Bacterial profile and their antimicrobial resistance patterns among patients with community-acquired pneumonia in southwestern Iran.

Background and Objectives: Community-acquired pneumonia (CAP) is one of the most common life-threatening infections, occurring in the community or within the first 48 hours of a patient's hospitalization. The present study aimed to investigate the frequency of pathogenic bacteria and their antibiotic resistance pattern in the sputum of patients with community-acquired pneumonia in Yasuj from 2018 to 2019. Materials and Methods: In the present study, 128 patients with CAP were included. Under aseptic conditions clinical samples including sputum collected from each patient were sent to the Microbiology Laboratory. Specific culture media and biochemical tests were used to identify the bacteria. Antimicrobial resistance patterns of the isolates were examined by disc diffusion. DNA was extracted from sputum using the phenol-chloroform method. The PCR method was used for the molecular detection of bacteria. Data were analyzed using SPSS software version 22 and the chi-square test. Results: The most common clinical symptoms in patients were sputum (68.8%), fever (64.1%), shortness of breath (60.2%), cough (50.8%), and chest pain (24.2%). A total of 133 bacteria were identified by culture and 117 bacteria by PCR. In the current study, the most prevalent organisms were Streptococcus pneumoniae (24.1%), Hemophilus influenzae (18%), Staphylococcus aureus (13.5%), and Moraxella catarrhalis (11.4%). Antibiogram test showed that most of the Gram-negative bacteria were resistant to levofloxacin (22.6%), rifampin (20.8%) and ceftriaxone (17%), and the highest resistance rate to clindamycin (43.1%), ciprofloxacin (43.1%) and amoxicillin (41.4%) were detected in the Gram-positive bacteria. Cefepime was the most effective antibiotic against Gram negative bacteria. Conclusion: S. pneumoniae was the most prevalent bacteria identified by culture and PCR methods in patients with CAP, indicating an important role of this bacterium in the pathogenesis of CAP. According to the results, cefepime can be used to treat patients with CAP with Gram-negative bacteria. In the present study, S. pneumoniae, S. aureus, P. aeruginosa, H. influenzae, M. catarrhalis, and K. pneumoniae have been isolated from the CAP patient population with varying frequencies. This is consistent with various studies in different parts of the world.

Identification and detection of pathogenic bacteria from patients with hospital-acquired pneumonia in southwestern Iran; evaluation of biofilm production and molecular typing of bacterial isolates.

BACKGROUND: Hospital-acquired pneumonia (HAP) is the second most common nosocomial infection in intensive care units (ICUs). The present study aims to determine the prevalence of pathogenic bacteria, their biofilm formation, and molecular typing from patients with HAP in southwestern Iran. METHODS: Fifty-eight patients with HAP participated in this cross-sectional study. Sputum and endotracheal aspirate were collected from each patient for isolation and detection of bacteria. Biofilm formation was evaluated using Congo red agar or Microtiter plate assay. The antimicrobial susceptibility patterns of the isolates were investigated. The multiplex polymerase chain reaction (M-PCR) technique was used to determine the Staphylococcal Cassette Chromosome mec (SCCmec) types of methicillin-resistant Staphylococcus aureus (MRSA) strains. All S. aureus isolates were typed using the agr typing method. A repetitive element sequence-based PCR (rep-PCR) typing method was used for typing of Gram-negative bacteria. Data were analyzed using the Statistical Package for the Social Sciences (SPSS) software version 15 and the chi-square test. RESULTS: Bacteria were isolated in 52 (89.7%) of patients. Acinetobacter baumannii (A. baumannii) was the most prevalent organism (37%), followed by S. aureus, Pseudomonas aeruginosa (P. aeruginosa), and Escherichia coli (E. coli). Using the PCR method, 56 bacteria were detected. A. baumannii was the most prevalent (35.7%) organism. A. baumannii and P. aeruginosa were biofilm-producing. All Gram-negative isolates were colistin-sensitive, and most of the A. baumannii isolates were multidrug-resistant (MDR). MRSA was identified in 12 (80%) S. aureus isolates, and 91.6% of MRSA were SCCmec type III. The agr type III was the most predominant. The rep-PCR analysis showed seven different patterns in 20 A. baumannii, six patterns in 13 P. aeruginosa, and four patterns in 6 E. coli. CONCLUSION: A. baumannii was more prevalent than S. aureus in ventilator-associated pneumonia (VAP), while S. aureus is a major pathogen in non-ventilator hospital-acquired pneumonia (NV-HAP), possibly due to the tendency of the former to aquatic environments. Based on the rep-PCR typing method, it was concluded that bacteria were transmitted from patients or healthcare workers among different wards. Colistin can be used as a treatment in Gram-negative MDR isolates.

Antimicrobial Susceptibility Pattern in the Bacteria Isolated from Surgical Site Infection: Emphasis on Staphylococcus Aureus; Yasuj City, Southwest Iran.

BACKGROUND: Surgical site infections (SSIs) in surgical wards remains the most common cause of postoperative complications and realistically is the third most common origin of healthcare-related conditions. Staphylococcus aureus is undoubtedly the most common bacteria causing SSIs. The current study aimed at investigating the antimicrobial susceptibility pattern in bacteria isolated from SSIs, evaluation of tetracycline resistance genes, and SCCmec typing in S. aureus isolates isolated from patients with SSIs from 2018 to 2019 in Yasuj, Kohgiluyeh, and Boyer-Ahmad Province, Iran. METHODS: This study diligently investigated 240 potential patients. Antimicrobial susceptibility testing was performed properly by the disk diffusion method. For the final confirmation of isolated bacteria, PCR was used. The presence of tet genes and SCCmec typing was carried out by multiplex PCR. RESULTS: The results showed that the most common isolated pathogens included S. aureus, E. coli, P. aeruginosa, Coagulase-negative Staphylococci, and K. pneumonia in 58.8%, 19.8%, 9.2%, 6.8% and 5.4% of cases, respectively. The majority of the Gram positive isolates were resistant against penicillin (86%) and Gram negative were resistant against ciprofloxacin (75.6%). In isolates of Staphylococcus aureus, the mecA gene was detected in 63.6% of isolates. The predominant SCCmec types were type III (59.1%) and type I (18.4%). The tetK and tetM genes were detected in 80.7% and 71.9% of the S. aureus isolates, respectively. There was a statistically significant difference between tet genes (tetK and tetM) from the viewpoint of resistance to tetracycline (p = 0.024). CONCLUSIONS: According to the results of the current study, it is recommended to administer vancomycin, amikacin, and imipenem in Yasuj to treat SSIs.

Sonochemical incorporated of cytosine in Cu-H2bpdc as an antibacterial agent against standard and clinical strains of Proteus mirabilis with rsbA gene.

The cytosine embedded copper based metal-organic framework (Bio-MOF) was synthesized by facile one-step sonochemical method by simply mixing of 4-4, biphenyldicarboxylic, cytosine and copper nitrate (Bio-Cu-H2bpdc-Cy). The prepared bio-MOF was characterized by XRD, FTIR and FE-SEM techniques. The effect of Cu-H2bpdc-Cy on the expression of the rsbA gene was evaluated in the clinical and standard Proteus mirabilis and study of MIC of Cu-H2bpdc-Cy by microdilution against them that have the rsbA gene. According to different concentrations of MIC, MBC concentrations was cultured on blood agar culture medium. Regarding to the concentration of MIC, gene expression changes were obtained by real-time PCR. MIC for standard and clinical strains of Proteus mirabilis was 1.6 and 1.8 mg/ml, and also MBC was obtained to be 1.8 and 2.0 mg/ml, respectively. Finally, in the real time PCR method, expression of the rsbA gene in presences of bio-Cu-H2bpdc-Cy was reduced, but has no effect on the gene expression of the Housekeeping DNA Gyrase-B gene. Considering the effect of Cu-H2bpdc-Cy on the rsbA gene in Proteus mirabilis bacteria, it is possible to use of Cu-H2bpdc-Cy agent as a therapeutic supplement against this bacterium.

Sonochemical-solvothermal synthesis of guanine embedded copper based metal-organic framework (MOF) and its effect on oprD gene expression in clinical and standard strains of Pseudomonas aeruginosa.

The guanine incropped Cu based metal-organic framework (Guanine-Cu-MOF) was synthesized by facile one-step sonochemical method by simply mixing of 4-4, biphenyldicarboxylic, guanine and copper nitrate (Bio-Cu-H2bpdc-Gu). The prepared guanine-MOF was characterized by using X-Ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and Field emission scanning electron microscopy (FE-SEM) techniques. The morphology of prepared material was sponge-shaped which it was well documented, together with the presence of existing functional groups. The effect of prepared material on oprD Gene Expression was investigated in Clinical and Standard Strains of Pseudomonas aeruginosa (PAO-1) and minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of prepared samples against P. aeruginosa strains were determined through the broth micro-dilution method. The expression of oprD gene in strains affected by Cu-H2bpdc-Gu was quantitatively investigated through real-time PCR. MIC of Bio-Cu-H2bpdc-Gu was 400 µg/mL for the standard and clinical strains of P. aeruginosa, while, MBC of this compound was 700 µg/mL for standard strain and 800 µg/mL for clinical strains. The highest and the lowest rate of oprD gene expression were found to be 3.6 and 1.1 fold in the strains, respectively.

The frequency of Klebsiella pneumonia encoding genes for CTX-M, TEM-1 and SHV-1 extended-spectrum beta lactamases enzymes isolated from urinary tract infection.

BACKGROUND: The extended- spectrum ß-lactamase producing bacteria are widely spread worldwide. The productions of these enzymes cause bacterial resistance to a wide range of antibiotics. The aim of this study was to investigated the frequency of K. pneumonia encoding genes for CTX-M, TEM-1 and SHV-1 extended-spectrum beta lactamases enzymes isolated from urinary tract infection. METHODS: This study is cross-sectional study. All K. pneumonia isolates from urine samples, which had grown on media culture more than 105 were delivered to the medical microbiology laboratory. K. pneumonia susceptibility of 198 samples were confirmed by disk diffusion. The gene frequency of genes was determined using PCR, and analyzed using SPSS version 21 software. FINDING: Most of the K. pneumonia isolated from urine producing ß-lactamase were resistant to cotrimoxazole (53.2%) followed by cefotaxime (50%), ceftazidime, ceftriaxone (40.3%), nalidixic acid (17.8%), amikacin and imipenem (1.6%) and meropenem (0%) respectively. Out of the 198 confirmed isolates of K. pneumonia, 62 cases (31.3%) have the gene phenotype of broad spectrum ß-lactamase enzymes and highest frequency of gene phenotype was related to the SHV-1 gene (85.5%). Then in the terms of abundance from highest to lowest CTXM-3 (56.5%), CTXM-1 (27.4%), TEM-1 (16.1%) and CTXM-2 (8.1%), were respectively. CONCLUSION: This study showed that K. pneumonia isolated from urine producing ß-lactamase were resistance to a wide range of antibiotics. Due to the increasing resistance of most antibiotics, control and supervision in the use of antibiotics and identification of broad spectrum ß-lactamase enzymes by phenotypic methods appears to be essential.

Ultrasound assisted extraction of phenolic acids from broccoli vegetable and using sonochemistry for preparation of MOF-5 nanocubes: Comparative study based on micro-dilution broth and plate count method for synergism antibacterial effect.

The aim of this work was comparison study of dilution and plating method for evaluation of the synergism effect of metal-organic framework nanocubes (MOF-5-NCs) and broccoli extract (Brassica oleracea) on antibacterial activity of standard and clinical Pseudomonas aeruginosa strains. For this purpose, sonochemical synthesis of MOF-5-NCs was performed and it was characterized using XRD, FT-IR, FESEM and EDS techniques. Maceration extraction (ME) and ultrasound assisted extraction (UAE) methods in three different solvents were prepared and applicability of their extracts were compared in some cases such as radical scavenging and antioxidant activity. The HPLC/UV analysis was applied for separation, identification and evaluation of phenolic acids in prepared broccoli extracts. Then, antimicrobial activity of MOF-5NCs and broccoli extract against gram-negative bacteria, Pseudomonas aeruginosa was evaluated by detection of minimal inhibition concentration (MIC), minimal bactericidal concentration (MBC) and zone of inhibition (ZOI). The results of in vitro assays showed that dilution method due to flase estimation of 4% viability percentage which is not logic by consideration of MBC well could not be able to estimate MBC. Therefore, plate count method was performed for precise calculation of MBC. MIC of broccoli extract and MOF-5-NCs on Pseudomonas aeruginosa strains were 7.81mgmL-1 and 3.13mgmL-1, respectively.

High Frequency of Class 1 Integrons in Escherichia coli Isolated From Patients With Urinary Tract Infections in Yasuj, Iran.

BACKGROUND: Most urinary tract infections (UTI) are caused by Escherichia coli. Integrons have an important role in distributing antibiotic resistance genes among bacteria. OBJECTIVES: The aim of this study was to investigate the presence of class 1, 2 and 3 integrons and their association with antibiotic resistance in E. coli isolated from patient with UTI in Yasuj, Iran. PATIENTS AND METHODS: In this cross-sectional study a total of 200 E. coli were collected from 1820 patients diagnosed with UTI that had been referred to two clinical laboratories between February 2013 and November 2014 in Yasuj city, southwest of Iran. Susceptibility of isolates to 11 different antibiotics was determined by the disk agar diffusion method. multiplex-polymerase chain reaction (PCR) was used for detection of class 1, 2 and 3 integrons. The data were analyzed using the SPSS software (version 16) and the chi-square test. A P value of < 0.05 was considered statistically significant. RESULTS: The highest rate of resistance was observed toward cephalothin (99%) and amoxicillin (76%) while only two (1%) isolates showed resistance to imipenem. Overall, 79% of isolates were multi drug resistant (MDR). Class 1 and 2 integrons were detected in 104 (52%) and 5 (2.5%) isolates respectively, while none of the isolates were positive for class 3 integrons. A significant association was observed between the presence of integrons and resistance to co-trimoxazole, nalidixic acid, ciprofloxacin, amoxicillin, ceftazidime and tetracycline (P < 0.05). CONCLUSIONS: High MDR isolates of E. coli were observed in this study. The significant association between class 1 integrons and resistance to ciprofloxacin, nalidixic acid, co-trimoxazole, amoxicillin, ceftazidime and tetracycline showed that class 1 integrons have an important role in resistance to these antibiotics in this region.

Genetic similarity between adenoid tissue and middle ear fluid isolates of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis from Iranian children with otitis media with effusion.

BACKGROUND: Otitis media with effusion (OME) is a common disease among children, in the pathogenesis of which bacterial infections play a critical role. It was suggested that adenoid tissue could serve as a reservoir for bacterial infection, the eustachian tubes being the migration routes of bacteria into the middle ear cavity. The aim of this study was to investigate the genetic similarity between isolates of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis, obtained from adenoid tissue and middle ear fluid. METHODS: A total of 60 specimens of middle ear fluids (MEFs) and 45 specimens of adenoid tissue were obtained from 45 children with OME. All the samples were inoculated on culture media for bacterial isolation and identification. The genetic similarity between bacterial isolates was determined by pulsed-field gel electrophoresis (PFGE). RESULTS: The same bacterial species were simultaneously isolated from adenoid tissue and MEFs of 14 patients, among which, 6 pairs of M. catarrhalis, 5 pairs of S. pneumoniae and 3 pairs of H. influenzae were identified. CONCLUSIONS: Based on the genetic similarities between isolate pairs, found by PFGE analysis, this study suggested that M. catarrhalis, S. pneumoniae and H. influenzae colonize the adenoid tissue, then migrate to the middle ear cavity and, hence, contribute to the total pathogenesis of OME.

Hepatitis B Infection among high risk population: a seroepidemiological survey in Southwest of Iran.

BACKGROUND: Hepatitis B virus (HBV) infection remains a major global health problem. This study aimed to assess the prevalence and risk behaviors for HBV infection among high risk groups in Kohgiloyeh and Boyerahmad province, in Southwest of Iran. METHODS: Blood samples were collected from 2009 subjects, between 2009 and 2010 in Kohgiloyeh and Boyerahmad province, in southwest of Iran. Recruited subjects were the high risk groups for HBV infection, including inmates, injecting drug users, health care workers, patients on maintenance haemodialysis, hemophilic patients and patients with a history of blood transfusion. Their serum samples were tested for the presence of antibodies to hepatitis B core antigen (HBc IgM, IgG) by enzyme-linked immunosorbent assay (ELISA). Seropositive specimens were tested for HBsAg. Demographic features of participants were recorded during sample collecting. RESULTS: HBsAg was detected in 24 of the 2009 subjects, giving an overall prevalence of 1.2%. All HBsAg positive cases were males. The prevalence of HBsAg among injection drug users was 3.2%. Significant correlation was found between HBV infection and drug abuse, level of education and place of residence (p<0.05), while no significant correlation was found between HBV infection and previous history of blood transfusion, unprotected sexual behavior, and thalassemia. CONCLUSION: Based on the findings of this study, incarceration and drug abuse are the most important risk factors for acquiring HBV infection in this region. Modifying behavior, improving the individual education and expanding the HBV vaccination coverage may reduce the rate of infection in the region.

Characterization of Alloiococcus otitidis strains isolated from children with otitis media with effusion by Pulsed-Field Gel Electrophoresis.

OBJECTIVE: Alloiococcus otitidis is a slow growing organism which has been isolated in a few studies on patients with otitis media with effusion (OME). According to the literature review, there is no study about the molecular typing of A. otitidis. In this study, the characteristics of A. otitidis isolates from patients with OME were investigated via Pulsed-Field Gel Electrophoresis (PFGE) typing method. METHODS: A total of 50 children with OME, who underwent myringotomy or who had an insertion of a ventilation tube, were included in this study. The isolates were identified to the species level as A. otitidis using standard biochemical methods, following which the amplification and sequencing of the 16S rRNA gene were carried out. The molecular characteristic of A. otitidis was investigated by PFGE technique. RESULTS: Fifteen isolates of A. otitidis were identified in the middle ear fluid of the patients. All the isolates were susceptible to ampicillin, amoxicillin/clavulanate and fluoroquinolones. All of the 15 isolates were typed by PFGE method and were found to include 13 different PFGE types. CONCLUSION: The current study, being the first reports on the molecular typing of A. otitidis by PFGE method, shows that A. otitidis is a heterogenic organism in Iranian children who have OME.

High prevalence of hepatitis C infection among high risk groups in Kohgiloyeh and Boyerahmad Province, Southwest Iran.

BACKGROUND: Detection of Hepatitis C virus (HCV)-infected people in each community assists with infection prevention and control.  This study aims to evaluate the prevalence of HCV infection among high risk groups in Kohgiloyeh and Boyerahmad Province, Southwest Iran. METHODS: This was a cross-sectional study conducted from 2009-2010 in Kohgiloyeh and Boyerahmad Province. High risk groups for HCV were the subjects of this study. Blood samples were taken from 2009 individuals at high risk for HCV that included inmates, injecting drug users (IDUs), health care workers, patients on maintenance hemodialysis, hemophilic patients, and those with histories of blood transfusions. Patients were residents of Yasuj, Gachsaran, and Dehdasht (3 main townships in the province). Samples were analyzed by ELISA for anti-HCV antibodies. Demographic features of participants were recorded by a questionnaire during sample collection. Data were analyzed by SPSS version 13 software. RESULTS: Of 2009 subjects, HCV antibodies were detected in 172 (8.6%). Rate of infection was higher in males (11.4%) compared to females (3.2%). Rate of infection in inmates was 11.7% while this rate was 42.4% in IDUs, 4.2% in health care workers, and 6.1% in thalassemic patients. Significant correlation was found between HCV infection, history of imprisonment, and thalassemia. CONCLUSION: Results of this study have provided epidemiologic features of HCV and its risk factors in Kohgiloyeh and Boyerahmad Province, Southwest Iran. This information may assist in preventing the spread of HCV infection in this and other similar settings in the region. The findings of this study may help in improving surveillance and infection control in the community through management and monitoring of infected individuals.

Evaluation of crude sesquiterpenoid extract of Phellinus fastuosus as a natural preservative.

It has been revealed that the use of synthetic food preservatives has variety of various side effects and hence search of safe and effective natural preservative has become a need. With the afore said objective the present study to screen the possibility of using sesquiterpenoid extract of local folk mushroom Phellinus fastuosus as food preservative was undertaken. Microbial growth inhibition by sesquiterpenoid extract of Phellinus was evaluated in the media with natural ingredient such as milk agar (MA), tomato juice agar (TJA), wheat flour agar (WFA) and pineapple juice agar (PAJA) with the composition with Phellinus extract, sodium benzoate and combinations. Three strains of bacteria and one strain of fungus were used astest organisms. The sesquiterpenoid extract of Phellinus at 0.02% concentration significantly inhibited the growth of all test organisms on natural media and the results were comparable with sodium benzoate. Similarly combination of Phellinus extract and sodium benzoate completely inhibited the growth of all microorganisms in all media, suggesting the possibility of using the Phellinus extract as food preservative.