Iranian Journal of Microbiology
Volume:10 Issue: 2, Apr 2018

Colistin belongs to polymyxin family of antibiotics which are polypeptide bactericidal agents acting mainly by disruption of outer-membrane in Gram-negative bacteria (GNB). This antibiotic group (including polymyxin B and colistin) was approved for clinical use in the late 1950s but fell out of favour soon because of the reported high incidence of nephrotoxicity. With increasing the emergence of extensively-drug resistant (XDR)-GNB and paucity of new marketed antibiotics, polymyxins have recently regained significant clinical interest. They are currently considered as the last-line defense against problematic XDR-GNB notably carbapenem-resistant Enterobacteriaceae (CRE) and Acinetobacter baumannii. Colistin revival in clinical settings has increased the inevitable risk of emerging resistance. Resistance to colistin in GNB is known to be mediated by chemical modification or complete loss of the antibiotic target, LPS. Recently the transmissible plasmid mediated resistance mechanism has been identified in Enterobacteriaceae posing a significant threat to infection control programs. Despite having a very similar chemical structure and indistinguishable antimicrobial activity in vitro, colistin and polymyxin B (PMB) differ mainly in the form administered parenterally. While PMB is administered directly as its active form, colistin is formulated as an inactive prodrug, colistin methanesulfonate (CMS) which itself lacks antibacterial activity and requires to be converted in vivo to colistin in a reaction which occurs slowly and incompletely. As a consequence, plasma concentrations of colistin rise slowly resulting in lower plasma concentrations in renally competent patients. Indeed, it is estimated that only

The antibiotic resistance among Enterococcus faecium strains has increased worldwide. Additionally, biofilm-forming isolates of E. faecium play an important role in human infections. This study was conducted to investigate the prevalence of virulence and antibiotic resistance genes between biofilm-producing and non-biofilm-producing E. faecium strains.
In this study, 228 E. faecium isolates from clinical and environmental specimens were obtained from different wards of hospitals in Lorestan province (Iran). Then, the pattern of antibiotic resistance and minimum inhibitory concentration (MIC) against β-lactams, glycopeptides, aminoglycosides and other common antibiotics was investigated using disk diffusion and agar dilution methods. Biofilm formation was investigated using polystyrene microtiter plates. PCR assay was conducted for antibiotic resistance and biofilm related genes. Pulse field gel electrophoresis (PFGE) was used to determine the clonal spread of isolates.
Most of isolates (78%) were resistant to penicillin, but all were susceptible to linezolid and tigecycline. The biofilm-producing isolates were more resistant to β-lactams, glycopeptides and aminoglycosides compared to non-biofilm-producing strains. In biofilm-producing isolates, pilA, pilB, efaAfm and esp were the dominant virulence genes and vanA and pbp5 genes were the dominant resistant genes. PFGE analysis exhibited a similar pattern between the clinical and environmental isolates, suggesting the presence of a common origin of the infection by E. faecium.
The results of the antibiotic resistance, biofilm assay, and PFGE analysis suggest that there is a common clone of persistent and biofilm-producing strains of E. faecium, which could rapidly disseminate in patients and the environment.

Staphylococcus aureus is an important pathogen that can be colonized in the nose and increase the risk of spreading infections in hospitals. The present study aimed at determining the phenotypic and genotypic characterization of S. aureus strains isolated from patients and healthcare workers (HCWs) from a teaching hospital in Isfahan, Iran.
This cross-sectional study was performed on 262 nasal swabs and 23 clinical isolates that were collected from a teaching hospital during February and April 2016. Staphylococcal cassette chromosome mec (SCCmec) and multilocus sequence typing (MLST) were performed for selected isolates.
Overall, 23% and 18% of healthcare workers and patients were carriers, respectively. Methicillin-resistant S. aureus (MRSA) rate was 13%, 33% and 52% in nasal HCWs, nasal patients, and clinical samples, respectively. The molecular typing of MRSA isolates revealed that the most common SCCmec type is SCCmec type III (88%). The highest rate of resistance was observed against tetracycline and erythromycin, with 48.7%. The most frequently detected toxin genes among S. aureus isolates were hla (99%) and sea (44%), moreover, pvl genes were detected in (40%) of MRSA isolates. The results of MLST showed 7 different sequence types (STs): ST859 (2/9), ST6 (2/9), ST639 (1/9), ST343 (1/9), ST239 (1/9), ST291 (1/9) and ST25 (1/9).
Our results revealed that ST clones associated with healthcare-associated MRSA (HA-MRSA) are actively circulating among nasal carriage in our healthcare setting, and thus, effective infection control policies are needed to reduce nasal carriage in healthcare settings.

Variable number tandem repeat (VNTR) patterns and resistance against three commonly used hospital disinfectants [0.5% (w/w) chlorhexidine digluconate (CHG) and 75% (w/w) alcohol (A), CHG-A; Quaternary ammonium compounds (QACs) and biguanides (B), QAC-B; and 70% (w/w) isopropanol (ISP) and 0.25% (w/w) QACs, ISP-QAC], as well as frequently used antibiotics, were evaluated among 115 Staphylococcus epidermidis blood isolates recovered from a children’s hospital in Tehran, Iran.
Multi-locus variable number tandem repeat analysis (MLVA) was performed using primers targeting 5 VNTR loci on the genome of S. epidermidis isolates. Micro-broth dilution method and detection of qacA/B and smr genes were carried out for evaluating resistance against the disinfectants.
Out of the 115 isolates, 115 (100%) and 113 (98.3%) were susceptible to linezolid and quinupristin/dalfopristin, respectively. A total of 55.7% of the isolates were found to be multidrug resistant (MDR). All isolates had MICs of CHG-A and ISP-QAC of 8 folds lower and MIC of QAC-B 6 folds lower than that suggested by the manufacturers. The genes qacA/B and smr were found in 28 (24.3%) and 14 (12.2%) isolates, respectively. MLVA typing of the S. epidermidis isolates resulted in 106 VNTR patterns and 102 MLVA types for the 112 S. epidermidis isolates, considering that 3 were not typeable.
MLVA typing of S. epidermidis isolates show a great diversity and that the isolates are still susceptible to the concentrations of disinfectants recommended for use by the manufacturers. In addition, the relatively high percentage of the MDR S. epidermidis isolates could cause MDR infections and act as reservoirs to transfer resistance determinants to S. aureus population. Therefore, it is important that suitable infection control strategies are employed to avoid the distribution of MDR isolates between personnel and patients in this medical centre.

Multidrug resistance and in particular, carbapenem resistant Gram-negative bacteria is spreading worldwide at an alarming rate. Among the clinically significant carbapenemases, the New Delhi Metallo-β-lactamase (NDM) is one of the most formidable. NDM efficiently hydrolyses β-lactams and is the last-resort among carbapenems. Hence, therapeutic options for NDM producer bacteria become restricted to a handful of antibiotics. The present study was undertaken to detect the prevalence of the blaNDM-variants Metallo β- lactamases (MBLs) among isolates of Pseudomonas aeruginosa recovered from various clinical samples of hospitalized patients in Baghdad, Iraq.
A total of 100 isolates of Gram-negative bacteria obtained from various clinical samples were subjected to antibiotic susceptibility testing by the disc-diffusion method against meropenem (10 µg), imipenem (10 µg), doripenem (10 µg), polymyxin B (10 µg), colistin (10 µg), amikacin (30 µg), gentamicin (10 µg), aztreonam (30 µg), ciprofloxacin (5 µg), levofloxacin (5 µg), ofloxacin (5 µg), cefepime (30 µg), ceftazidime (30 µg), piperacillin-tazobactam (100\10 µg), tigecycline (15 µg) and tetracycline (10 µg). The results were interpreted according to the guidelines suggested by the Clinical Laboratory Standards Institute. Presence of blaNDM was detected by PCR and it was confirmed by DNA sequencing of the gene present in the isolates that exhibited carbapenem resistance.
In the present study, four isolates of P. aeruginosa carried the blaNDM, three isolates harboured blaNDM-1 and one isolate harboured blaNDM-2. All isolates were resistant to imipenem and meropenem. The blaNDM-1 carrying isolates remained susceptible to colistin and β-lactamase inhibitors piperacillin-tazobactam.
We are reporting emergence of the P. aeruginosa carrying the blaNDM-variant, which exhibited resistance to imipenem and meropenem for the first time in Iraq.

Multidrug resistant Salmonella strains have been observed around the world in recent years. Many mechanisms contribute to the spread of antimicrobial resistance genes. This study aimed at determining the distribution and transmission of class 1, 2 and 3 integrons among MDR Salmonella isolates collected from a selection of chicken broilers in the north of Iran.
PCR assays were used to detect genes for tetracyclines (tetA, tetB and tetG), chloramphenicol (cat1 and floR), and streptomycin (strA). Also, the presence of class 1, 2 and 3 integrons in all MDR isolates was evaluated using specific primers for the integrase genes of integrons intI1, intI2 and intI3.
Class 1, 2 and 3 integrons were present in 36%, 42% and 4% of the MDR isolates, respectively. Out of the tetracyclines resistant isolates, 47 (100%) and 5 (10.6%) carried tetA, tetB genes, respectively, while no isolate was positive for the tetG gene. All 36 chloramphenicol- resistant strains carried floR and cat1 genes. Nine (18%) Salmonella Infantis isolates harbored the strA gene, conferring resistance to sterptomycin.
This study found a high frequency of antimicrobial resistance genes among Salmonella isolates; therefore, management strategies are needed to prevent food-borne diseases caused by MDR Salmonella from food supplies.

There are very few analysis tools to examine seminal fluid specimens, so bacterial infections on male infertility has always been the subject of discussion. These infectious processes lead to deterioration of spermatogenesis, impairment of sperm function, and/or obstruction of the seminal tract. In this study, we aimed at determining the role of bacterial infection on semen parameters including motility, count and normal morphology in infertile male patients.
In this cohort study, 150 infertile males having abnormal semen parameters (study group) and 150 healthy fertile males (control group) were included. A total of 300 semen samples were collected after 3 to 5 days of sexual abstinence. Volume, pH, concentration, normal morphology, and motility were evaluated. Samples were seeded using a calibrated loop on agar and EMB plates, which were incubated overnight. The microorganisms were identified by Gram staining technique, catalase and coagulase tests.
The prevalence of seminal infection among infertile males in Qom was 21%. Among these infected samples 61.9%, 14.28%, 14.28% and 9.25% were contaminated with Staphylococcus aureus, coagulase negative staphylococci, Streptococcus and Escherichia coli, respectively. All the identified bacteria except Streptococcus caused a significant decrease in sperm concentration. Sperm motility was significantly lower in E. coli contaminated samples than in the control group, and the presence of E. coli and S. aureus led to a decline in normal morphology of the sperms.
Sperm bacterial contamination is quite frequent and could contribute to the deterioration of the sperm quality of infertile males.

Paratuberculosis (PTb) (John's disease) is an incurable chronic intestinal infection that mainly affects ruminants. PTb is caused by Mycobacterium avium subspecies paratuberculosis (MAP) with a global distribution. Despite evidences on MAP contribution in Crohn's disease its causal role is still a matter of controversy. In ruminant farming, vaccination is broadly accepted as an effective control measure of PTb. This article describes preparation and field trial of an inactivated PTb vaccine made from the MAP 316F strain.
Formulation of the vaccine was conducted based on the method traditionally used in the UK. Identity of the MAP strain was authenticated by PCR-IS900 and PCR-F57 tests. In the field, a group of 100 lambs (3-8 weeks old) were subcutaneously inoculated with the vaccine preparation under study. These animals, pre-vaccination, were all PTb ELISA negative. Serum level of antibody was determined by ELISA on days 0, 30, 60, 120 and 240, post-vaccination.
In PCR-900 and PCR-F57, the MAP 316F strain produced two fragments of 560 and 704 bp length respectively, a confirmation of its identity as MAP bacterium. In the field trial and at the arranged time intervals, the achieved blood serum levels of antibody, attributable to the vaccine formulation, displayed considerably high values.
Given that the PTb-caused economical losses in the Iranian environment are dramatically high and also the fact that future of state policy on control of PTb remains unknown, we belive vaccination of animals is the best recommendable practice.

Probiotics are defined as live micro-organisms conferring a health benefit on the host. Although most probiotics are bacteria, some yeasts such as Saccharomyces and Kluyveromyces, has been found to have effective probiotic properties. The objective of this study was to isolate and identify indigenous Saccharomyces and Kluyveromyces yeast strains and to compare some probiotic characteristics between these two strains in vitro.
Strains were isolated on yeast glucose chloramphenicol agar medium from 205 samples and identified by morphological, physiological and biochemical assays. The effects of different conditions such as pH and temperature on the survival and growth of the isolates were studied. In addition, resistance to acidic pH (1.5, 2, 3 and 5), pepsin and different concentrations of bile salts (1%, 3% and 5%), as well as proteolytic, lipolytic and hemolytic activity of selected isolates were assessed. Finally, the best isolates were selected for investigation of their viability in samples of dairy products.
126 isolates were identified using biochemical and molecular techniques as yeast strains. Five isolates were found to have effective probiotic properties, belonging to Kluyveromyces marxianus (S97, S101 and S106) and Saccharomyces cerevisiae (S28, S34). These isolates were able to grow at 37°C, pH=1.5, withstand to concentration of 5% oxbile and pepsin and exhibit the proteolytic activity. The isolates of K. marxianus showed better viability in dairy (yogurt).
In the in-vitro comparative experiments, the isolates of K. marxianus showed better probiotic potentials.

Rare actinomycetes are a promising source of novel metabolites of pharmaceutical importance. The current study focussed on selective isolation of specific genera of rare actinomycetes and screening the isolates for biosynthetic genes particularly polyketide synthases (PKS) and non ribosomal peptide synthetases (NRPS).
The soil samples were subjected to various pre-treatments like 1.5% phenol treatment, 0.3% chloramine T treatment, benzethonium chloride treatment, etc. and plated on selective media supplemented with specific antibiotics targeting rare genera of actinomycetes. The putative rare actinomycete isolates were screened for bioactivity using agar cross streak method and agar well diffusion method. The ability of the isolates to produce anti-quorum sensing compounds was tested against Serratia marcescens. The isolates were also screened for the presence of biosynthetic gene clusters associated with PKS-I, PKS-II and NRPS pathways using the degenerate primer sets K1F-M6R, KSα/KSβ and A3F-A7R, respectively. The expression of these gene clusters was tracked by physicochemical screening of the extracts of isolates using spectroscopic and chromatographic techniques.
In this study, 1.5% phenol treatment was found to be the most promising followed by heat treatment and chloramine treatment. Our studies showed that ISP5 agar was the best for isolation of rare genera followed by ISP7, Starch Caesin agar and ISP2 supplemented with antibiotics like gentamicin, nalidixic acid and streptomycin. Micromonospora was the most abundant genus followed by Dactylosporangium. Actinomadura, Nocardiopsis and Actinoplanes were almost equal in number. Primary screening showed that 92% of the isolates were active against one of the test organisms. Thirty seven isolates were found to produce anti-quorum sensing (QS) compounds. NRPS sequences were detected in thirty nine isolates (42.8%), whereas PKS-I and PKS-II sequences were detected in seventeen and twenty eight strains (18.6% and 30.7%), respectively.
Nine type I and type II polyketide-producing isolates as well as six peptide-producing isolates were found. The peptide extract of isolate KCR3 and a polyketide extract of isolate NCD10 were found to possess anti-tumor activity exhibiting an IC50 value of 3 μg/ml and 2.5 μg/ml against HeLa cells.

Cytomegalovirus (CMV) infection is the most common viral opportunistic infection causing gastrointestinal diseases such diarrhea and colitis in immunocompromised patients. The development and performance of a robust and sensitive PCR assay are usually evaluated to detect CMV DNA in human fecal specimens. In this study, our aim was to detect CMV DNA in stool samples taken from patients with HIV/AIDS, cancer, and transplant recipient patients with chronic and persistent diarrhea using a non-invasive method.
A total of 633 immunocompromised patients (451 males and 182 females) suffering from persistent or chronic diarrhea were included in this study. Among them, 392 were HIV/AIDS patients, 151 had cancer and were receiving chemotherapy, and 90 were recipients of a solid organ or bone marrow transplant. CMV genome was extracted from the stool samples using phenol: chloroform: isoamyl alcohol method. CMV DNA was identified by polymerase chain reaction using sequence specific primers on genomic DNA.
Looking at the frequency of CMV DNA in 392 HIV/AIDS patients, we found that only 5 patients (1.27%) were positive for CMV genome, while this frequency was 4.63% (7/151) and 5.5% (5/90) in patients with cancer receiving chemotherapy and in those with solid organ or bone marrow transplant, respectively.
The results of this study revealed that the cause of chronic or persistent diarrhea in HIV/AIDS, cancer, and graft recipient patients might be related to CMV infection. Accordingly, we recommend a non-invasive method, such as stool sample, as a first line of diagnosis of enteritis when the physician suspects that a patient has CMV infection.