Mohammad holds a Bachelor’s degree in Medical Laboratory Sciences and MSc in Medical Microbiology. He also obtained his PhD, in Microbiology in 2014, followed by postdoctoral training, at the University of Sydney. Given his interest towards teaching he also completed a Graduate Certificate Degree in Educational Studies (Higher Education) in 2015 at the University of Sydney.
During and upon finishing his PhD, he worked on characterising genomic regions that carry antibiotic resistance genes in Acinetobacter baumannii, which is a bacterium that causes a range of hospital acquired infections and is highly resistant to antibiotics. Mohammad’s work on A. baumannii has made significant contribution to increase our understanding on pathways leading to the success of one of the two globally distributed clones of A. baumannii, global clone 1 (GC1). In early 2018, he received the UTS Chancellor’s Postdoctoral Research Fellow (CPDRF) and moved to the University of Technology Sydney where he has begun looking at the biofilm formation of this superbug.
- Professional Member of Australian Society for Microbiology (MASM)
- Member of American Society for Microbiology
Can supervise: YES
Mohammad's research interests are broadly focused on mechanisms of antibiotic resistance in Gram-negative pathogens that are relevant to Public Health. His research involves exploring bacterial genomes to find novel insertion sequences (IS), transposons, integrons and genomic islands to help explain how complex antibiotic resistance islands have been crafted leading to multiply-antibiotic resistance phenotypes.
His general interests include examining genomic diversity, clonality and epidemiology of Acinetobacter baumannii, which is a nosocomial microorganism that causes a range of infections. This organism has now become a global threat due to development of high levels of antibiotic resistance. He is also interested in studying biofilm formation in A. baumannii, which is one of the main factors that makes this microorganism resistant to extreme environmental conditions, e.g. desiccation, allowing it to survive in hospital environments for a very long period of time.
Subject coordinator Infection and Immunity Research 60124
Cummins, ML, Hamidian, M & Djordjevic, ASP 2020, 'Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae.', Microorganisms, vol. 8, no. 2.View/Download from: Publisher's site
Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.
Douraghi, M, Kenyon, JJ, Aris, P, Asadian, M, Ghourchian, S & Hamidian, M 2020, 'Accumulation of Antibiotic Resistance Genes in Carbapenem-Resistant Acinetobacter baumannii Isolates Belonging to Lineage 2, Global Clone 1, from Outbreaks in 2012-2013 at a Tehran Burns Hospital', MSPHERE, vol. 5, no. 2.View/Download from: Publisher's site
Hamidian, M, Lazenby, J, To, J, Hartstein, R, Soares, J, McNamara, S & Whitchurch, CB 2020, 'Complete genome sequence of stenotrophomonas maltophilia Strain CF13, recovered from sputum from an australian cystic fibrosis patient', Microbiology Resource Announcements, vol. 9, no. 32.View/Download from: Publisher's site
© 2020 Hamidian et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Stenotrophomonas maltophilia isolate CF13 is a multidrug-resistant isolate that was recovered in Sydney, Australia, in 2011, from a sputum sample from an individual with cystic fibrosis. The genome sequence of CF13 was completed using long- and short-read technologies.
Hamidian, M & Nigro, SJ 2019, 'Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii.', Microbial genomics, vol. 5, no. 10.View/Download from: Publisher's site
Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of high levels of resistance to many antibiotics, particularly those considered to be last-resort antibiotics, such as carbapenems. Although alterations in the efflux pump and outer membrane proteins can cause carbapenem resistance, the main mechanism is the acquisition of carbapenem-hydrolyzing oxacillinase-encoding genes. Of these, oxa23 is by far the most widespread in most countries, while oxa24 and oxa58 appear to be dominant in specific regions. Historically, much of the global spread of carbapenem resistance has been due to the dissemination of two major clones, known as global clones 1 and 2, although new lineages are now common in some parts of the world. The analysis of all publicly available genome sequences performed here indicates that ST2, ST1, ST79 and ST25 account for over 71 % of all genomes sequenced to date, with ST2 by far the most dominant type and oxa23 the most widespread carbapenem resistance determinant globally, regardless of clonal type. Whilst this highlights the global spread of ST1 and ST2, and the dominance of oxa23 in both clones, it could also be a result of preferential selection of carbapenem-resistant strains, which mainly belong to the two major clones. Furthermore, ~70 % of the sequenced strains have been isolated from five countries, namely the USA, PR China, Australia, Thailand and Pakistan, with only a limited number from other countries. These genomes are a vital resource, but it is currently difficult to draw an accurate global picture of this important superbug, highlighting the need for more comprehensive genome sequence data and genomic analysis.
Hamidian, M, Hawkey, J, Wick, R, Holt, KE & Hall, RM 2019, 'Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1.', Microbial genomics, vol. 5, no. 1.View/Download from: Publisher's site
Resistance to carbapenem and aminoglycoside antibiotics is a critical problem in Acinetobacter baumannii, particularly when genes conferring resistance are acquired by multiply or extensively resistant members of successful globally distributed clonal complexes, such as global clone 1 (GC1) . Here, we investigate the evolution of an expanding clade of lineage 1 of the GC1 complex via repeated acquisition of carbapenem- and aminoglycoside-resistance genes. Lineage 1 arose in the late 1970s and the Tn6168/OCL3 clade arose in the late 1990s from an ancestor that had already acquired resistance to third-generation cephalosporins and fluoroquinolones. Between 2000 and 2002, two distinct subclades have emerged, and they are distinguishable via the presence of an integrated phage genome in subclade 1 and AbaR4 (carrying the oxa23 carbapenem-resistance gene in Tn2006) at a specific chromosomal location in subclade 2. Part or all of the original resistance gene cluster in the chromosomally located AbaR3 has been lost from some isolates, but plasmids carrying alternate resistance genes have been gained. In one group in subclade 2, the chromosomally located AbGRI3, carrying the armA aminoglycoside-resistance gene, has been acquired from a GC2 isolate and incorporated via homologous recombination. ISAba1 entered the common ancestor of this clade as part of the cephalosporin-resistance transposon Tn6168 and has dispersed differently in each subclade. Members of subclade 1 share an ISAba1 in one specific position in the chromosome and in subclade 2 two different ISAba1 locations are shared. Further shared ISAba1 locations distinguish further divisions, potentially providing simple markers for epidemiological studies.
Hamidian, M, Wick, RR, Hartstein, RM, Judd, LM, Holt, KE & Hall, RM 2019, 'Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2', MICROBIAL GENOMICS, vol. 5, no. 10.View/Download from: Publisher's site
Hamidian, M, Wick, RR, Judd, LM, Holt, KE & Hall, RM 2019, 'Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece.', Microbiology resource announcements, vol. 8, no. 41.View/Download from: Publisher's site
Acinetobacter baumannii isolate A388, recovered in Greece in 2002, represents a distinct antibiotic-resistant lineage of global clone 1 (GC1) producing the OXA-58 carbapenemase. We present the complete 4.332-Mbp genome sequence (chromosome plus 1 plasmid), generated by combining long (MinION) and short (Illumina HiSeq) read sequencing data.
Holt, KE, Kenyon, JJ, Hamidian, M, Schultz, MB, Pickard, DJ, Dougan, G & Hall, RM 2019, 'Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.', Microbial genomics, vol. 5, no. 7.View/Download from: Publisher's site
Wyres, KL, Hawkey, J, Hetland, MAK, Fostervold, A, Wick, RR, Judd, LM, Hamidian, M, Howden, BP, Löhr, IH & Holt, KE 2019, 'Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.', The Journal of antimicrobial chemotherapy, vol. 74, no. 3, pp. 577-581.View/Download from: Publisher's site
Recent reports indicate the emergence of a new carbapenemase-producing Klebsiella pneumoniae clone, ST307. We sought to better understand the global epidemiology and evolution of this clone and evaluate its association with antimicrobial resistance (AMR) genes. We collated information from the literature and public databases and performed a comparative analysis of 95 ST307 genomes (including 37 that were newly sequenced). We show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the blaCTX-M-15 ESBL gene and several other AMR determinants. Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance has occasionally emerged.
Hamidian, M & Hall, RM 2018, 'Genetic structure of four plasmids found in Acinetobacter baumannii isolate D36 belonging to lineage 2 of global clone 1.', PloS one, vol. 13, no. 9, pp. e0204357-e0204357.View/Download from: Publisher's site
Four plasmids ranging in size from 4.7 to 44.7 kb found in the extensively antibiotic resistant Acinetobacter baumannii isolate D36 that belongs to lineage 2 of global clone 1 were examined. D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. The smallest plasmid pD36-1 (4.7 kb) carries no resistance genes but includes mobA and mobC mobilisation genes related to those found in pRAY* (pD36-2, 6,078 bp) that also carries the aadB gentamicin, kanamycin and tobramycin resistance gene cassette. These two plasmids do not encode a Rep protein. Plasmid pRAY* was found to be mobilised at high frequency by the large conjugative plasmid pA297-3 but a pRAY* derivative lacking the mobA and mobC genes was not. The two larger plasmids, pD36-3 and pD36-4, encode Rep_3 family proteins (Pfam1051). The cryptic plasmid pD36-3 (6.2 kb) has RepAci1 and pD36-4 (44.7 kb) encodes two novel Rep_3 family proteins suggesting a co-integrate. Plasmid pD36-4 includes the sul2 sulfonamide resistance gene, the aphA1a kanamycin/neomycin resistance gene in Tn4352::ISAba1 and a mer module in a hybrid Tn501/Tn1696 transposon conferring resistance to mercuric ions. New examples of dif modules flanked by pdif sites (XerC-XerD binding sites) that are part of many A. baumannii plasmids were also identified in pD36-3 and pD36-4 which carry three and two dif modules, respectively. Homologs of three dif modules, the sup sulphate permease module in pD36-3, and of the abkAB toxin-antitoxin module and the orf module in pD36-4, were found in different contexts in diverse Acinetobacter plasmids, consistent with module mobility. A novel insertion sequence named ISAba32 found next to the pdif site in the abkAB dif module is related to members of the ISAjo2 group which also are associated with the pdif sites of dif modules. Plasmids found in D36 were also found in some other members of GC1 lineage 2.
Hamidian, M & Hall, RM 2018, 'The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 - Structure, origin and evolution.', Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy, vol. 41, pp. 26-39.View/Download from: Publisher's site
In multiply resistant Acinetobacter baumannii, complex transposons located in the chromosomal comM gene carry antibiotic and heavy metal resistance determinants. For one type, known collectively as AbaR, the ancestral form, AbaR0, entered a member of global clone 1 (GC1) in the mid 1970s and continued to evolve in situ forming many variants. In AbaR0, antibiotic and mercuric ion resistance genes are located between copies of a cadmium-zinc resistance transposon, Tn6018, and this composite transposon is in a class III transposon, Tn6019, carrying arsenate/arsenite resistance genes and five tni transposition genes. The antibiotic resistance genes in the AbaR0 and derived AbaR3 configurations are aphA1b, blaTEM, catA1, sul1, tetA(A), and cassette-associated aacC1 and aadA1 genes. These genes are in a specific arrangement of fragments from well-known transposons, e.g. Tn1, Tn1721, Tn1696 and Tn2670, that arose in an IncM1 plasmid. All known GC1 lineage 1 isolates carry AbaR0 or AbaR3, which arose around 1990, or a variant derived from one of them. Variants arose via deletions caused by one of three internal IS26s, by recombination between duplicate copies of sul1 or Tn6018, or by gene cassette addition or replacement. A few GC2 isolates also carry an AbaR island with different cassette-associated genes, aacA4 and oxa20.
Hamidian, M & Hall, RM 2017, 'Acinetobacter baumannii ATCC 19606 Carries GIsul2 in a Genomic Island Located in the Chromosome', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 61, no. 1.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2017, 'Origin of the AbGRI1 antibiotic resistance island found in the comM gene of Acinetobacter baumannii GC2 isolates.', Journal of Antimicrobial Chemotherapy, vol. 72, no. 10, pp. 2944-2947.View/Download from: Publisher's site
Hamidian, M, Nigro, SJ & Hall, RM 2017, 'Problems with the Oxford Multilocus Sequence Typing Scheme for Acinetobacter baumannii: Do Sequence Type 92 (ST92) and ST109 Exist?', Journal of Clinical Microbiology, vol. 55, no. 7, pp. 2287-2289.View/Download from: Publisher's site
Hamidian, M, Nigro, SJ, Hartstein, RM & Hall, RM 2017, 'RCH51, a multiply antibiotic-resistant Acinetobacter baumannii ST103IP isolate, carries resistance genes in three plasmids, including a novel potentially conjugative plasmid carrying oxa235 in transposon Tn6252.', Journal of Antimicrobial Chemotherapy, vol. 72, no. 7, pp. 1907-1910.View/Download from: Publisher's site
To determine the identity and context of genes conferring antibiotic resistance in a sporadic multiply antibiotic-resistant Acinetobacter baumannii recovered at Royal Children's Hospital, Brisbane.The antibiotic resistance phenotype for 23 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of RCH51 was determined using the Illumina HiSeq platform. Antibiotic resistance determinants were identified using ResFinder. Plasmids were recovered by transformation.Isolate RCH51 belongs to the uncommon STs ST103 IP (7-3-2-1-7-1-4) and ST514 OX (1-52-29-28-18-114-7). It was found to be resistant to sulfamethoxazole, tetracycline, gentamicin, tobramycin and kanamycin and also exhibited reduced susceptibility to imipenem (MIC 2 mg/L) and meropenem (MIC 6 mg/L). RCH51 carries the oxa235 , sul2 , floR , aadB and tet39 resistance genes, all located on plasmids. The largest of the three plasmids, pRCH51-3, is 52 789 bp and carries oxa235 in the ISAba1-bounded transposon Tn 6252 , as well as sul2 and floR . pRCH51-3 represents a new A. baumannii plasmid family that is potentially conjugative as it contains several genes predicted to encode transfer functions. However, conjugation of pRCH51-3 was not detected. The aadB and tet39 resistance genes were each found in small plasmids identical to the known plasmids pRAY*-v1 and pRCH52-1, respectively.The resistance gene complement of RCH51 was found in three plasmids. pRCH51-3, which carries the oxa235 , sul2 and floR resistance genes, represents a new, potentially conjugative A. baumannii plasmid type.
Hamidian, M, Venepally, P, Hall, RM & Adams, MD 2017, 'Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1.', Genome Announcements, vol. 5, no. 35, pp. 1-2.View/Download from: Publisher's site
Extensively antibiotic-resistant Acinetobacter baumannii isolate AB0057 recovered in the United States in 2004 was one of the first global clone 1 isolates to be completely sequenced. Here, the complete 4.05-Mb genome sequence (chromosome and one plasmid) has been revised using Illumina HiSeq data and targeted sequencing of PCR products.
Harmer, CJ, Hamidian, M & Hall, RM 2017, 'pIP40a, a type 1 IncC plasmid from 1969 carries the integrative element GIsul2 and a novel class II mercury resistance transposon.', Plasmid, vol. 92, pp. 17-25.View/Download from: Publisher's site
The 167.5kb sequence of the conjugative IncC plasmid pIP40a, isolated from a Pseudomonas aeruginosa in 1969, was analysed. pIP40a confers resistance to kanamycin, neomycin, ampicillin, sulphonamides and mercuric ions, and several insertions in a type 1 IncC backbone were found, including copies of IS3, Tn1000 and a novel mercury resistance transposon, Tn6182. The antibiotic resistance genes were in two locations. Tn6023, containing the aphA1 kanamycin and neomycin resistance gene, is in a partial copy of Tn1/Tn2/Tn3 (blaTEM, ampicillin resistance) in the kfrA gene, and the sul2 sulphonamide resistance gene is in the integrative element GIsul2 in the position of ARI-B islands. The 11.5kb class II transposon Tn6182 is only distantly related to other class II transposons, with at most 33% identity between the TnpA of Tn6182 and TnpA of other group members. In addition, the inverted repeats are 37bp rather than 38bp, and the likely resolution enzyme is a tyrosine recombinase (TnpI). Re-annotation of GIsul2 revealed genes predicted to confer resistance to arsenate and arsenite, but resistance was not detected. The location of GIsul2 confirms it as the progenitor of the ARI-B configurations seen in many IncC plasmids isolated more recently. However, GIsul2 has integrated at the same site in type 1 and type 2 IncC plasmids, indicating that it targets this site. Analysis of the distribution of GIsul2 revealed that it in addition to its chromosomal integration site at the 3'-end of the guaA gene, it has also integrated into other plasmids, increasing its mobility.
Blackwell, GA, Hamidian, M & Hall, RM 2016, 'IncM Plasmid R1215 Is the Source of Chromosomally Located Regions Containing Multiple Antibiotic Resistance Genes in the Globally Disseminated Acinetobacter baumannii GC1 and GC2 Clones', MSPHERE, vol. 1, no. 3.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2016, 'The resistance gene complement of D4, a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate, resides in two genomic islands and a plasmid', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 71, no. 6, pp. 1730-1732.View/Download from: Publisher's site
Hamidian, M, Ambrose, SJ & Hall, RM 2016, 'A large conjugative Acinetobacter baumannii plasmid carrying the sul2 sulphonamide and strAB streptomycin resistance genes', PLASMID, vol. 87-88, pp. 43-50.View/Download from: Publisher's site
Hamidian, M, Holt, KE, Pickard, D & Hall, RM 2016, 'A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 71, no. 1, pp. 269-271.View/Download from: Publisher's site
Harmer, CJ, Hamidian, M, Ambrose, SJ & Hall, RM 2016, 'Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands', PLASMID, vol. 87-88, pp. 51-57.View/Download from: Publisher's site
Holt, K, Kenyon, JJ, Hamidian, M, Schultz, MB, Pickard, DJ, Dougan, G & Hall, R 2016, 'Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1', MICROBIAL GENOMICS, vol. 2, no. 2.View/Download from: Publisher's site
Holt, KE, Hamidian, M, Kenyon, JJ, Wynn, MT, Hawkey, J, Pickard, D & Hall, RM 2016, 'Genome sequence of Acinetobacter baumannii strain A1, an early example of antibioticresistant global clone 1', Genome Announcements, vol. 3, no. 2.View/Download from: Publisher's site
� 2015 Holt et al. Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to global clone 1 (GC1). Here, we present its complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina), long-read sequencing (PacBio), and manual finishing.
Hamidian, M, Hawkey, J, Holt, KE & Hall, RM 2015, 'Genome sequence of Acinetobacter baumannii strain D36, an antibiotic-resistant isolate from lineage 2 of global clone 1', Genome Announcements, vol. 3, no. 6.View/Download from: Publisher's site
© 2015 Hamidian et al. Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia in 2008 and belongs to a distinct lineage of global clone 1 (GC1). Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4 plasmids), generated via long read sequencing (PacBio).
Hamidian, M, Holt, KE & Hall, RM 2015, 'Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 70, no. 9, pp. 2519-2523.View/Download from: Publisher's site
Hamidian, M, Holt, KE & Hall, RM 2015, 'The complete sequence of Salmonella genomic island SGI1-K', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 70, no. 1, pp. 305-306.View/Download from: Publisher's site
Hamidian, M, Holt, KE & Hall, RM 2015, 'The complete sequence of Salmonella genomic island SGI2', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 70, no. 2, pp. 617-619.View/Download from: Publisher's site
Hawkey, J, Hamidian, M, Wick, RR, Edwards, DJ, Billman-Jacobe, H, Hall, RM & Holt, KE 2015, 'ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data', BMC GENOMICS, vol. 16.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2014, 'pACICU2 is a conjugative plasmid of Acinetobacter carrying the aminoglycoside resistance transposon TnaphA6', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 4, pp. 1146-1148.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2014, 'Resistance to third-generation cephalosporins in Acinetobacter baumannii due to horizontal transfer of a chromosomal segment containing ISAba1-ampC', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 10, pp. 2865-2866.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2014, 'Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 1, pp. 77-80.View/Download from: Publisher's site
Hamidian, M, Holt, KE, Pickard, D, Dougan, G & Hall, RM 2014, 'A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 4, pp. 955-958.View/Download from: Publisher's site
Hamidian, M, Kenyon, JJ, Holt, KE, Pickard, D & Hall, RM 2014, 'A conjugative plasmid carrying the carbapenem resistance gene bla(OXA-23) in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 10, pp. 2625-2628.View/Download from: Publisher's site
Hamidian, M, Wynn, M, Holt, KE, Pickard, D, Dougan, G & Hall, RM 2014, 'Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 2, pp. 557-558.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2013, 'ISAba1 targets a specific position upstream of the intrinsic ampC gene of Acinetobacter baumannii leading to cephalosporin resistance', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 68, no. 11, pp. 2682-2683.View/Download from: Publisher's site
Hamidian, M, Hancock, DP & Hall, RM 2013, 'Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 68, no. 1, pp. 244-245.View/Download from: Publisher's site
Hamidian, M, Nigro, SJ & Hall, RM 2012, 'Variants of the gentamicin and tobramycin resistance plasmid pRAY are widely distributed in Acinetobacter', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 67, no. 12, pp. 2833-2836.View/Download from: Publisher's site
Post, V, Hamidian, M & Hall, RM 2012, 'Antibiotic-resistant Acinetobacter baumannii variants belonging to global clone 1', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 67, no. 4, pp. 1039-1040.View/Download from: Publisher's site
Hamidian, M & Hall, RM 2011, 'AbaR4 replaces AbaR3 in a carbapenem-resistant Acinetobacter baumannii isolate belonging to global clone 1 from an Australian hospital', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 66, no. 11, pp. 2484-2491.View/Download from: Publisher's site
Hamidian, M, Sanaei, M, Azimi-Rad, M, Tajbakhsh, M, Dabiri, H & Zali, M-R 2011, 'fla-typing, RAPD analysis, isolation rate and antimicrobial resistance profile of Campylobacter jejuni and Campylobacter coli of human origin collected from hospitals in Tehran, Iran', ANNALS OF MICROBIOLOGY, vol. 61, no. 2, pp. 315-321.View/Download from: Publisher's site
Hamidian, M, Sanaei, M, Bolfion, M, Dabiri, H, Zali, M-R & Walther-Rasmussen, J 2011, 'Prevalence of putative virulence markers in Campylobacter jejuni and Campylobacter coli isolated from hospitalized children, raw chicken, and raw beef in Tehran, Iran', CANADIAN JOURNAL OF MICROBIOLOGY, vol. 57, no. 2, pp. 143-148.View/Download from: Publisher's site
Hamidian, M, Tajbakhsh, M, Tohidpour, A, Rahbar, M, Zali, MR & Walther-Rasmussen, J 2011, 'Detection of novel gyrA mutations in nalidixic acid-resistant isolates of Salmonella enterica from patients with diarrhoea', INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, vol. 37, no. 4, pp. 360-364.View/Download from: Publisher's site
Hamidian, M, Tajbakhsh, M, Walther-Rasmussen, J & Zali, M-R 2009, 'Emergence of Extended-Spectrum beta-Lactamases in Clinical Isolates of Salmonella enterica in Tehran, Iran', JAPANESE JOURNAL OF INFECTIOUS DISEASES, vol. 62, no. 5, pp. 368-371.
Jafari, F, Hamidian, M, Rezadehbashi, M, Doyle, M, Salmanzadeh-ahrabi, S, Derakhshan, F & Zali, MR 2009, 'Prevalence and antimicrobial resistance of diarrheagenic Escherichia coli and Shigella species associated with acute diarrhea in Tehran, Iran', Canadian Journal of Infectious Diseases and Medical Microbiology, vol. 20, no. 3.View/Download from: Publisher's site
A study was performed to determine the prevalence and antimicrobial resistance of Shigella species and diarrheagenic Escherichia coli isolates cultured from patients with acute diarrhea in Tehran, Iran. Between May 2003 and May 2005, 1120 diarrheal specimens were collected and assayed for bacterial enteropathogens by conventional and molecular methods. Etiological agents were isolated from 564 (50.3%) specimens, and included 305 (54%) E coli, 157 (27.8%) Shigella species, and 102 (18%) from other genera of bacteria. The predominant E coli was Shiga toxin-producing E coli (105 isolates [34.5%]) and the predominant Shigella serotype was Shigella sonnei (88 isolates [56.1%]). A high rate of antibiotic resistance was observed among E coli, with 40 of 53 (75.5%) Shiga toxin-producing E coli isolates resistant to amoxicillin and tetracycline, and eight (5.2%) E coli isolates resistant to more than six antibiotics. Most Shigella isolates were resistant to tetracycline (95%) and trimethoprim- sulfamethoxazole (91.7%), with greatest antibiotic resistance observed among S sonnei (53 of 88 [60.2%] isolates). Antibiotic resistance is widespread in diarrheagenic E coli and Shigella in children with acute diarrhea in Tehran, Iran; hence, updated strategies for appropriate use of antimicrobial agents in Iran are needed. ©2009 Pulsus Group Inc. All rights reserved.
Jafari, F, Shokrzadeh, L, Hamidian, M, Salmanzadeh-Ahrabi, S & Zali, MR 2008, 'Acute diarrhea due to enteropathogenic bacteria in patients at hospitals in Tehran', JAPANESE JOURNAL OF INFECTIOUS DISEASES, vol. 61, no. 4, pp. 269-273.
Mirsalehian, A, Nakhjavani, F, Peymani, A, Jabalameli, F, Mirafshar, SM & Hamidian, M 2008, 'Frequency of extended spectrum β-Lactamase producing Enterobacteriaceae in intensive care units', Tehran University Medical Journal, vol. 65, no. 1, pp. 33-38.
© 2008, Tehran University of Medical Sciences. All rights reserved. Background: The incidence of ESBL producing species have been steadily increased in recent years, resulting in limitation of infection control issues and therapeutic options.The purpose of this study was to evaluate prevalence of Enterobacteriaceae and also assess epidemiology ESBL producing strains isolated from patients admitted in ICUs. Methods: A total of one hundred fifty isolates were collected from urine, sputum, blood, wound and other clinical samples from patient admitted in ICU and then were identified by biochemical tests.All of the samples were screened by DAD method according to The NCCLS Guideline. The species that met NCCLS screening criteria was further tested for Clavulanic Acid effect by confirmatory method. Results: A total of one hundred fifty isolates,133(89.3%) were found to be resistant at least on of the indicators cephalosporin tested according to NCCLS Guideline. 121(80.6%) of the isolates were resistant to all the indicators tested.89(59.3) isolateds were confirmed as ESBL producers. The number of isolates ESBL producing was as follow: Klebsiella pneumoniae 33 (76.74%), E.coli 20 (60.60%), Enterobacter cloacae 8 (47.05%), Citrobacter diversus 6 (54.54%), Enterobacter aerogenes 7 (53.84%), Citrobacter freundii 4 (40%), Klebsiella oxytoca 6 (62.5%), Proteus mirabilis 4 (50%), Serratia marcescens 2 (40%), Proteus Volgaris 0%.All of the isolates sensitive to imipenem. Conclusion: The present study shows high prevalence of ESBL producing Enterobacteriaceae from patients admitted in ICU.The increased rate of these species in most cases due to the administration of inadequate and irrational antimicrobial therapy.To overcome this problem, it needs to develop new antimicrobial agents, limiting the Unnecessary Use of antimicrobial and increasing compliance with infection control issues.
Akbari-Nakhjavani, F, Mirsalehian, A, Hamidian, M, Kazemi, B, Mirafshar, M, Jabal Ameli, F, Pajand, O & Peymani, A 2007, 'Antimicrobial susceptibility testing of Escherichia coli strains isolated from urinary tract infections to fluoroquinolones and detection of gyrA mutations in resistant strains', Daru, vol. 15, no. 2, pp. 94-99.
Widespread uses of fluoroquinolones have resulted in increasing incidences of resistance against these agents all over the world. The aim of this study was to assess, susceptibility of Escherichia coli strains from patients with Urinary Tract Infection against common fluoroquinolones and detection of mutations in the gyrA gene. Antimicrobial susceptibility testing of 164 E.coli isolates from patients with UTI, was evaluated by disk agar diffusion (DAD) and MIC methods. Polymerase chain reaction of E.coli strains were performed by amplification of Quinolone Resistance Determining Region (QRDR) of gyrA gene. PCR products were tested by Conformational Sensitive Gel Electrophoresis (CSGE) and those with hetrodublexes were selected and examined by DNA sequencing. According to disc agar diffusion, 49.3% were resistant to nalidixic acid, 41.4% to norfloxacin, 44.5% to ofloxacin and 40.2 % to ciprofloxacin. By Minimal Inhibitory Concentration (MIC) testing a high-level of resistance (42.1%) to ciprofloxacin was observed. Mutations in codons 83 and 87 in all 81 isolates were positive by CSGE method.
Nakhjavani, FA, Mirsalehian, A, Hamidian, M, Kazemi, B, Mirafshar, M & Jabalameli, F 2007, 'Antimicrobial susceptibility testing for Escherichia coli strains to fluoroquinolones, in urinary tract infections', Iranian Journal of Public Health, vol. 36, no. 1, pp. 89-92.
Background: Urinary Tract Infections (UTIs) are one of the most common infections diseases diagnosed all over the world. Meanwhile most episode of UTIs is caused by Echerichia coli (up to 85%) and frequently fluoroquinolones are preferred as initial agents for empiric therapy of UTIs. Widespread use of fluoroquinolones has resulted in an increasing incidence of resistance these agents all over the world The aim of this study was to assess, susceptibility of Escherichia coli strains from UTI patients against common fluoroquinolones. Methods: Antimicrobial susceptibility testing was determined by disk agar diffusion (DAD) and Minimal Inhibitory Concentration methods as described by the National Committee for Clinical Laboratory Standards (NCCLS). Results: One hundred sixty four clinical isolates of E. coli were collected by urine cultures from patients with UTI. The extent of resistant to nalidixic acid, ofloxacin, norfloxacin and ciprofloxacin, by disk diffusion method was 49.3%, 44.5%, 41.4% and 40.2%, respectively. Resistance to ciprofloxacin by MIC method was 42.1%. Conclusion: This study represents high level resistant of E. coli isolates from UTI patients. It is because of inappropriate and incorrect administration of antimicrobial agents in blind cases. This problem remarks significance of performing antimicrobial susceptibility testing before empiric antibiotic therapy. To overcome this problem use of unnecessary antibiotics therapy should be limited.
Hamidian, M, Wick, R, Hartstein, R, Judd, L, Holt, K & Hall, R 2019, 'Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clone 1 and 2'.
2. Abstract The Acinetobacter baumannii global clone 1 (GC1) isolate AB307-0294, recovered in the USA in 1994, and the global clone 2 (GC2) isolate ACICU, isolated in 2005 in Italy, were among the first A. baumannii isolates to be completely sequenced. AB307-0294 is susceptible to most antibiotics and has been used in many genetic studies and ACICU belongs to a rare GC2 lineage. The complete genome sequences, originally determined using 454 pyrosequencing technology which is known to generate sequencing errors, were re-determined using Illumina MiSeq and MinION (ONT) technologies and a hybrid assembly generated using Unicycler. Comparison of the resulting new high-quality genomes to the earlier 454-sequenced version identified a large number of nucleotide differences affecting protein coding features, and allowed the sequence of the long and highly-repetitive bap and blp1 genes to be properly resolved for the first time in ACICU. Comparisons of the annotations of the original and revised genomes revealed a large number of differences in the protein coding features (CDSs), underlining the impact of sequence errors on protein sequence predictions and core gene determination. On average, 400 predicted CDSs were longer or shorter in the revised genomes and about 200 CDS features were no longer present. 3. Impact statement The genomes of the first 10 A. baumannii strains to be completely sequenced underpin a large amount of published genetic and genomic analysis. However, most of their genome sequences contain substantial numbers of errors as they were sequenced using 454 pyrosequencing, which is known to generate errors particularly in homopolymer regions; and employed manual PCR and capillary sequencing steps to bridge contig gaps and repetitive regions in order to finish the genomes. Assembly of the very large and internally repetitive gene for the biofilm-associated proteins Bap and BLP1 was a recurring problem. As these strains continue to be used for genetic stu...
Wyres, K, Hawkey, J, Hetland, MAK, Fostervold, A, Wick, R, Judd, L, Hamidian, M, Howden, B, Löhr, I & Holt, K 2018, 'Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307'.
Abstract Recent reports indicate the emergence of a new carbapenemase producing Klebsiella pneumoniae clone, ST307. Here we show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the bla CTX-M-15 extended-spectrum beta-lactamase (ESBL) gene plus other antimicrobial resistance determinants. Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance is now emerging.