonella enterica sub-species enterica serovar Gallinarum, biovar Gallinarum (S. Gallinarum/bvSG) and biovar Pullorum (S. Pullorum/bvSP) are the etiologic agents of fowl typhoid (FT) and pullorum disease (PD), respectively. A limited number of studies from South Asian countries had detected differentiating genes among both biovars. Molecular assa...

Background: Wastewater is a major source of Antibiotic-Resistant Bacteria (ARB) and a hotspot for the exchange of Antibiotic-Resistant Genes (ARGs). The occurrence of Carbapenem-Resistant Bacteria (CRB) in wastewater samples is a major public health concern. Objectives: This study aimed to analyze Antibiotic resistance in bacteria from wastewater s...

Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found...

Background Multidrug resistance (MDR) in the family Enterobacteriaceae is a perniciously increasing threat to global health security. The discovery of new antimicrobials having the reversing drug resistance potential may contribute to augment and revive the antibiotic arsenal in hand. This study aimed to explore the anti-Enterobacteriaceae capabili...

Biofilm-associated foodborne Salmonella infections in poultry have become increasingly challenging for veterinarians, particularly in developing countries, and warrant thorough investigation. We assessed the biofilm-forming tendency of poultry isolates of Salmonella enterica, namely Salmonella Typhimurium (n = 23), Salmonella Infantis (n = 28), and...

Background Infections caused by avian pathogenic Escherichia coli (APEC) result in significant economic losses in poultry industry. APEC strains are known to form biofilms in various conditions allowing them to thrive even under harsh and nutrient-deficient conditions on different surfaces, and this ability enables them to evade chemical and biolog...

Urinary tract infections (UTIs) are predominantly caused by uropathogenic Escherichia coli (E. coli). There is rapid increase in antimicrobial resistance in UTIs, also declared as a serious health threat by World Health Organization (WHO). Present study was designed to investigate the antimicrobial resistance status with specific focus on ESBLs and...

Biofilm-associated bacterial infections are problematic for physicians due to high antimicrobial resistance in biofilm-forming bacteria. Staphylococcus species, particularly Staphylococcus epidermidis, cause severe infections particularly associated with clinical implants. In this study, we have detected the biofilm formation potential of clinical...

Rapid emergence of resistance in Salmonella enterica serovar Typhi (Salmonella Typhi) against most of the available therapeutic options for typhoid has rendered its treatment more difficult. This study sought to determine the current scenario of antimicrobial resistance in local isolates of Faisalabad following several treatment failure reports. Ou...

Background Surface-enhanced Raman spectroscopy (SERS) is an effective tool for identifying biofilm forming bacterial strains. Biofilm forming bacteria are considered a major issue in the health sector because they have strong resistance against antibiotics. Staphylococcus epidermidis is commonly present on intravascular devices and prosthetic joint...

Background Outer membrane proteins (OMPs) of Gram-negative bacteria have been known as potential vaccine targets due to their antigenic properties and host specificity. Here, we focused on the exploration of the immunogenic potential and protective efficacy of total OMPs of Salmonella enterica serovar Typhi due to their multi epitope properties, ad...

Pathogenic bacteria, such as enteropathogenic (EPEC) and enterotoxigenic Escherichia coli (ETEC), cause diarrhea in mammals. In particular, E. coli colonize and infect the gastrointestinal tract via type 1 fimbriae (T1F). Here the major zymogen granule membrane glycoprotein 2 (GP2) acts as host cell receptor. GP2 is also secreted by the pancreas an...

Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its synergistic resistance mechanisms resulting in the ineffectiveness of the used antimicrobials. This study aimed to characterize P. aeruginosa isolates for antimicrobial susceptibility, biofilm formation virulence genes, and molecular mechanisms responsi...

Antibiotics are generally applied for treatment or as subtherapeutic agents to overcome diseases caused by pathogenic bacteria including Escherichia coli, Salmonella and Enterococcus species in poultry. However, due to their possible adverse effects on animal health and to maintain food safety, probiotics, prebiotics, and synbiotics have been propo...

Cardiac conduction disease (CCD), which causes altered electrical impulse propagation in the heart, is a life-threatening condition with high morbidity and mortality. It exhibits genetic and clinical heterogeneity with diverse pathomechanisms, but in most cases, it disrupts the synchronous activity of impulse-generating nodes and impulse-conduction...

Salmonella is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, an...

Avian pathogenic E. coli is not only pathogenic for commercial poultry but can also cause foodborne infections in humans utilizing the same attachment and virulence mechanisms. Our aim was to identify genes of avian pathogenic E. coli involved in adhesion to chicken and human cells in order to understand the colonization and pathogenesis of these b...

Antibiotics are generally applied for treatment or as subtherapeutic agents to overcome diseases caused by pathogenic bacteria including Escherichia coli, Salmonella and Enterococcus species in poultry. However, due to their possible adverse effects on animal health and to maintain food safety, probiotics, prebiotics, and synbiotics have been propo...

Haemorrhagic septicaemia is mainly caused by an opportunistic pathogen, Pasteurella multocida, a major threat to the livestock dependent economies. The main endotoxins are lipopolysaccharides. The lipid A, a key pathogenic part of lipopolysaccharides, anchors it into the bacterial cell membrane. Hence, profiling of the lipid A is important to under...

Biofilms are complex, sessile microbial communities that are problematic in clinical settings due to their association with survival and pathogenicity of bacteria. The biofilm formation supporting conditions for zoonotic serovars of Salmonella and avian pathogenic E. coli (APEC) from poultry have not been well studied yet. Clinical isolates of zoon...

Rhodococcus sp. Eu-32 has shown an extended novel dibenzothiophene desulfurization sulfur-specific 4S pathway and could remove significant amounts of organic sulfur from coal. Here, we present the draft genome sequence of Eu-32 with a genome size of approximately 5.61 Mb, containing 5065 protein coding sequences with a G+C content of 65.1%. The Rho...

We evaluated prevalence and distribution of antibiotic resistant E. coli in three categories: animals (goats, pigs, poultry, cattle, sheep), humans (butchers, meat sellers, animal farm workers, buyers) and animal food products (milk, cheese, beef, chicken, yoghurt) from selected animal farms in South-West Nigeria. The biofilm formation, phylogroupi...

Objective: To determine the prevalence and genetic relatedness of blaCTX-M-type extended spectrum-β-lactamase (ESBL)-producing Escherichia coli at the human-animal interface in Pakistan. Materials and Methods: A total of 150 human, cattle, and poultry fecal samples (50 each) were screened for ESBL-producing E. coli using ESBL CHROMagar®. Bacterial...

Cadmium is an important widely distributed heavy metal in the environment due to its several industrial uses, while milk thistle is an important herb and is a source of several antioxidant particularly silymarin which is a pharmacological active substance present in seeds of milk thistle plant (Silybum marianum). The current study investigated path...

Hereditary Spastic paraplegias (HSPs) are heterogeneous group of degenerative disorders characterized by progressive weakness and spasticity of the lower limbs, combined with additional neurological features. This study aimed to identify causative gene variants in two nonrelated consanguineous Pakistani families segregating HSP. Whole exome sequenc...

Aims: The aim of this study was the molecular identification of Salmonella enterica serovar Infantis (S. Infantis) isolated from poultry samples and their antimicrobial resistance and virulence profiling. Methods and results: A total of 149 isolates, belonging to genus Salmonella, originally isolated from 340 suspected poultry post mortem specim...

Multidrug resistant (MDR) Pseudomonas aeruginosa having strong biofilm potential and virulence factors are a serious threat for hospitalized patients having compromised immunity. In this study, 34 P. aeruginosa isolates of human origin (17 MDR and 17 non-MDR clinical isolates) were checked for biofilm formation potential in enriched and minimal med...

The pathogenesis of Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever in humans, is mainly attributed to the acquisition of horizontally acquired DNA elements. Salmonella pathogenicity islands (SPIs) are indubitably the most important form of horizontally acquired DNA with respect to pathogenesis of this bacterium. The insert...

Comparison of de novo assembled contig lengths between all strains. The x-axis shows the percentage of length of the assembled genome for any strain and y-axis shows the length of contigs in kilobases used for a particular length percentage of assembled genome. (TIF)

%GC content of a ST11 de novo assembled contigs. (TIF)

%GC content of a ST5 de novo assembled contigs. (TIF)

%GC content of a ST6 de novo assembled contigs. (TIF)

%GC content of a ST18 de novo assembled contigs. (TIF)

Whole genome sequencing and assembly statisitics of SalmonellaTyphi Strains. (XLSX)

Comparison of de novo assembled contig lengths between all strains with respect to the reference genome size [S. Typhi, Acc: AL513382]. The x-axis shows the percentage of length assembled with respect to the reference genome for any strain and y-axis shows the length of contigs in kilobases used for a particular length percentage. (TIF)

Comparative distribution of # contigs with GC percentage in a certain range. The x value is the GC percentage intervals. The y value is the number of contigs which GC content lies in the corresponding interval. (TIF)

%GC content of a ST8 de novo assembled contigs. (TIF)

%GC content of a ST16 de novo assembled contigs. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST6. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST19. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST26. (TIF)

Comparison of growth of contig lengths. On the x-axis, contigs are ordered from the largest to smallest. The y-axis gives the size of the x largest contigs in the assembly. (TIF)

%GC content of a ST7 de novo assembled contigs. (TIF)

%GC content of a ST25 de novo assembled contigs. (TIF)

%GC content of a ST38 de novo assembled contigs. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST5. (TIF)

%GC content of a ST17 de novo assembled contigs. (TIF)

%GC content of a ST19 de novo assembled contigs. (TIF)

%GC content of a ST22 de novo assembled contigs. (TIF)

%GC content of a ST26 de novo assembled contigs. (TIF)

Distribution of total contig lengths (y-axis) at different read coverage depths (x-axis, grouped in bins). (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST8. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST11. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST16. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST17. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST22. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST25. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST7. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST18. (TIF)

Distribution of contig lengths (y-axis) at different read coverage depths (x-axis) of ST38. (TIF)

The zoonotic serovars of Salmonella enterica particularly Typhimurium and Enteritidis pose a continuous global threat to poultry industry and public health. We report the prevalence of Salmonella Typhimurium and Salmonella Enteritidis serovars in local poultry, phenotypic antimicrobial resistance profiling, and molecular detection of antimicrobial...

Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on Escherichia coli biofilm formation have investigated nonpathogenic E. coli K-12 strains. Due t...

Efficacious typhoid vaccines for young children will significantly reduce the disease burden in developing world. The Vi polysaccharide based conjugate vaccines (Vi-rEPA) against Salmonella Typhi Vi positive strains has shown high efficacy but may be ineffective against Vi negative S. Typhi. In this study, for the first time, we report the synthesi...

The first report of plasmid-mediated colistin resistance among Enterobacteriaceae in China sounded alarms in the medical community worldwide (1).…

The snapshot of extended spectrumb-lactamases (ESBL) bugs is greatly linked with the E. coliin humans, animals and environment and badly affecting the One Health concept. Proposed study was aimed for the detection of genetic diversity between ESBL producing isolates under One Health initiative. A total of 150 samples, including humans (n=50), cattl...

Background Paratyphoid fever caused by Salmonella enterica serovar Paratyphi A is becoming a serious health problem in Asian countries particularly Pakistan, China and India and situation is aggravated by current unavailability of a licensed vaccine. This study was designed to purify the O-specific polysaccharides (OSP) produced by an isolate of Sa...

The epidemiological aspects of Theileria orientalis in Pakistan are poorly studied and further investigations using sensitive and precise molecular techniques are required. This study reports the first molecular characterisation of T. orientalis detected from imported (Bos taurus) and local cattle (Bos indicus × Bos taurus) and buffaloes (Bubalus b...

Currently licensed typhoid vaccines are based on Vi capsular polysaccharides. Recent molecular reports from typhoid endemic countries state that Salmonella enterica serovar Typhi (S. Typhi) Vi negative strains occur naturally and cause typhoid fever which is indistinguishable from disease caused by Vi positive strains. Vaccine based on Vi polysacch...

Salmonella enterica serovar Typhi (S. Typhi) is a human restricted pathogen. It biosynthesizes a virulence capsu-lar polysaccharide named as Vi antigen. S. Typhi regulates expression of genes involved in the biosynthesis of Vi antigen in response to osmolarity. Beside Vi-positive isolates, Vi-negative (acapsulated) isolates are also pathogenic. How...

Currently licensed typhoid vaccines are based on Vi capsular polysaccharides. Recent molecular reports from typhoid endemic countries state that Salmonella enterica serovar Typhi (S. Typhi) Vi negative strains occur naturally and cause typhoid fever which is indistinguishable from disease caused by Vi positive strains. Vaccine based on Vi polysacch...

PCR assays can be performed for the rapid detection and discrimination of biovars Gallinarum and Pullorum from poultry isolates. Earlier confirmation of infection is more effective in elimination of disease from flocks.

Isolation and molecular detection of Salmonella enterica serovar Gallinarum from local poultry farms

Typhoid, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem worldwide especially in developing countries. Lipopolysaccharides are one of the main virulence factors of S. Typhi. Hydrophobic lipid A anchors the lipopolysaccharides into the bacterial outer membrane and also serves as the epicenter of endotoxicity, which...

This study aimed to determine the drug susceptibility patterns and genetic elements related to drug resistance in isolates of Salmonella enterica serovar Typhi (S. Typhi) from the Faisalabad region of Pakistan. The drug resistance status of 80 isolates were evaluated by determining antimicrobial susceptibility, MICs, drug resistance genes involved,...

Background and Objective: Wound infections are often difficult to treat due to various bacterial pathogens. Pseudomonas aeruginosa is one of the common invaders of open wounds. Precise diagnosis of this etiological agent in wound infections is of critical importance particularly in treatment of problematic cases. The existing diagnostic methods hav...

Objectives: Production of extended spectrum beta -lactamases (ESBLs) by clinical isolates of pathogenic E. coli is a very serious therapeutic threat. This study was aimed to investigate the prevalence of ESBLs and associated drug resistance in E. coli isolates from urine and pus, and to report the drift from 2005 to 2009-10. Methodology: Among 173...

Objective Discrimination of Salmonella Typhi Vi negative strains from Vi positive strains, extraction and purification of Lipopolysaccharides, O-specific polysaccharide antigen, and determination of antigenicity. Methods Lipopolysaccharide (LPS) is an essential structural component of the outer cell membrane of Salmonella species. It plays a main...

Rotavirus infection is very common in developing countries and occurs at least once in children under the age of 5 years. The rate of detection of rotavirus infection in various age groups (0-5 years) in patients with gastroenteritis admitted to hospital from the Faisalabad region, Pakistan is reported. Out of 300 fecal samples, 189 (57.3%) were po...

Bacillary dysentery, common in developing countries, is usually caused by Shigella species. A major problem in shigellosis is the rapid emergence of multidrug-resistant strains. This is the first detailed molecular study on drug resistance of Shigella isolates from the Faisalabad region of Pakistan. Ninety-five Shigella isolates obtained after scre...

Uropathogenic E.coli (UPEC) are among major pathogens causing urinary tract infections. Virulence factors are mainly responsible for the severity of these emerging infections. This study was planned to investigate the distribution of virulence genes and cytotoxic effects of UPEC isolates with reference to phylogenetic groups (B2, B1, D and A) to un...

Objectives: Currently fluoroquinolones and cephalosporins are at the forefront of typhoid treatment. The objective of this study was to assess the current drug resistance status of S. Typhi isolates from Faisalabad region by conventional and molecular methods. Methodology: Drug resistance pattern of 30 clinical isolates (2011) against 8 drugs (nali...

The objective of this work was the phylogenetic characterization of local clinical isolates of uropathogenic E. coli with respect to drug resistance. A total of 59 uropathogenic E. coli responsible for community acquired urinary tract infections were included in this study. A triplex PCR was employed to segregate each isolate into four different ph...