Shigella: Antibiotic-Resistance Mechanisms And New Horizons For Treatment

Shigella spp. are a common cause of diarrheal disease and have remained an important pathogen responsible for increased rates of morbidity and mortality caused by dysentery each year around the globe. Antibiotic treatment of Shigella infections plays an essential role in reducing prevalence and death rates of the disease. However, treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. Drug resistance in Shigella spp. can result from many mechanisms, such as decrease in cellular permeability, extrusion of drugs by active efflux pumps, and overexpression of drug-modifying and -inactivating enzymes or target modification by mutation. Therefore, there is an increasing need for identification and evolution of alternative therapeutic strategies presenting innovative avenues against Shigella infections, as well as paying further attention to this infection. The current review focuses on various antibiotic-resistance mechanisms of Shigella spp. with a particular emphasis on epidemiology and new mechanisms of resistance and their acquisition, and also discusses the status of novel strategies for treatment of Shigella infection and vaccine candidates currently under evaluation in preclinical or clinical phases.

Study of genetic diversity, biofilm formation, and detection of Carbapenemase, MBL, ESBL, and tetracycline resistance genes in multidrug-resistant Acinetobacter baumannii isolated from burn wound infections in Iran

Background

Antimicrobial resistance in multidrug-resistant Acinetobacter baumannii (MDR-AB) isolated from burn wound infections is a major concern in intensive care or burns units worldwide, and molecular studies are considered critical strategies for control of MDR-AB outbreaks in this regard. Thus, in this study, antibiotic resistance, biofilm-forming ability, molecular epidemiology of MDR A. baumannii strains recovered from patients with burns were investigated in three major hospital centers of Iran.

Methods

In this cross-sectional research, 163 non-repetitive A. baumannii strains were tested for susceptibility to antimicrobial agents. Polymerase chain reaction (PCR) was performed to characterize ambler classes A, B, and D β-lactamases, ISAba1 and integrons, biofilm formation was also investigated. Clonal relatedness was analyzed using Pulsed-Field Gel Electrophoresis (PFGE).

Results

Among 163 A. baumannii strains collected, 94.5% of them were Carbapenem-Non-Susceptible A. baumannii (CNSAB) and also 90.1 and 52.2% of them were Metallo-β-Lactamases (MBL) and Extended-Spectrum β-Lactamases (ESBL) producing isolates, respectively. Colistin and polymyxin B exhibited excellent activity against CNSAB strains. High prevalence of bla_{OXA − 23-like} (85.1%), bla_VIM (60.5%), bla_{PER − 1} (42.3%), tetB (67.8%), and Class 1 integrons (65.6%) were identified in CNSAB strains. ISAba1 element was associated with 42 (25.8%) and 129 (98.5%) of bla_OXA-51-like and bla_OXA-23-like genes, respectively. 6 clusters with the ability to form strong biofilms were found to be dominant and endemic in our entire areas.

Conclusions

Results of the present study show that antimicrobial resistance in CNSAB isolates from burn wound infections in monitored hospitals in Iran is multifactorial, and also findings of the study suggested that local antibiotic prescription policies should be regularly reviewed, and efficient infection control measures should be observed. Therefore, further strengthening of surveillance of antimicrobial resistance is urgently needed in these regions.

Investigating of four main carbapenem-resistance mechanisms in high-level carbapenem resistant Pseudomonas aeruginosa isolated from burn patients

BACKGROUND

Pseudomonas aeruginosa is an opportunistic pathogen involved in many infections. Carbapenem-resistant P.aeruginosa has emerged as an important cause of infection in different hospitals worldwide. We aimed to determine frequencies of the four main resistance mechanisms [metallo-beta lactamase (MBL) production (bla_IMP, bla_VIM, bla_SPM and bla_NDM), overproduction of the MexAB-OprM and MexXY efflux pumps, overproduction of chromosome-encoded AmpC β-lactamase, and reduced OprD expression] in high-level carbapenem-resistant P.aeruginosa isolated from patients with burns.

METHODS

In a descriptive study, 107 P. aeruginosa isolates were collected from patients with burn injuries and tested for antibiotic susceptibility, by an E-test for carbapenems, an E-test for metallo-β-lactamase producer isolates, and PCR to detect MBL genes. Furthermore, high-level carbapenem-resistant isolates were tested by real-time PCR for the expression levels of the mexB, mexY, ampC, and oprD genes.

RESULTS

Amongst all P. aeruginosa isolates, 78.5%, 46.7%, and 15% were imipenem-, meropenem-, and doripenem-resistant, respectively; 72% of isolates were multidrug-resistant. The bla_IMP and bla_VIM genes were detected in 17.9% and 1.2% of isolates; respectively. The bla_SPM and bla_NDM genes were not observed. Among the resistant isolates, mexB overexpression (63.2%) was the most frequent mechanism, followed by mexY overexpression (52.6%), ampC overexpression (36.8%), and reduced oprD expression (21.1%).

CONCLUSION

Emerging antimicrobial resistance in burn wound bacterial pathogens is a serious therapeutic challenge for clinicians. In the present study, most of the isolates were MDR. This finding indicated an alarming spread of resistant isolates and suggested that infection control strategies should be considered. Resistance to carbapenems is influenced by several factors, not all of which were evaluated in our study; however, the results showed that production of MBLs and overexpression of the mexB gene were the most frequent mechanisms in carbapenem-resistant isolates.

Viral Coinfection among COVID-19 Patient Groups: An Update Systematic Review and Meta-Analysis

BACKGROUND

Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients.

METHODS

We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies.

RESULTS

Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively.

CONCLUSION

The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.

Evaluation of GeneXpert MTB/RIF for determination of rifampicin resistance among new tuberculosis cases in west and northwest Iran

Despite a Mycobacterium tuberculosis control programme and anti-tuberculosis drugs, drug-resistant tuberculosis (DR-TB) is one of the most serious public health issues worldwide. Rapid laboratory diagnosis of M. tuberculosis is needed for the diagnosis of multidrug-resistant (MDR) TB and to find the optimal treatment protocol. The purpose of this study was to detect resistance to rifampicin in new cases of TB using the GeneXpert MTB/RIF (M. tuberculosis/rifampicin) assay and the standard proportional method in west and northwest Iran. In this descriptive cross-sectional study, sputum samples were enrolled and screened for M. tuberculosis using Ziehl–Neelsen stain and mycobacterial culture. Samples from individuals with smear-positive TB were cultured on Lowenstein–Jensen medium; afterwards, the presence of resistance to rifampicin was examined by the GeneXpert MTB/RIF and standard proportional methods. A total of 400 new cases of suspected TB were collected, 162 (40.5%) of which were smear- and culture-positive for M. tuberculosis. The frequencies of rifampicin resistance in new smear-positive TB cases were 3.1% and 4.3% for GeneXpert and standard proportional method, respectively. Sensitivity and specificity of GeneXpert were 71% and 100%, respectively, compared with the proportional method. GeneXpert can be a quick and helpful method for the diagnosis of rifampicin-resistant TB in regions with high rates of DR-TB or MDR-TB. GeneXpert MTB-RIF assay must be used as an early diagnostic method whose results must be confirmed by the standard proportional method. The GeneXpert and proportional methods complement but do not replace each other.

Dissemination of carbapenem-resistant Acinetobacter baumannii in patients with burn injuries

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii has emerged as an important cause of infection in burn patients. This study aimed to characterize the antimicrobial susceptibility pattern, determine the prevalence of oxacillinase and metallo-beta-lactamase (MBL) genes, and type the A. baumannii isolates obtained from burn patients.

METHODS

During a 1-year period, a total of 40 nonduplicated isolates of A. baumannii were obtained from burn patients who were hospitalized in the Taleghani Burn Hospital in Ahvaz, in the southwest of Iran. Testing for antimicrobial susceptibility was carried out by disk diffusion and E-test. To screen MBL production, a double disk synergy and MBL E-test were performed. The presence of bla_OXA-23-like, bla_OXA-24-like, bla_OXA-51-like and bla_OXA-58-like, bla_VIM, bla_IMP and bla_SPM, and bla_NDM was sought by polymerase chain reaction (PCR). Repetitive extragenic palindromic sequence-based PCR was carried out for determination of isolates clonality.

RESULTS

Overall, 92.5% of isolates were carbapenem-resistant. Polymyxin B, colistin, and ampicillin-sulbactam were the most effective agents in vitro, with a susceptibility rate of 100%, 97.5%, and 72.5%, respectively. According to the double disk synergy and E-test, 55.6% and 97.3% of isolates were MBL producers, respectively. Furthermore, 70% of isolates harbored bla_OXA-23-like and 20% were positive for bla_OXA-24-like. However, no encoding genes were detected for bla_VIM, bla_IMP and bla_SPM, bla_NDM, and bla_OXA-58-like. Repetitive extragenic palindromic sequence-based PCR revealed that carbapenem-resistant isolates belonged to four clones, including A, B, C, and D; the predominant clones were B and C.

CONCLUSION

The rate of carbapenem resistance was high, and it appeared that bla_OXA-23-like and bla_OXA-24-like contributed to the carbapenem resistance of A. baumannii isolates. This result suggests that the two predominant clones of A. baumannii were spread among burn patients. In order to prevent future dissemination of resistant isolates among burn patients, an effective infection control plan is necessary.

Worldwide prevalence of microbial agents' coinfection among COVID-19 patients: A comprehensive updated systematic review and meta-analysis

BACKGROUND

To provide information about pathogens' coinfection prevalence with SARS-CoV-2 could be a real help to save patients' lives. This study aims to evaluate the pathogens' coinfection prevalence among COVID-19 patients.

METHOD

In order to find all of the relevant articles, we used systematic search approach. Research-based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID-19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed.

RESULTS

A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID-19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95-26.46; I2 : 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I2 : 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity.

CONCLUSION

We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

Frequency of quinolone resistance genes among extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains isolated from urinary tract infections

Background

As an opportunistic pathogen, Escherichia coli (E. coli) is widely recognized as the main cause of nosocomial infections as well as some disorders especially those associated with urinary tract infections (UTIs). This study, therefore, sets out to determine the extent of antibiotic resistance to quinolones and to measure the frequency of qnr genes (A, B, and S) within extended-spectrum beta-lactamase (ESBL) and non-ESBL-producing strains of E. coli isolated from UTI-diagnosed patients as well as to investigate their antimicrobial susceptibility patterns for some selected antibiotics in southwest Iran.

Methods

Two hundred E. coli strains were isolated from UTI-diagnosed patients, hospitalized in nine different wards of Ahvaz Golestan Hospital between November 2015 and March 2016. The isolates were confirmed through well-practiced phenotypical methods. Moreover, the antimicrobial susceptibility test was successfully performed using a disk diffusion method. ESBL production among the isolates was screened by double disk synergism test (DDST), and the qnr genes were identified using a multiplex PCR.

Results

Out of the 200 samples collected, 167 isolates were confirmed to be E. coli strains. Maximum and minimum resistance were reported against nalidixic acid and chloramphenicol with 65.3% and 17.4%, respectively. Most of the isolates were resistant to all three types of quinolones studied in this research. Using multiplex PCR, the qnr genes were found in 100 (59.88%) strains (qnrA = 10, qnrB = 21, qnrS = 41, qnrB-S = 21, qnrB-A = 1, qnrA-S = 3, qnrA-B-S = 3), 58% of which was found among ESBL-producing isolates.

Conclusions

Resistance to quinolones antibiotics was highest among ESBL-producing isolates harboring, especially qnrS among other determinants of the qnr gene. There is a need for sensitive antibiotic stewardship especially in hospitals of Ahvaz, Khuzestan province. Further research is needed to ascertain the gravity of quinolones resistance in Iran and to quickly act against its spread among other nosocomial pathogens.

Prevalence of nontuberculous mycobacteria and high efficacy of d-cycloserine and its synergistic effect with clarithromycin against Mycobacterium fortuitum and Mycobacterium abscessus

Background

The prevalence of pulmonary disease caused by nontuberculous mycobacteria (NTM) is reportedly on the rise in the world. Some of the species are resistant to various antibiotics; hence, limited treatment options are available. The aims of this study were to investigate the prevalence of NTM and to determine the effect of d-cycloserine against Mycobacterium fortuitum and Mycobacterium abscessus isolated from clinical specimens to find out the synergistic effect of d-cycloserine and clarithromycin.

Methods

A total of 95 nonduplicate pulmonary isolates of NTM were collected from three major Regional Tuberculosis (TB) Centers. NTM isolates were identified by conventional tests and PCR sequence analysis of the rpoB gene. PCR sequencing of erm-41 was performed for detecting the inducible resistance to macrolides. In vitro susceptibilities and activities of d-cycloserine-clarithromycin combinations were accessed using the broth microdilution method.

Results

Among 714-positive acid-fast bacilli from TB-suspected cases, 95 isolates were identified as NTM (13.3%). The prevalence of identified isolates was as follows: M. fortuitum 46 (48.4%), Mycobacterium simiae 16 (16.8%), Mycobacterium kansasii 15 (15.7%), M. abscessus 7 (7.3%), Mycobacterium thermoresistibile 4 (4.2%), Mycobacterium elephantis 3 (3.2%), Mycobacterium porcinum 2 (2.1%), and Mycobacterium chimaera 2 (2.1%). In addition, rpoB sequence analysis could identify all NTM isolates. The effect of d-cycloserine was better than that of clarithromycin. The synergistic effect of d-cycloserine with clarithromycin was observed for six (100%) and five (71.5%) strains of M. fortuitum and M. abscessus, respectively.

Conclusion

In the present study, we demonstrated a wide range of NTM in processed samples from different provinces of Iran. Our observations indicated that d-cycloserine was very active against M. abscessus and M. fortuitum; hence, d-cycloserine, either alone or in combination with clarithromycin, may be promising for the treatment of M. abscessus- and M. fortuitum-associated diseases.

Anti tuberculosis drug resistance in west of iran

Background and Objective:

Mycobacterium tuberculosis has developed resistance to antituberculosis drugs and becoming a major and alarming public health problem in worldwide. This study was aimed to determine antituberculosis drug resistance rate and to identify multidrug resistant tuberculosis (MDR-TB) in West of Iran.

Materials and Methods:

Of 130 samples were included between December 2011 and July 2012 in the study from that 112 cases were M. tuberculosis. The proportional method was carried out according to the Clinical and Laboratory Standards Institute on Lowenstein-Jensen against isoniazid, rifampicin, streptomycin, ethambutol, pyrazinamide, para aminosalicylic acid, ethionamide, cycloserine (CYC). The microdilution method was carried out using 7H9 broth with 96 well-plates.

Results:

From 112 isolates, resistance was observed to isoniazid 18 (16.07%), rifampicin 16 (14.28%), streptomycin 25 (22.32%), ethambutol 15 (13.39%), pyrazinamide 27 (24.10%), para aminosalicylic acid 19 (16.96%), CYC 4 (3.57%), and ethionamide 14 (12.5%) cases. 16 isolates were MDR.

Conclusion:

The high prevalence of MDR-TB in our study is assumed to be due to recent transmission of drug-resistant strains. Overall, the rate of drug resistance in our study was high, which is in line with findings of some high-burden countries. Hence that early case detection, rapid drug susceptibility testing, and effective anti-TB treatment is necessary.

Genotyping of coa and aroA Genes of Methicillin-Resistant Staphylococcus aureus Strains Isolated From Nasal Samples in Western Iran

Background:

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen frequently isolated in both hospital and community environments. Methicillin-resistant Staphylococcus aureus is considered a major nosocomial pathogen that causes severe morbidity and mortality.

Objectives:

The main objective of this study was to determine the genotypes of MRSA strains isolated from the nares of hospitalized and community patients in Kermanshah Hospital, western Iran, by PCR-restriction fragment length polymorphism (PCR-RFLP).

Materials and Methods:

Of 1387 patients, 1217 patients were screened for more than 48 hours after admission in hospital wards and 170 patients were screened in the hemodialysis unit of Kermanshah Hospital, which is the largest hospital in western Iran. S. aureus was identified by standard biochemical tests, including colonial morphology, production of coagulase, and DNase and the API20 Staph test. Methicillin-resistant Staphylococcus aureus was identified by the Oxacillin strip test.

Results:

In total, 258 S. aureus isolates were recovered from 1387 samples, of which 96 isolates were MRSA, 82 were hospital acquired, and 14 were community acquired. Digestion of the aro A gene revealed only one distinctive RFLP pattern in the 258 isolates.

Conclusions:

Methicillin-resistant Staphylococcus aureus is an increasingly common cause of nosocomial infections. Our results are in agreement with those of other studies reporting that a few specialized clones are responsible for most cases of MRSA nasal carriage. In this study, MRSA strains isolated from different wards of hospital were closely related when analyzed by coagulase gene typing. Identifying patients colonized with MRSA during hospitalization and rapidly typing them with these methods may facilitate detection of outbreaks and prevention of the spread of organisms in hospitals.

Genotyping of multidrug-resistant strains of Pseudomonas aeruginosa isolated from burn and wound infections by ERIC-PCR

PURPOSE

To determine the genetic diversity of MDR P. aeruginosa strains isolated from burn and wound infections in Ahvaz, Iran, by ERIC-PCR.

METHODS

From total 99 strains of P. aeruginosa defined as MDR by using drug susceptibility testing, 66 were subjected to ERIC-PCR analysis, comprises 53 strains isolated from burn infection, and 13 randomly selected strains from wound infection with higher resistance to combinations of more numbers of drugs.

RESULTS

Eight clusters (I to VIII), and 50 single clones were generated for tested MDR isolates analyzed by ERIC-PCR. The high heterogeneity was observed among the isolates from burn infections including 16 isolates which were categorized in eight clusters and 37 single clones. The isolates in clusters II, III, VI, VIII showed 100% similarity.

CONCLUSIONS

The high level of genotypic heterogeneity in P. aeruginosa strains demonstrated no genetic correlation between them. Extremely high drug resistance in isolates from burn, suggests that efficient control measures and proper antibiotic policy should be observed.

Association between depression with glycemic control and its complications in type 2 diabetes

AIMS

This study aims to determine the association between depression with glycemic control (HbA1c) and its complications.

MATERIALS AND METHODS

This was a cross-sectional study that included 514 diabetic patients. The patients were randomly selected from among all type 2 diabetes patients referred to health and medical centers in Khorramabad town (Iran). Two questionnaires used for data collection. The first questionnaire included demographic information, diabetes and its complications and the second questionnaire was Beck Depression Inventory (BDI-II) which was used to assess depression. The stata software version 14 was used for data analysis. Then, for evaluate the association between depression with glycemic contol and its complications, Univariate and multiple logistic regression analysis were employed.

RESULTS

The prevalence of depression in diabetic patients under study was 46.3% and for female and male was 49.6 and 36.8%; respectively. The results showed that 48.6% of diabetic patients did not have appropriate glycemic control status (HbA1c > 8). There was no significant association between glycemic control expressed as HbA1c levels and depression (OR: 1.11, 95% CI: 0.87-1.57). By contrast, sex (OR: 2.03, CI 95%: 1.03-3.99), residence (OR: 1.92, 95% CI: 1.28-2.91) and sexual complications (OR: 5.54, 95% CI: 1.07-27.87) have a significant statistical association with depression.

CONCLUSION

The study highlights the high prevalence of depression in diabetic patients. However, there was no significant association between depression and glycemic control. The implementation of mental health screening for rapid diagnosis and timely treatment of depression seems essential in diabetic patients.

Effectiveness of breastfeeding education on the weight of child and self-efficacy of mothers - 2011

BACKGROUND

Breastfeeding is the most natural and essential way for feeding newborn babies. This is an ideal approach for physical and emotional development of babies, as well as for the recovery of mothers. This study was aimed to determine the effect of breastfeeding education based on the health belief model (HBM) toward primiparous women.

MATERIALS AND METHODS

In a case-control group, quasi-experimental study, 88 subjects were allocated in control and experimental groups. Subjects who were assigned to the experimental group were provided a program consisting of group education based on HBM during their prenatal period. Instrument for data gathering was made by the researchers and standard questionnaire from Dennis and Faux for Breastfeeding Self-efficacy Scale (BSES). Baseline interviews were conducted before delivery and follow-up visits were conducted after 30 days and at the fourth month after delivery. Data were analyzed using SPSS (version 16) with c(2), independent sample t-tests, and paired t-test.

RESULTS

Mean age of pregnant women who participated in the study was 22 ± 3.29 years. After the program, the experimental group had significantly better scores in terms of self-efficacy, knowledge, and attitude scores statistically. In the fourth month, the mean of child weight in the experimental group was significantly higher than that of the control group (P=0.001) and exclusive breastfeeding was significantly higher than in the control group (P=0.007).

CONCLUSION

Prenatal education in this study based on HBM was successful, and knowledge, attitude, self-efficacy, and related indicators improved. The necessity of producing standard education package and education of pregnant mothers, especially in their first pregnancy, by health professionals is perceived.

Frequency of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis Strains Isolated from Patients in West of Iran

BACKGROUND AND OBJECTIVE

Tuberculosis (TB) is a devastating infectious disease causing high mortality and morbidity worldwide. The most serious threat related to tuberculosis control is the recent emergence of drug-resistant tuberculosis strains. The aim of the present study was to identify various types of mutations in the rpoB region in rifampicin-resistant strains isolated from sputum of tuberculosis patients.

MATERIALS AND METHODS

Drug susceptibility of 125 Mycobacterium tuberculosis isolates was determined using the CDC standard conventional proportional method. Target DNA of M. tuberculosis was amplified by polymerase chain reaction, hybridized, and scanned. We used the low cost density array (LCD-array) to detect mutations within the 90-bp rpoB region. Each array is a transparent, prestructured polymer support using a nonfluorescent detection principle based on the precipitation of a clearly visible dark substrate.

RESULTS

Of the 125 M. tuberculosis isolates, 35 (28%) were found to be rifampicin-resistant and using the LCD array revealed point mutations at nine different codons as follows: S512T (AGC→ACC) (20%), D516V (GAC→GTC) (20%), H526D (CAC→GAC) (6%), H526R (CAC→CGC) (20%), H526Y (CAC→TAC) (23%), and S531W (TCG→TGG) (8%), and the most frequent site mutations were L511P (CCG→CTG) (46%), followed by S531l (TCG→TTG) (40%) and D516Y (GAC→TAC) (26%).

CONCLUSION

Our data significantly differs from previously reported mutation frequencies for codon 526 (CAC to GAC) among Italian isolates (40.1%) and Greek isolates (17.6%). Phenotypic testing is time-consuming and requires laboratory resources. Microarray rpoB is useful in detecting rifampicin resistance-determining region-associated site mutations of rifampicin-resistant M. tuberculosis isolates.

Identification of Carbapenem-Resistant Klebsiella pneumoniae with Emphasis on New Delhi Metallo-Beta-Lactamase-1 (blaNDM-1) in Bandar Abbas, South of Iran

BACKGROUND AND OBJECTIVE

The spread of carbapenem-resistant Klebsiella pneumoniae especially bla_NDM-1-carrying isolates is a great concern worldwide. In this study we describe the molecular basis of carbapenem-resistant K. pneumoniae in three teaching hospitals at Bandar Abbas, south of Iran.

MATERIALS AND METHODS

A total of 170 nonduplicate clinical isolates of K. pneumoniae were investigated. Antimicrobial susceptibility test was performed by disc diffusion method. PCR was carried out for detection of carbapenemase (bla_KPC, bla_IMP, bla_VIM, bla_NDM, bla_SPM, bla_OXA-48, and bla_OXA-181) and extended-spectrum β-lactamase (bla_CTX-M, bla_SHV, bla_TEM, bla_VEB, bla_GES, and bla_PER). Clonal relatedness of bla_NDM-1-positive isolates was evaluated by multilocus sequence typing (MLST).

RESULTS

Tigecycline was the most effective antimicrobial agent with 96.5% susceptibility. In addition, 6.5% of the isolates were carbapenem resistant. Bla_NDM-1 was identified in four isolates (isolate A-D) and all of them were multidrug-resistant. MLST revealed that bla_NDM-1-positive isolates were clonally related and belonged to two distinct clonal complexes, including sequence type (ST) 13 and ST 392. In addition to bla_NDM-1, isolate A coharbored bla_SHV-11, bla_CTX-M-15, and bla_TEM-1, isolate B harbored bla_SHV-11 and bla_CTX-M-15, and isolates C and D contained both bla_SHV-1 and bla_CTX-M-15.

CONCLUSION

Our results indicate that NDM-1-producing K. pneumoniae ST 13 and ST 392 are disseminated in our region. Moreover, one of our major concerns is that these isolates may be more prevalent in the near future. Tracking and urgent intervention is necessary for control and prevention of these resistant isolates.

A review on EBV encoded and EBV-induced host microRNAs expression profile in different lymphoma types

Previous literature supports the variations in microRNAs expression levels among lymphoma patients due to EBV infection. These alterations can be observed in both EBV-encoded-microRNAs and EBV-induced cellular microRNAs. Moreover, changes in the microRNA profile could be significant in disease progression. This study aimed to assess published literature to obtain a microRNA profile for both EBV-encoded microRNAs and EBV-induced cellular microRNAs among lymphoma patients. We searched common available electronic databases by using relevant keywords. The result demonstrated that EBV infection could alter the microRNA expression levels among lymphoma patients. In Burkitt lymphoma, hsa-miR197 and miR510 were most frequently assessed human micro RNAs. Also, miR-BART6-3P and miR-BART17-5P were the most frequent viral micro RNAs in Burkitt lymphoma. Other human important micro RNAs were hsa-miR155 (in Diffuse large B cell lymphoma (DLBCL)), hsa-miR145 (in Nasal natural killer T cell lymphoma (NNKTCL)), miR-96, miR-128a, miR-128b, miR-129, and miR-205 (in Classic Hodgkin lymphoma (CHL)), miR-21, miR-142-3P, miR-126, miR-451 and miR-494-3P (in Nasal natural killer cell lymphoma (NNKCL)). Also, viral assessed micro RNAs were miR-BART1-5P (in DLBCL and NNKTCL), miR-BART-5 (in CHL), and EBV-miR-BART20-5P (in NNKCL). In conclusion, it could be suggested that EBV-encoded-microRNAs and EBV-induced cellular-microRNAs can be utilized as helpful factors for different types of lymphoma diagnoses or prognostic factors. Moreover, the mentioned microRNAs can also be promising therapeutic targets and can be used to modulate the oncogenes.

Comparison of different phenotypic and genotypic methods for the detection of methicillin-resistant Staphylococcus aureus

Background:

Staphylococcus aureus is known as a powerful pathogen that causes various infections. Emergence of methicillin-resistant S. aureus (MSRA) is responsible for nosocomial and community-acquired infections worldwide.

Aims:

The present study aimed to evaluate the performance and ability of eight different phenotypic and genotypic methods for the detection of MSRA.

Materials and Methods:

A total of 186 S. aureus isolates were defined as methicillin-susceptible S. aureus (MSSA; 95) and MSRA (91) using polymerase chain reaction (PCR) as the gold standard. Susceptibility to methicillin was investigated using oxacillin, methicillin, cefotetan, cefoxitin, and cefmetazole disks, by oxacillin Adata Tab and strips. For all S. aureus isolates minimal inhibitory concentrations of oxacillin were determined using the broth microdilution method according to Clinical and Laboratory Standards Institute guidelines.

Results:

Among the diagnostic methods studied, broth microdilution and the cefoxitin disk had the highest specificity (98.9 and 94.7%), sensitivity (100 and 98.9%), and concordance with PCR results (98.9 and 93.6%). The cefotetan and cefmetazole disks had the lowest concordance with PCR results.

Conclusion:

Our results suggest that microdilution and cefoxitin disk methods have high sensitivities compared with other methods for detection of MSRA. The cefoxitin disk method may be preferred in clinical laboratories because it is easy to perform and does not require special equipment.

Clonal evolution multi-drug resistant Acinetobacter baumannii by pulsed-field gel electrophoresis

BACKGROUND

Acinetobacter baumannii is usually multi-drug resistant (MDR), including third generation cephalosporins, amino glycosides and fluoroquinolone. Resistance to these antibiotics is mediated by multiple factors such as: lactamases, efflux pumps and other mechanisms of resistance. Pulsed-field gel electrophoresis (PFGE) was then used to investigate the genetic relationships among the MDR isolates.

AIM

The aim of this study was to determine MDR isolates and the existence of OXAs genes among MDR isolates of A. baumannii collected from Kermanshah hospitals in west of Iran.

MATERIALS AND METHODS

Forty-two MDR A. baumannii were collected from patients at Kermanshah hospitals. The isolates were identified by biochemical tests and API 20NE kit. The susceptibility to different antibiotics by disk diffusion method was determined. Polymerase chain reaction (PCR) was performed for detection of blaOXA-23-like , blaOXA-24-like , blaOXA-51-like and blaOXA-58-like betalactamase genes in isolates and clonal relatedness was done by PFGE (with the restriction enzyme ApaI) and patterns analyzed by Bionumeric software.

RESULTS

This study showed high resistant to ciprofloxacin, piperacillin, ceftazidime and also resistant to other anti-microbial agents and more spread blaOXA-23-like gene (93%) in MDR isolate. The PFGE method obtained six clones: A (10), B (9), C (5), D (4), E (11) and F (3) that clone E was outbreak and dominant in different wards of hospitals studied.

CONCLUSION

An isolate from the emergency ward of these hospitals had indistinguishable isolates PFGE profile and similar resistance profile to isolates from intensive care unit (ICU), suggesting likely transmission from ICU to emergency via patient or hospital staff contact.

Frequency distribution of virulence factors in uropathogenic Escherichia coli isolated from Kermanshah in 2011-2012

BACKGROUND

Uropathogenic Escherichia coli (UPEC) can cause urinary tract infection (UTI). To prevent urine flow lavage, UPEC has acquired several virulence factors called adhesins. These adhesins are expressed and controlled by different genes.

AIM

This study was aimed to determine some of the most important genes that control virulence factors of UPEC (pyelonephritis associated pili [pap], S fimbrial adhesion [sfa] and A fimbrial adhesion [afa] genes), which code for adhesins and phenotypic factors.

MATERIALS AND METHODS

In total, 205 UPEC isolates from in- and out-patients with UTI were obtained. Polymerase chain reaction was used for gene amplification. One drop of bacterial suspension, one of red blood cells and one of peripheral blood smear were mixed for hemagglutination (HA). Formation of a clump was considered to be positive. Bacteria were grown on blood agar to determine hemolysis. Surface hydrophobicity was determined using the SAT test.

RESULT

Frequencies of pap, afa and sfa were 42 (20.5%), 17 (8.3%) and 44 (21.5%), respectively. Frequencies of HA, hemolysis and hydrophobicity were 138 (67.3%), 56 (27.3%) and 39 (19%), respectively. Among HA-positive bacteria, 103 (74.6%) were mannose resistant. Our results highlight higher frequency of HA than that of other virulence factors, indicating a crucial role of this virulence factor in UPEC.

DISCUSSION

We concluded that major differences exist in the prevalence of virulence factors among different UPEC isolated from different countries. The association observed between pathogenicity and virulence factors may promote UPEC survival and growth within the urinary tract. Detecting these genes as the primary controllers of UPEC virulence factors may aid in better management of related infections.

Verification of Frequency in Species of Nontuberculous Mycobacteria in Kermanshah Drinking Water Supplies Using the PCR-Sequencing Method

BACKGROUND

Nontuberculous mycobacteria are habitants of environment, especially in aquatic systems. Some of them cause problems in immunodeficient patients. Over the last decade, 16S rRNA gene sequencing was established in 45 novel species of nontuberculous mycobacteria. Experiences revealed that this method underestimates the diversity, but does not distinguish between some of mycobacterium subsp. To recognize emerging rapidly growing mycobacteria and identify their subsp, rpoB gene sequencing has been developed.

OBJECTIVES

To better understand the transmission of nontuberculous mycobacterial species from drinking water and preventing the spread of illness with these bacteria, the aim of this study was to detect the presence of bacteria by PCR-sequencing techniques.

MATERIALS AND METHODS

Drinking water samples were collected from different areas of Kermanshah city in west of IRAN. After decontamination with cetylpyridinium chloride, samples were filtered with 0.45-micron filters, the filter transferred directly on growth medium waiting to appear in colonies, then DNA extraction and PCR were performed, and products were sent to sequencing.

RESULTS

We found 35/110 (32%) nontuberculous mycobacterial species in drinking water samples, isolates included Mycobacterium goodii, Mycobacterium aurum, and Mycobacterium gastri with the most abundance (11.5%), followed by Mycobacterium smegmatis, Mycobacterium porcinum, Mycobacterium peregrinum, Mycobacterium mucogenicum, and Mycobacterium chelonae (8%).

CONCLUSIONS

In this study, we recognized the evidence of contamination by nontuberculous mycobacteria in corroded water pipes. As a result of the high prevalence of these bacteria in drinking water in Kermanshah, this is important evidence of transmission through drinking water. This finding can also help public health policy makers control these isolates in drinking water supplies in Kermanshah.

Clinical Symptoms and Types of Samples Are Critical Factors for the Molecular Diagnosis of Symptomatic COVID-19 Patients: A Systematic Literature Review

BACKGROUND

Currently, a novel coronavirus found in 2019 known as SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Various parameters including clinical manifestations and molecular evaluation can affect the accuracy of diagnosis. This review aims to discuss the various clinical symptoms and molecular evaluation results in COVID-19 patients, to point out the importance of onset symptoms, type, and timing of the sampling, besides the methods that are used for detection of SARS-CoV-2.

METHODS

A systematic literature review of current articles in the Web of Science, PubMed, Scopus, and EMBASE was conducted according to the PRISMA guideline.

RESULTS

Of the 12946 patients evaluated in this investigation, 7643 were confirmed to be COVID-19 positive by molecular techniques, particularly the RT-PCR/qPCR combined technique (qRT-PCR). In most of the studies, all of the enrolled cases had 100% positive results for molecular evaluation. Among the COVID-19 patients who were identified as such by positive PCR results, most of them showed fever or cough as the primary clinical signs. Less common symptoms observed in clinically confirmed cases were hemoptysis, bloody sputum, mental disorders, and nasal congestion. The most common clinical samples for PCR-confirmed COVID-19 patients were obtained from throat, oropharyngeal, and nasopharyngeal swabs, while tears and conjunctival secretions seem to be the least common clinical samples for COVID-19 diagnosis among studies. Also, different conserved SARS-CoV-2 gene sequences could be targeted for qRT-PCR detection. The suggested molecular assay being used by most laboratories for the detection of SARS-CoV-2 is qRT-PCR.

CONCLUSION

There is a worldwide concern on the COVID-19 pandemic and a lack of well-managed global control. Hence, it is crucial to update the molecular diagnostics protocols for handling the situation. This is possible by understanding the available advances in assays for the detection of the SARS-CoV-2 infection. Good sampling procedure and using samples with enough viral loads, also considering the onset symptoms, may reduce the qRT-PCR false-negative results in symptomatic COVID-19 patients. Selection of the most efficient primer-probe for target genes and samples containing enough viral loads to search for the existence of SARS-CoV-2 helps detecting the virus on time using qRT-PCR.

Evaluate the frequency distribution of nonadhesive virulence factors in carbapenemase-producing Acinetobacter baumannii isolated from clinical samples in Kermanshah

Background:

Acinetobacter baumannii which is a Gram-negative bacterium can cause several different infections. The appearance of carbapenemase-producing A. baumannii in recent years has made the treatment process more difficult. The identification of virulence factors (VFs), such as nonadhesives in A. baumannii, helps to fight against related infections.

Materials and Methods:

A total of 104 samples from teaching hospitals in Kermanshah, Iran, were collected during a 24 months period (2011-2013). Sample identification was first carried out by biochemical tests, and then their susceptibility to carbapenems was determined using the Kirby–Bauer method. For confirmation of carbapenemase-producing A. baumannii, polymerase chain reaction (PCR) was done for carbapenemase-encoding genes. In addition, the frequency of nonadhesive VFs in carbapenemase-producing isolates was determined by PCR.

Results:

There were 50 isolates that were identified as carbapenemase-producing A. baumannii. The PCR results showed; 40 isolates (80%) for traT, 17 isolates (34%) for cvaC, and 8 isolates (16%) for iutA, and these encode serum resistance, colicin V and aerobactin, respectively. No significant correlation was observed between these three genes.

Conclusions:

The mechanism of A. baumannii virulence has always been in question. The role of VFs has also been recognized in other Gram-negative bacteria. According to the prevalence of traT, cvaC and iutA, as nonadhesive VFs, we can suggest that they could be the main mechanism of carbapenemase-producing A. baumannii pathogenesis.

Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran

BACKGROUND AND AIMS

Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis.

METHODS

A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification.

RESULTS

A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%).

CONCLUSIONS

The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.

HPV infections in retinoblastoma: a systematic review

BACKGROUND

Retinoblastoma is the most common primary intraocular malignancy in children less than 4 years. Retinoblastoma (RB) contains about 3%-5% of all childhood cancers. Recent studies demonstrated that interacting between RB tumor suppressor and oncoproteins of DNA tumor viruses such as human papillomavirus (HPV). The objective of the current systematic review study was to present conducted studies in the field of HPV infection and its possible role in retinoblastoma.

METHODS

For this systematic review, all relevant original research studies were assessed by searching in electronic databases include PubMed, Embase, Scopus, Google Scholar, and Web of Science by using relevant keywords. The study was designed based on the PRISMA criteria. All publications with English literature and original researches are considered for screening.

RESULTS

Conducted search results lead to 4070 studies. The title and abstract screening lead to 11 studies. Data extraction was performed on 8 included studies. The prevalence of the HPV was ranged from 0 to 69%, and HPV genotype 16 and 18 were the most detected types. The most used method for the detection of the viruses was PCR, and the most assessed sample was formalin-fixed, paraffin-embedded tissue blocks.

CONCLUSION

The association between HPV and retinoblastoma is still inconsistent. The prevalence of the HPV in RB was ranged from 0 to 69%, which indicates a wide range and highlights the importance of further investigation for more accurate statistical of HPV prevalence in RB. Thus, further worldwide studies of larger sample sizes of cohorts should be investigated to clarify this uncertainty.