Determination Of Antibiotic Resistance Profile Research Articles

Evaluation of distribution and susceptibility of microorganisms isolated from joint fluid cultures: five-year data

Aims: Septic arthritis is joint inflammation. It is an orthopedic emergency that requires prompt diagnosis and treatment. In this study, it was aimed to examine the distribution and antibiotic resistance profiles of microorganisms isolated from joint fluid samples taken from patients who applied to the orthopedic clinic of our hospital in the last five years. 
 Methods: In our study, 1162 joint fluid samples were sent to the medical microbiology laboratory of our hospital from the orthopedics and traumatology clinic between January 01, 2018 and December 31, 2022. Joint fluid samples taken from clinically appropriate patients under sterile conditions were incubated in a BacT/Alert 3D (Biomerieux, France) culture device. Bacteria isolated from 164 specimens with growth detected, were identified by matrix-mediated laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) based VITEK MS (Biomerieux, France). Antibiotic susceptibility tests were performed on the VITEK 2 Compact (Biomerieux, France) device.
 Results: Staphylococcus aureus (S. aureus) (29.3%) and coagulase negative Staphylococci (CNS) (29.3%) were the most commonly grown microorganisms. Other microorganisms grown were Streptococcus spp. (9.1%), Enterococcus spp. (6.1%), Pseudomonas aeruginosa (P. aeuruginosa) (7.3%), Escherichiae coli (E. coli) (4.3%) and Klebsiella pneumoniae (K. pneumoniae) (4.3%). When antibiotic susceptibility results were evaluated according to EUCAST restricted reporting criteria, linezolid in Gram-positive strains, amikacin in Enterobacterales, colistin and tigecycline in nonfermentative Gram-negative bacteria were found to be the most susceptible antibiotics. 
 Conclusion: The continuous change in antibiotic susceptibility profiles in joint infections, the long duration of treatment and follow-up, and the increase in polymicrobial infections require regular monitoring of culture and antibiotic susceptibility tests. In our study, the distribution of microorganisms isolated from joint fluid samples of our hospital and the determination of antibiotic resistance profiles will contribute to the clinician in terms of guiding empirical treatment.

Determination of antibiotic resistance profile of bacterial community from environmental water using antibiotic-resistant bacterial contamination detection (ABCD) kit

Quick and easy monitoring approaches are needed to assess sources, clinical relevance, and incidences of antibiotic resistance in environmental bacterial communities. In the present work, antibiotic-resistant bacterial contamination detection (ABCD) kits were developed for the same. The method was standardized with strains of Escherichia coli TS7, Staphylococcus arlettae HWI8, Enterococcus faecalis HWI19, and Aerococcus viridans HWII16 with known antibiogram using six clinically important antibiotics. The method was verified with different water sources having different physicochemical parameters successfully. Only 1 ml of sample water is required to be mixed with an optimized concentration of the antibiotic solution and incubated for 6h; subsequently, a color change to pink may be observed within a specified amount of time upon the addition of the bacterial detection PVDF membrane to monitor the presence of resistant bacteria. There is no color change in the case of antibiotic-susceptible bacterial communities or the absence of a resistant community. Moreover, the time taken for color change is inversely related to the magnitude of the antibiotic-resistant communities in terms of enumeration. Up to our understanding, this is the 1st report which can determine an antibiotic-resistance profile of any water source by observing only color change within a maximum of 7 h (6 h for co-culture of bacteria and antibiotics + 1 h for color change detection) time without the aid of any microbiology laboratory or skilled manpower.

Determination of antibiotic resistance profiles of Lactococcus garivieae isolated from rainbow trout (Oncorhynchus mykiss) farms in Muğla, Turkey

This study was aimed to determine the current antibiotic resistance of Lactococcus garvieae, which causes significant economic losses in rainbow trout (Oncorhynchus mykiss) farms. For the study, three farms located around a stream were visited in two consecutive disease outbreaks. Bacteria were isolated from the diseased fish and all bacterial isolates were identified using conventional and molecular methods. Then, they were examined for 5 different antibiotic resistance genes and their antibiotic susceptibility profiles were determined using the disc diffusion technique. The results of the study revealed that all 16 isolates had a different antibiotic resistance profile and each should be considered as a separate strain. Additionally, they showed that there may be different L. garvieae strains within and between farms, using the same water source. Comparison of the results with previous studies from the region and different regions of the country revealed that antibiotic resistance is increasing in L. garvieae, and screenings on a limited number of isolates may not give an accurate picture of the final status of antibiotic resistance. These outcomes of the study are discussed in terms of treatment strategies that trout farms in the region should follow when treating lactococcosis.

Determination of antibiotic resistance profiles and biofilm production of Staphylococcus spp. isolated from Anatolian water buffalo milk with subclinical mastitis.

Mastitis is one of the most crucial diseases of dairy animals. Especially subclinical mastitis (SCM) has negative impacts on of dairy economy in term of reducing milk quality and quantity also premature culling and cost of therapy. Staphylococci are important etiological agents in SCM. The aim of the study was to investigate the biofilm production and antibiotic resistance profiles of Staphylococcus spp. other than S. aureus isolated from milks of Anatolian water buffalo with subclinical mastitis. Twenty-two coagulase negative staphylococci (CNS) identified phenotypically were also identified with PCR as Staphylococcus spp. other than S. aureus. Biofilm productions were investigated both by Congo Red Agar Method and PCR. The antibiotic resistance profiles of the isolates were determined by Disc Diffusion Method and they were antibiotyped. Only three (13.6%) isolates were biofilm positive both phenotypically and genotypically. All isolates except for two were resistant against at least two antibiotics. Multidrug-resistance among the isolates was low (13.6%). Antibiotyping results showed that the similarities among the strains were between 30-100%. Genotyping of the strains revealed that a genetic heterogeneity was found among CNS isolates and their similarities were between 43% and 93%. In conclusion, CNS isolates identified as subclinical mastitis agents in buffaloes showed a high antibiotic resistance profile especially against oxacillin and vancomycin. Further studies should be conducted to investigate new mechanisms and/or genes responsible for antibiotic resistance in buffaloes.

Prevalence of Antibiotic Resistant Bacteria in Nigerian Fermented Food Condiments

Food borne diseases remain a growing public health problem gotten through the consumption of contaminated food and water. A world health organization report, 2015 estimated 600million episodes of illness due to contaminated food worldwide. Amongst all age groups, Africa bore the greatest burden of diarrhoeal diseases. Gram-negative bacteria have become a significant challenge to the control of infection as a result of acquisition of antibiotic resistant genes. This is especially of concern in Nigeria where fermented condiments are important part of daily meals and sometimes consumed without cooking. This work thus identifies Gram negative bacteria from fermented condiments and evaluates the antibiotic resistance profile of the bacterial isolates. The fermented condiments- Iru (Parkia biglobosa) (67), Ogiri-igbo (Ricinus communis) (58), Ukpaka (Pentaclethra macrophylla) (22) and Okpei (Prosopis africana) (42), were obtained from markets in Abuja, Gboko, Lokoja, Okenne, Abeokuta, Ibadan, Ijebu-Ode, Ilorin, Lagos, Ondo and Ore. Coliform and faecal coliform test was done. Isolation of the Gram-negative bacteria was done using MacConkey agar. Taxonomic studies were carried out on the isolated Gram negative bacteria. Determination of antibiotic resistance profile of the Gram-negative bacteria was done by disc diffusion method. Ukpaka (Pentaclethra macrophylla) samples had the highest percentage occurrence of coliforms (100%). Faecal coliform were more prevalent in Ukpaka (20%) and Iru (16.67%). Klebsiella pneumonia was prevalent in the 3 of the fermented condiments (Iru, Ogiri and Ukpaka). Escherichia coli was the most frequent Gram-negative bacteria in Okpei samples. The relatively high recovery rates of Gram-negative bacteria shows possible contamination of fermented condiments by human pathogens. The isolates from Ukpaka showed the highest resistance (55.3%) to Cotrimoxazole. The effect of the resistance of Gram-negative bacteria to antibiotics could be transmission of resistant strains from farm to house, treatment failure and a limited choice of antibiotics used for treatment.

Prevalence of Antibiotic Resistant Bacteria in Nigerian Fermented Food Condiments

Food borne diseases remain a growing public health problem gotten through the consumption of contaminated food and water. A world health organization report, 2015 estimated 600million episodes of illness due to contaminated food worldwide. Amongst all age groups, Africa bore the greatest burden of diarrhoeal diseases. Gram-negative bacteria have become a significant challenge to the control of infection as a result of acquisition of antibiotic resistant genes. This is especially of concern in Nigeria where fermented condiments are important part of daily meals and sometimes consumed without cooking. This work thus identifies Gram negative bacteria from fermented condiments and evaluates the antibiotic resistance profile of the bacterial isolates. The fermented condiments- Iru (Parkia biglobosa) (67), Ogiri-igbo (Ricinus communis) (58), Ukpaka (Pentaclethra macrophylla) (22) and Okpei (Prosopis africana) (42), were obtained from markets in Abuja, Gboko, Lokoja, Okenne, Abeokuta, Ibadan, Ijebu-Ode, Ilorin, Lagos, Ondo and Ore. Coliform and faecal coliform test was done. Isolation of the Gram-negative bacteria was done using MacConkey agar. Taxonomic studies were carried out on the isolated Gram negative bacteria. Determination of antibiotic resistance profile of the Gram-negative bacteria was done by disc diffusion method. Ukpaka (Pentaclethra macrophylla) samples had the highest percentage occurrence of coliforms (100%). Faecal coliform were more prevalent in Ukpaka (20%) and Iru (16.67%). Klebsiella pneumonia was prevalent in the 3 of the fermented condiments (Iru, Ogiri and Ukpaka). Escherichia coli was the most frequent Gram-negative bacteria in Okpei samples. The relatively high recovery rates of Gram-negative bacteria shows possible contamination of fermented condiments by human pathogens. The isolates from Ukpaka showed the highest resistance (55.3%) to Cotrimoxazole. The effect of the resistance of Gram-negative bacteria to antibiotics could be transmission of resistant strains from farm to house, treatment failure and a limited choice of antibiotics used for treatment.

Determination of Antibiotic Resistance Profile and Virulence Genes in Escherichia coli Isolates from Palestinian Patients

Introduction: Escherichia coli (E. coli) is considered one of the most frequent intestinal and extraintestinal pathogen.
 Methods: A total of 49 isolates of E. coli were collected from different clinical samples, from different hospitals in Northern West Bank-Palestine, during January-March 2019.
 Aims: To detect the distribution of Type III secretion system (T3SS) genes, class 1, 2 and 3 integrons, virulence factors (fyuA, papGIII, iutA and sfa⁄foc) using multiplex PCR and antibiotic resistance using disc diffusion method.
 Results: In this study, E. coli isolates showed high resistance rate against different types of antibiotics and 71.4% of the isolates were multidrug resistant (MDR). Only class 1 integron was detected in these isolates with prevalence 57%, and 65.7% of MDR isolates carried integron genes. The prevalence of T3SS genes was 0.0%. In addition, results of this study showed that the prevalence of virulence genes papGIII, sfa⁄foc, fyuA and iutA was 4.1%, 40%, 64%, and 79.6%, respectively.
 Conclusions: The isolates of E. coli showed high resistance rate against different types of antibiotics. The co-occurrence of class 1 integrons and antimicrobial resistance genes in these isolates is an additional threat for spread of the antimicrobial resistance traits which may further complicate future strategies for treatment the infections caused by this pathogen. In addition, E. coli isolated from Palestinian patients showed one or more virulence factors that could increase their pathogenic potential.

Antibiotic resistance among ocular pathogens: current trends from the ARMOR surveillance study (2009-2016).

BackgroundThe Antibiotic Resistance Monitoring in Ocular micRoorganisms study is an ongoing surveillance study that tracks antibiotic resistance among bacterial isolates from ocular infections across the United States. We report antibiotic resistance rates and trends from 2009 through 2016.Materials and methodsStaphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Pseudomonas aeruginosa, and Haemophilus influenzae from various ocular infections were obtained from participating United States centers. Isolates were sent to a central laboratory for determination of antibiotic resistance profiles. Minimum inhibitory concentrations were determined by broth microdilution according to the Clinical and Laboratory Standards Institute for drugs from more than ten antibiotic classes, and isolates were classified as susceptible or resistant based on systemic breakpoints, wherever available. Resistance rates were also evaluated based on decade of patient life and longitudinally over the 8-year time period.ResultsA total of 1,695 S. aureus, 1,475 CoNS, 474 S. pneumoniae, 586 H. influenzae, and 599 P. aeruginosa were collected from 87 sites. Resistance was high among staphylococci and pneumococci, with methicillin resistance detected in 621 (36.6%) S. aureus and 717 (48.6%) CoNS isolates. Multidrug resistance (≥3 drug classes) was observed among staphylococci, particularly in methicillin-resistant (MR) isolates (MR S. aureus [MRSA]: 76.2%; MR CoNS [MRCoNS]: 73.5%). Differences in methicillin resistance among staphylococci were observed based on patient age, with higher rates observed in older patients (P<0.0001). For certain organism-antibiotic combinations, there were significant changes in resistance over time, including a decrease in methicillin resistance among S. aureus (but not CoNS); no notable trends were observed for S. pneumoniae.ConclusionAntibiotic resistance was prevalent among gram-positive organisms, and MR staphylococcal isolates were more likely to be multidrug resistant. Although a small decrease in methicillin resistance was observed among S. aureus over time, the continued high prevalence of in vitro methicillin resistance should be considered when treating patients with ocular infections.

The Relationship Between Class I and II Integrons and Antibiotic Resistance Among Escherichia coli Isolates From Urinary Tract Infections

Objective: the aim of this study was determination of antibiotic resistance profile, investigation of class I and II integrons among Escherichia coli (E. coli) isolates from urinary tract infections. This study was conducted for the investigation of the prevalence of class I and II Integrons among E. coli Isolates from urinary tract infections. Materials and Methods: A total of 100 E. coli clinical isolates were collected from urinary tract infections in Borujerd city, Iran, from… to …. All the isolates were identified with standard laboratory procedures as described everywhere. The antibiotic susceptibility profile was conducted against adopted antibiotic disks following CLSI 2016 guidelines. All the isolates were enrolled in the PCR technique for the presence of class I and II integrons. Results: the highest resistance was against amoxicillin (72%), ciprofloxacin (69%), nalidixic acid (55%) and tetracycline (51%). The prevalence of class I and II integrons was 31% and 21%, respectively. A significant relation was observed between resistance to trimethoprim-sulfamethoxazole (p<0.001), nalidixic acid (p<0.01) and tetracycline (p<0.005) with the presence of class I integron. The rate of class I integron in the E. coli isolates was high, possibly playing a role in the spread of multidrug resistant isolates. Conclusion: considering the significant relation observed between the presence of class I integron among multidrug-resistant isolates, establishment implementation of proper procedures to control and suitable treatment strategies in hospitals seems essential for the prevention of more spread of these isolates.

Identification of Anaerobic Gram-Negative Bacilli Isolated from Various Clinical Specimens and Determination of Antibiotic Resistance Profiles with E-Test Methods

The aim of this study was to identify gram-negative anaerobic bacilli isolated from various clinical specimens that were obtained from patients with suspected anaerobic infections and to determine the antibiotic resistance profiles by using the antibiotic concentration gradient method. The study was performed in Afyon Kocatepe University Ahmet Necdet Sezer Research and Practice Hospital, Medical Microbiology Laboratory between 1 November 2014 and 30 October 2015. Two hundred and seventyeight clinical specimens accepted for anaerobic culture were enrolled in the study. All the samples were cultivated anaerobically by using Schaedler agar with 5% defibrinated sheep blood and Schaedler broth. The isolated anaerobic gram-negative bacilli were identified by using both the conventional methods and automated identification system (VITEK 2, bioMerieux, France). Antibiotic susceptibility tests were performed with antibiotic concentration gradient method (E-test, bioMerieux, France); against penicillin G, clindamycin, cefoxitin, metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem for each isolate. Of the 28 isolated anaerobic gram-negative bacilli; 14 were identified as Bacteroides fragilis group, 9 were Prevotella spp., and 5 were Fusobacterium spp. The highest resistance rate was found against penicillin (78.5%) and resistance rates against clindamycin and cefoxitin were found as 17.8% and 21.4%, respectively. No resistance was found against metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem. As a result, isolation and identification of anaerobic bacteria are difficult, time-consuming and more expensive when compared with the cost of aerobic culture. The rate of anaerobic bacteria isolation may be increased by obtaining the appropriate clinical specimen and appropriate transportation of these specimens. We believe that the data obtained from the study in our center may offer benefits for the follow up and treatment of infections caused by anaerobic bacteria and may contribute to the current literature. Because of high resistance rate detected against penicillin, this antibiotic should not be used as a first choice in empirical treatment. Cefoxitin may be used in empirical antimicrobial treatment of anaerobic gram-negatives; but the rate of antibiotic resistance should be detected for more useful and proper treatment. The prior selection of the most effective antibiotic, may contribute to decrease the rate of high resistance. In our study, no resistance was observed against carbapenem group antibiotics and metronidazole; so these antibiotics should be reserved as treatment options in the future for infections caused by resistant gram-negative anaerobic bacteria.

Detection of New Virulence Genes in mecA-positive Staphylococcus aureus Isolated From Clinical Samples

Background Methicillin-resistant Staphylococcus aureus (MRSA) has become a main clinical and epidemiological concern for the past decades. These isolates have spread worldwide, causing health care– and community-associated infections. The aim of the present work was the determination of antibiotic resistance profile and simultaneous detection of psm-α and sasX genes in the clinical MRSA strains isolated from Tehran—the first report from Iran. Methods This descriptive study was performed on hospitalized patients during August to February 2015. Antibiotic susceptibility test for all S. aureus isolates was conducted on Mueller-Hinton agar. The presence of mecA, sasX, and psm genes was detected by multiplex polymerase chain reaction method. Results Of 153 S. aureus, 79 (51.6%) of the strains carried the mecA gene. Molecular analysis of mecA-positive S. aureus showed that the prevalence of sasX and psm genes was 13.9% (11/79) and 7.6% (6/79), respectively. Conclusions This is the first report of sasX and psm genes among S. aureus isolates from Iran. Phenol-soluble modulins have recently appeared as a novel toxin family describing the virulence potential of vastly aggressive S. aureus. Current understanding is needed on S. aureus surface protein-encoding gene sasX, which plays a vital role in colonization and pathogenesis of MRSA.

Characterization and determination of antibiotic resistance profiles of a single clone Acinetobacter baumannii strains isolated from blood cultures

Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMérieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all were susceptible to TG and COL. The resistance rates of the environmental isolates to SCF, AMK, GEN, NT, LVF, TET and SXT were determined as 57.1%, 85.7%, 85.7%, 28.8%, 28.6%, 85.7% and 57.1%, respectively. PFGE analysis done by the use of ApaI enzyme revealed the presence of one major clone. Dendogram analysis indicated that environmental and clinical isolates were in the same clone indicating that the outbreak was possibly originated from the same internal ICUs. Our data emphasized that multidrug resistant A.baumannii isolates were quite common in our hospital, and enviromental cross-contamination throughout the year was confirmed by molecular methods. Despite the precautions such as continous education on effective hand washing, use of gloves and hospital cleaning, established in our hospital, this single clonal spread was attributed to staff shortage and poor adherence to infection control rules. In conclusion, for the prevention of dissemination of multidrug resistant A.baumannii strains and control of nosocomial infections, infection control strategies should be established and strict compliance to these rules should be provided.

Detection of tetracycline resistance genes by PCR methods.

Rapid, accurate, and sensitive determination of antibiotic resistance profiles of various human and animal pathogens becomes a vital prerequisite for successful therapeutic intervention in the face of the increased occurrences of drug-resistant bacterial infections. The current methods, which are dependent on cultivation of pathogens and phenotypic expression of antibiotic resistance, usually require excessive time, special microbiological equipment, and qualified personnel. However, even with all these requisites, for example, no bacteria can be grown from more than 80% of all clinical samples sent to clinical microbiology laboratories. Besides the cultivation limitations, the cultivation-based determination of an antibiotic resistance profile lacks the genotypic information, which is essential for understanding the epidemiology and routes of transmission of antibiotic resistance genes. These genes often reside on mobile genetic elements and can move freely between commensal and pathogenic microbiota, occurring even between taxonomically distant clinical and environmental microbiota. Therefore, development of genotyping methods for detection of antibiotic resistance genes is highly desirable for fast, accurate, and sensitive detection of antibiotic resistance genes in a broad range of pathogenic and commensal bacteria in both clinical and environmental samples. As a model for our studies we have chosen the genes conferring resistance to tetracyclines. Tetracyclines belong to a family of broad-spectrum antibiotics that include tetracycline, chlortetracycline, oxytetracycline, demeclocycline, methacycline, doxycycline, minocycline, and a number of other semisynthetic derivatives. These antibiotics inhibit protein synthesis in Gram-positive and Gram-negative bacteria by preventing the binding of aminoacyl-tRNA molecules to the 30S ribosomal subunit. The antibiotics of this group were introduced in the late 1950s and since then have been widely used in clinical and veterinary medicine, as well as for prophylaxis and growth promotion in food animals. Because of the possible misuse and overuse of these drugs, resistance to this class of antibiotics is widespread among many clinical isolates, thus limiting the utility of tetracyclines in treating infections. Despite this shortcoming, antibiotics of this class still remain in the active arsenal for dermatologists to treat skin infections such as acne and rosacea.