Ashraf A Khan

• Ph.D.
• SBRBPAS Expert (Microbiologist) at U.S. Food and Drug Administration

Plazomicin, a next-generation aminoglycoside, was recently approved by the U.S. Food and Drug Administration for the treatment of multidrug-resistant complicated urinary tract infections. It is highly effective against most aminoglycoside-modifying enzymes (AMEs). Here, we report that Salmonella enterica strains containing the newly identified gent...

Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, al...

The pervasive environmental metal contamination has led to selection of heavy-metal resistance genes in bacteria. The pco and sil clusters are located on a mobile genetic element and linked to heavy-metal resistance. These clusters have been found in Salmonella enterica serovars isolated from human clinical cases and foods of animal origin. This ma...

We analyzed antimicrobial resistance and virulence traits in multidrug-resistant (MDR) E. coli isolates obtained from imported shrimp using whole-genome sequences (WGSs). Antibiotic resistance profiles were determined phenotypically. WGSs identified key characteristics, including their multilocus sequence type (MLST), serotype, virulence factors, a...

Brucellosis is one of the most highly infectious zoonotic diseases worldwide and has substantial health and economic impact. Strenuous efforts are essential to combat and prevent this disease from the one-health perspective. Brucellosis is successfully eradicated from domestic animals in the United States, but control strategies continue to eradica...

Shiga toxin-producing Escherichia coli (STEC) is one of the most prominent food-borne pathogens in humans. The current study aims to detect and to analyze the virulence factors, antibiotic resistance, and plasmid profiles for forty-six STEC strains, isolated from clinical and food strains. Pulsed-field gel electrophoresis (PFGE) was used to determi...

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are recognized as an important group of bacterial enteropathogens. Here, we report the draft genome sequence of nine strains of non-O157 STEC isolated from ready-to-eat foods in Argentina. The whole-genome sequence data provide a better understanding of these isolates and will aid epidemiologic...

We report the draft genome sequences of 14 fluoroquinolone-resistant Escherichia coli strains that were isolated from imported shrimp. All isolates contained multiple point mutations in the quinolone resistance-determining regions (QRDRs) and non-QRDRs of gyrA, parC, and parE genes. The data improve the understanding of fluoroquinolone resistance a...

Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period coincided with a rapid rise in the incidence of S. Javiana infections in the U...

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen transmitted from animal to humans through contaminated food. Here, we report the draft genome sequences of six STEC isolates (six serotypes) from food (cheese, coriander, and pea protein pellets) in different countries; these isolates were resistant to tetracycline, with MIC valu...

We report here the draft genome sequences of 16 fluoroquinolone-resistant extraintestinal Escherichia coli isolates from human patients. These isolates had high MICs (32 to 256 μg/mL) for ciprofloxacin and contained point mutations in the quinolone resistance-determining region (QRDR) of both gyrA and parC that confer resistance to fluoroquinolone....

Antibiotic resistance has been on the rise due to the overuse of antibiotics in the agricultural industry. This has led to an increase in foodborne illnesses and a need for alternative modes of action to help mitigate bacterial growth. This study broaches the potential applications of hot water-treated (HWT) aluminum foil for use in the food packag...

Bacterial biofilm has become one of the most frequent health problems as it contributes to persistent chronic infections. Therefore, it is vital to find alternatives to currently used bactericidal agents to prevent bacterial contamination on surfaces effectively and prevent the biofilms formation. Several metallic materials are well known for their...

Whole-genome sequencing (WGS) is a valuable tool in research on foodborne pathogens. In this study, a total of 143 isolates of Salmonella serotypes Enteritidis, Typhimurium, and Heidelberg sourced from eggs and chickens were analyzed for their antimicrobial resistance profiles using WGS data. The isolates carried high rate of genes resistant to ami...

Bacillus cereus strains were isolated from dried foods, which included international brands of spices from South East Asia, Mexico and India purchased from several retail stores, samples of powdered infant formula (PIF), medicated fish feed and dietary supplements. The genetic diversity of 64 strains from spices and PIF was determined using a multi...

We report here the draft genome sequences of 15 ciprofloxacin-resistant Salmonella enterica strains with resistance to multiple other antibiotics, including aminoglycosides, β-lactams, sulfonamides, tetracycline, and trimethoprim, isolated from different imported foods. Three strains (NCTR75, NCTR281, and NCTR350) showed a high level of ciprofloxac...

Human pathogenic bacteria in the family Enterobacteriaceae may come into contact with food plants during cultivation, harvesting and processing. Attachment of such bacteria to plant surfaces as biofilms may allow their survival, but the resulting contamination of vegetables and fruits has resulted in many illnesses and disease outbreaks. This chapt...

Biofilm formation by microorganisms is common in almost all natural habitats, including foods. Biofilms formed on food surfaces and food contact equipment may result in serious health complications and economic losses due to food spoilage. In many bacterial pathogens, cell-to-cell communication (quorum sensing, QS) is a global gene regulatory mecha...

The purpose of this study was to determine the diversity and antimicrobial resistance of Listeria monocytogenes strains isolated from food-related environments in the United States. Nineteen unrelated strains of L. monocytogenes were recovered from approximately 1300 food and food processing environmental samples collected from 2007 to 2011 as part...

The objective of this study was to determine antimicrobial resistance and elucidate the resistance mechanism in nontyphoidal Salmonella enterica serovars isolated from food products imported into the United States from 2011 to 2013. Food products contaminated with antimicrobial-resistant nontyphoidal S. enterica were mainly imported from Taiwan, In...

Food contaminated with extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica has emerged as an important global issue due to the international food-product trade. Therefore, the purpose of this study was to investigate whether imported food products can serve as a reservoir for non-typhoidal Salmonella (NTS) that can transmit β-lactam-...

Sixty-one quinolone-resistant strains of Vibrio parahaemolyticus were isolated from 247 shrimp samples. These isolates had MICs of 256 and 4-8 µg/mL for nalidixic acid and ciprofloxacin respectively. Template DNA of the 61 isolates were screened by PCR for the quinolone resistance genes. Purified PCR amplicons of gyrA, gyrB and parC from these isol...

Cytolethal distending toxin B (cdtB) is a conserved virulence factor in Salmonella enterica serovar Typhi. Here we report the presence and functionality of cdtB in some nontyphoidal Salmonella (NTS) serovars, including Salmonella Javiana (cdtB+wt S. Javiana), isolated from imported food. To understand the role of cdtB in NTS serovars, a deletion mu...

Salmonella infection is one of the major food-borne illnesses in the United States. Several Gram-negative bacterial pathogens, including Salmonella Typhi, produce cytolethal distending toxin (CDT), which arrests growth, induces apoptosis of infected host cells and extends persistence of pathogenic bacteria in the host. The aim of this study was to...

A total of 60 Salmonella enterica serovar (ser.) Enteritidis isolates, 28 from poultry houses and 32 from clinical samples, were isolated during 2010. These isolates were subjected to testing and analyzed for antibiotic resistance, virulence genes, plasmids and plasmid replicon types. To assess genetic diversity, pulsed-field gel electrophoresis (P...

To determine the association of tetracycline resistance determinants with tigecycline sensitivity, tetracycline-resistant Salmonella spp. isolated from clinical and food samples were tested for the presence of tetracycline resistance determinants, tigecycline sensitivity, and the impact of tetA on tigecycline resistance. In addition, the impacts of...

Four popular ephedra-free dietary supplements were evaluated for their effects on heart rate (HR), blood pressure (BP), and electrocardiographic (ECG) parameters. Twelve healthy men participated in a study randomized for product sequence, with a 21-day washout period between supplement-administration phases. Throughout the study, Holter monitors we...

Sixty-three nalidixic acid-resistant Aeromonas sp. isolates were obtained from imported shrimp. Phylogenetic analysis of gyrB sequences indicated that 18 were A. enteropelogenes, 26 were A. caviae, and 19 were A. sobria. Double missense mutations in the quinolone resistance-determining region (QRDR) of gyrA at codon 83 (Ser→Val/Ile) and codon 92 (L...

This study describes the prevalence of arrays of class 1 integron cassettes and Qnr determinants (A, B, and S) in 19 fluoroquinolone-resistant Escherichia coli isolates from chicken litter. qnrS and qnrA were the predominant genes in these fluoroquinolone-resistant isolates, and an uncommon array of aacA4-catB3-dfrA1 gene cassettes from a class1 in...

A study was undertaken to isolate and characterize tetracycline and nalidixic acid-resistant Klebsiella spp. in farm-raised, imported shrimp sold in the United States. Sixty-seven multiple antibiotic-resistant Klebsiella spp. strains were isolated from imported shrimp samples. Using morphological and biochemical methods, fifty-three strains were te...

To determine the fluoroquinolone resistance determinants in Salmonella enterica serovar Schwarzengrund from imported foods. Antibiotic susceptibility of Salmonella Schwarzengrund to 16 antibiotics was examined using disc agar diffusion and Etest. Quinolone resistance determinants were examined by sequence analysis of gyrA, gyrB, parC and parE, PCR...

Dissemination of plasmid-mediated quinolone resistance among pathogenic bacteria is a concern for public health because of decreased sensitivity to fluoroquinolones and increased potentials to develop high fluoroquinolone resistance. Two qnrS1-positive isolates of Salmonella enterica Corvallis (468) and Typhimurium (484) from imported seafood (Thai...

A total of 39 Salmonella enterica serovar Saintpaul strains from imported seafood, pepper and from environmental and clinical samples were analyzed for the presence of virulence genes, antibiotic resistance, plasmid and plasmid replicon types. Pulsed-field gel electrophoresis (PFGE) fingerprinting using the XbaI restriction enzyme and plasmid profi...

The presence of virulence genes and integrons was determined in 81 strains of Aeromonas veronii isolated from farm-raised catfish. Polymerase chain reaction (PCR) protocols were used to determine the presence of genes for cytotoxic enterotoxin (act), aerolysin (aerA), two cytotonic enterotoxins (ast, alt), lipase (lip), glycerophospholipid:choleste...

A study was undertaken to investigate the occurrence of tetracycline-resistant genes and to characterize the integrons present in Escherichia coli isolated from catfish. Sixty-three tetracycline-resistant E. coli strains were isolated from the intestinal contents of 407 farm-raised catfish. All strains were resistant to multiple antibiotics. A poly...

A total of 210 Salmonella isolates, representing 64 different serovars, were isolated from imported seafood samples, and 55/210 isolates were found to be resistant to at least one antibiotic. Class 1 integrons from three multidrug-resistant Salmonella enterica strains (Salmonella enterica serovars Newport [strain 62], Typhimurium var. Copenhagen [s...

During 2001-2005, 210 Salmonella enterica strains were isolated from seafood samples imported into US. Strains of S. enterica serovar Weltevreden were the most predominantly found among the 64 different serovars isolated. A total of 37 Salmonella Weltevreden isolates were characterized by pulsed-field gel electrophoresis (PFGE), plasmid profiles an...

Fifty-two tetracycline-resistant Citrobacter spp. strains were isolated from farm-raised catfish. Morphological and biochemical characteristics indicated that 38 of the 52 citrobacters were Citrobacter freundii, 7 were C. amalonaticus and 7 were C. braakii. All isolates were resistant to multiple antibiotics. Polymerase chain reaction (PCR) protoco...

Several Salmonella enterica serotypes were isolated from unpasteurized orange juice samples analysed as a follow-up to an outbreak in 1999 of S. enterica serotype Muenchen in the Pacific Northwest regions of United States. Eleven S. enterica strains were serotyped and identified as S. enterica serotype Muenchen (2), S. enterica serotype Hidalgo (2)...

Mycobacterium vanbaalenii PYR-1 has the ability to degrade low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs). In addition to dioxygenases, cytochrome P450 monooxygenases have been implicated in PAH degradation. Three cytochrome P450 genes, cyp151 (pipA), cyp150, and cyp51, were detected and amplified by polymerase chain reactio...

Between June 2000 and December 2001, 500 food samples were collected from supermarkets and shops selling ready-to-eat food in Rosario, Argentina, and examined for Escherichia coli. Forty-nine E. coli isolates from food samples were further characterized for virulence genes by multiplex polymerase chain reaction (PCR) targeting the stx1, stx2, stx2e...

Eighty-one tetracycline-resistant Aeromonas sp. strains were isolated from farm-raised catfish. Morphological and biochemical characteristics indicated that 23 of the 81 aeromonads were Aeromonas hydrophila, 7 isolates were Aeromonas trota, 6 isolates were Aeromonas caviae, 42 isolates were Aeromonas veronii, and 3 isolates were Aeromonas jandaei....

Pyrolysis mass spectrometry was investigated for rapid characterization of food-borne bacterial pathogens. Nine isolates of Vibrio parahaemolyticus and one isolate each of Vibrio fluvialis, Vibrio hollisae, and Vibrio vulnificus were analyzed. Pyrolysis mass spectra, generated via an alternative ionization method, metastable atom bombardment, were...

Thirty multidrug-resistant Enterococcus spp. strains, including two from the milk of cows with mastitis, nine from chicken litter and 19 from turkey litter, were isolated. Twenty-five were identified by biochemical methods as E. gallinarum and five as E. faecalis. Most of the isolates were resistant to vancomycin, gentamicin, streptomycin, tetracyc...

Nineteen fluoroquinolone-resistant Escherichia coli strains were isolated from poultry litter. Sixteen of the 19 strains were serotyped to groups 6, 8, 53, 56, 153, and 174. Three strains were not serotyped to any known group. All isolates were resistant to multiple antibiotics. Most strains were resistant to gentamicin, kanamycin, chloramphenicol,...

Mycobacterium vanbaalenii PYR-1 is capable of degrading polycyclic aromatic hydrocarbons (PAHs) to ring cleavage metabolites. This study identified and characterized a putative phthalate degradation operon in the M. vanbaalenii PYR-1 genome. A putative regulatory protein (phtR) was encoded divergently with five tandem genes: phthalate dioxygenase l...

Mycobacterium vanbaalenii PYR-1 is capable of degrading a number of polycyclic aromatic hydrocarbons (PAHs) to ring cleavage metabolites via multiple pathways. Genes for the large and small subunits of a pyrene dioxygenase, nidA and nidB, respectively, were previously identified in M. vanbaalenii PYR-1 [Appl. Environ. Microbiol. 67 (2001) 3577]. A...

A fast, reliable, and inexpensive Triton X-100 boiling procedure for RNA isolation from both the Gram-positive and Gram-negative bacteria was developed. The yield of RNA was 0.2-2 mg per 10 ml bacterial culture. The method was tested on Gram-positive and Gram-negative bacteria of eight genera and nine species and yielded reproducible results. In pa...

Guillain-Barre Syndrome (GBS) is a neuromuscular disorder and campylobacteriosis is known to trigger the onset of the disorder. A polymerase chain reaction (PCR) protocol was developed that could specifically amplify a 497-bp region of the UDP-galactose 4-epimerase (galE) gene sequence in campylobacters responsible for triggering the onset of GBS....

Polycyclic aromatic hydrocarbon (PAH)-degrading genes nidA and nidB that encode the alpha and beta subunits of the aromatic ring-hydroxylating dioxygenase have been cloned and sequenced from Mycobacterium vanbaalenii PYR-1 [Khan et al., Appl. Environ Microbiol. 67 (2001) 3577-3585]. In this study, the presence of nidA and nidB in 12 other Mycobacte...

Campylobacteriosis, an infectious disease caused by Campylobacter jejuni and Campylobacter coli, is treated by fluoroquinolone antibiotics in clinical practices. However, use of these drugs in animal husbandry may select for fluoroquinolone-resistant campylobacters and, thereby, compromise the clinical treatment of infection. In this study, 21 fluo...

A polycyclic aromatic hydrocarbon (PAH)-utilizing Mycobacterium strain, PYR-1(T), was isolated from petroleum-contaminated estuarine sediments and has been shown by 16S rRNA gene sequencing to be closely related to Mycobacterium aurum ATCC 23366(T) and Mycobacterium vaccae ATCC 15438(T). In this investigation, the 16S rDNA, fatty acid methyl esters...

The epidemiology of four erythromycin-resistant methylase ( erm) genes, ermA, ermB, ermC and msrA, was determined in erythromycin-resistant staphylococci, enterococci and streptococci isolated from poultry litter. All isolates were resistant to multiple antibiotics. Southern hybridization indicated that 4 of the 20 staphylococci contained the ermC...

A Pseudomonas putida capable of degrading polychlorinated biphenyl was also found to transform 4-nitrocatechol to 3-nitro-2-hydroxy-6-oxohexa-2,4-dienoic acid (NHODA). Crude cell extract of this bacterium exhibited an enzyme (nitrocatechol dioxygenase, Ndo) activity catalyzing this transformation. The gene encoding Ndo was cloned in E. coli. The cl...

Outbreaks of Vibrio parahaemolyticus gastroenteritis in the United States (Texas, New York and Pacific Northwest) in 1997-98 emphasized the need to develop molecular methods for identification and differentiation of these organisms. When outbreak isolates were analyzed for the enterobacterial repetitive intergenic consensus sequences, the Texas and...

Identification of predominant human and animal intestinal tract anaerobes by conventional methods is cumbersome, time-consuming and less sensitive as compared to molecular methods. We have developed a molecular technique to identify most of the abundant intestinal microflora by polyermase chain reaction (PCR) amplification of a 16S rRNA gene fragme...

Nineteen fluoroquinolone-resistant Esche- richia coli strains were isolated from poultry litter. Sixteen of the 19 strains were serotyped to groups 6, 8, 53, 56, 153, and 174. Three strains were not serotyped to any known group. All isolates were resistant to multiple anti- biotics. Most strains were resistant to gentamicin, kana- mycin, chloramphe...

Mycobacterium sp. strain PYR-1 degrades high-molecular-weight polycyclic hydrocarbons (PAHs) primarily through the introduction of both atoms of molecular oxygen by a dioxygenase. To clone the dioxygenase genes involved in PAH degradation, two-dimensional (2D) gel electrophoresis of PAH-induced proteins from cultures of Mycobacterium sp. strain PYR...

The structural intermediates in the capsid assembly and DNA packaging pathway of Vibrio vulnificus bacteriophage 71A-6, a rod-shaped double-stranded DNA podovirus, were isolated by ultracentrifugation and studied by electron microscopy, SDS-PAGE and pulsed-field gel electrophoretic analysis. Bacteriophage 71A-6 synthesized rod-shaped capsids (mean...

Reports of antibiotic-resistant bacteria isolated from farms and animal carcasses are raising concerns that antibiotic use in agriculture may play a role in selecting for antibiotic resistance among foodborne bacteria. Emergence of antimicrobial resistance is a very controversial issue. Some contend that the indiscriminate use of antibiotics in agr...

The ermA, ermB, ermC and msrA/msrB genes were detected in multidrug-resistant Staphylococcus spp. strains by PCR. Among 25 human clinical staphylococcal isolates the ermA, ermB, ermC and the msrA/msrB genes were detected in 88, 72, 4 and 100% of the strains, respectively. Among 24 poultry isolates the ermA, ermB, ermC and the msrA/msrB genes were d...

A 81-kDa protein from Mycobacterium sp. strain PYR-1 was expressed in response to exposure of the strain to the polycyclic aromatic hydrocarbon pyrene and recovered by two-dimensional gel electrophoresis. The N-terminal sequence of the protein indicated that it was similar to catalase-peroxidase. An oligonucleotide probe designed from this sequence...

To isolate and characterize erythromycin-resistant methylase genes in multiple-antibiotic resistant staphylococci isolated from milk samples. 300 lactating cows. 23 erythromycin-resistant staphylococci were isolated from milk samples of 300 lactating cows. The prevalence of erythromycin-resistant methylase (erm) genes, ermC and ermA genes, and the...

A polyclonal antibody against microsomes of a fungus, Cunninghamella elegans, was used to screen a C. elegans cDNA library. A cDNA clone, containing an open reading frame (ORF) encoding a protein of 389 amino acids (aa), was obtained. GenBank comparison (BLAST) showed that the protein was closely related to P450 because a heme-binding region, which...

The transfer of ermA and ermC genes, the two most common resistance determinants of erythromycin resistance, was studied with Luria-Bertani broth in the absence of additional Ca(2+) or Mg(2+) ions. Fifteen human and five poultry isolates of Staphylococcus aureus, which were resistant to erythromycin but carried different genetic markers for erythro...

Salmonella typhimurium definitive type 104 (DT104) is a virulent pathogen for humans and animals with many strains having multiple drug resistance characteristics. The organism typically carries resistance to ampicillin, chloramphenicol, florfenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT-resistant). A multiplex PCR method was develop...

A polyclonal antibody was raised against microsomes prepared from Cunninghamella elegans and used to screen a C. elegans cDNA library. A cDNA clone from this screen was obtained, which corresponds to the C. elegans enolase gene. A single open reading frame (ORF) of 1311 bases was found, which encodes a protein of mol. wt 46882.9. The gene was found...

A comparative analysis of the two most dominant erythromycin-resistance determinant genes in Staphylococcus sppnamely, the ermA and ermC genes, was carried out. Sixty erythromycin-resistant strains of Staphylococcus spp. were tested, of which 24 were avian and 36 were clinical isolates. Our results indicated the prevalence of ermA over the ermC gen...

The epidemiology of the two common erythromycin-resistant methylase (erm) genes ermC and ermA was analyzed in 12 coagulase-negative Staphylococcus spp. and 34 coagulase-positive Staphylococcus spp. isolated from chicken. Southern hybridization indicated that only 2 of the 12 coagulase-negative Staphylococcus spp. strains contained the ermC gene on...

An improved, simple, cost-effective and non-radioactive procedure for in-gel hybridization is described for the detection of signal in dried agarose gels. Large and small digoxigenin-labelled DNA and oligonucleotide probes hybridized efficiently and specifically with the complementary DNA sequences in the gel. The signal-to-noise ratios for the gel...

Aeromonas trota is recognized as an important enteropathogen, and its haemolysin (aerolysin) is purported to be one of the virulence factors. Rapid detection and identification of A. trota is important for early and specific diagnosis of the infectious diseases that it causes. Synthetic oligonucleotide primers were used in a polymerase chain reacti...

The fungus, Cunninghamella elegans has been widely used in bioremediation and microbial models of mammalian studies in many laboratories. Using the polymerase chain reaction to randomly amplify the insert directly from the single non-blue plaques of a C. elegans cDNA library, then partly sequencing and comparing with GenBank sequences, we have iden...

A gram-negative, rod-shaped bacterium capable of utilizing L-asparagine as its sole source of carbon and nitrogen was isolated from soil and identified as Enterobacter cloacae. An intracellularly expressed L-asparaginase was detected and it deaminated L-asparagine to aspartic acid and ammonia. High-pressure liquid chromatography analysis of a cell-...

Aeromonas trota AK2, which was derived from ATCC 49659 and produces the extracellular pore-forming hemolytic toxin aerolysin, was mutagenized with the transposon mini-Tn5Km1 to generate a hemolysin-deficient mutant, designated strain AK253. Southern blotting data indicated that an 8.7-kb NotI fragment of the genomic DNA of strain AK253 contained th...