Prevalence Of Clinical Isolates Research Articles

The prevalence of multidrug-resistant Staphylococcus aureus isolated from different clinical samples

Abstract Background: Antibiotic resistance is a major global issue, with Staphylococcus aureus being one of the most common resistant bacterial forms. Objective: The study’s goal was to determine the prevalence of multidrug-resistant (MDR) S. aureus isolated from clinical specimens. Materials and Methods: The standard microbiological techniques used for isolates identification were subsequently validated by the VITEK-2 system. Antibiotic susceptibility was assessed using the disc diffusion technique. MDR bacteria were those that were resistant to three or more antibiotics. Results: S. aureus prevalence in clinical isolates was 27.9%. There was significant resistance toward all antibiotics used in the study except for tetracycline. About 98.2% of the isolates were MDR. Conclusion: Our results underscore the need for continued antibiotic resistance monitoring in S. aureus isolates associated with hospital-acquired infections.

Identification of Vancomycin Resistant Enterococcus Genes in Clinical Isolates

Vancomycin resistant enterococci (VRE) nosocomial diseases are rapidly spreading across the world. To treat these diseases is becoming a great challenge due to antibiotic resistance. The present study was aimed to estimate the prevalence of vancomycin resistant enterococci and to find out genes responsible for causing vancomycin resistance. One hundred different blood, wound and urine samples were collected from hospitalized patients at tertiary care health hospital, Lahore. On the basis of colony morphology, isolates of Enterococci were identified, Gram staining and biochemical tests including catalase test, Bile esculin test, growth in 6.5% NaCl, litmus milk reduction were performed. All the clinical isolates were checked for vancomycin resistant and 15% of all the samples were vancomycin resistant. Polymerase chain reaction (PCR) was performed for vancomycin resistance, enterococcal isolates to identify van genes responsible for resistance. In our study the presence of vanA gene was found in all 15 vancomycin resistant samples. vanB gene was not detected in any of the sample. The study highlights the increased VRE prevalence in clinicalisolates obtained from local hospital. The presence of vanA gene in all resistant samples is suggestive of its role as resistant gene. On the basis of these results there is an urgent need of establishing a rational antibiotic use policy for better management of enterococcal infections.

How Mycobacterium tuberculosis drug resistance has shaped anti-tubercular drug discovery.

Drug resistance is an increasing problem for the treatment of tuberculosis. The prevalence of clinical isolates with pre-existing resistance needs to be considered in any drug discovery program. Non-specific mechanisms of resistance such as increased efflux or decreased permeability need to be considered both in developing individual drug candidates and when designing novel regimens. We review a number of different approaches to develop new analogs and drug combinations or improve efficacy of existing drugs that may overcome or delay the appearance of clinical resistance. We also discuss the need to fully characterize mechanisms of resistance and cross- resistance to existing drugs to ensure that novel drugs will be clinically effective.

Hospital Premises as a Potential Reservoir of Antimicrobial Resistance

Soil in hospital premises can be a potential reservoir of organisms with Antimicrobial Resistance (AMR) due to their spread from hospital environment including pre-treated hospital waste. Thus, studying AMR in the soil samples from hospital premises at periodic interval could be helpful in monitoring the trend of its load and spectrum in hospital environment. Prevalence of Extended-Spectrum Beta-Lactamase (ESBL), carbapenemase and New Delhi Metallo-Beta-Lactamase (NDM) varieties of AMR were estimated in Escherichia coli and Klebsiella pneumoniae as indicator organisms in surface soil samples from hospital premises viz. hospital grounds and pedestrian tracks in relation to the pre-monsoon and post-monsoon seasons at an interval of four years between 2014 and 2018. There was significant increase in the prevalence of ESBL (mainly CTX-M variety), carbapenemase and NDM varieties of AMR in isolates from soil samples collected from hospital premises during post-monsoon season compared to pre-monsoon isolates regardless of the year of sampling although monsoon season did not affect the prevalence of AMR in clinical samples processed during the same period. There was gradual rise in resistance to other antibiotics viz. co-trimoxazole, tetracycline, fluoroquinolones and amoxyclav in soil samples collected from hospital premises during the four years interval. Prevalence of various categories of AMR were higher in samples collected during the post-monsoon season compared to prevalence in clinical isolates from hospital attending population during the corresponding period regardless of the year of sampling. Increasing prevalence of various categories of AMR recorded in hospital premises could indicate inadequate containment measures towards prevention of their spread from hospital environment warranting adaption of requisite measures for prevention.

Prevalence of Antibiotic Resistance and Class 1 Integrons in Clinical and Environmental Isolates ofPseudomonas aeruginosa

Background: Many clinical isolates of Pseudomonas aeruginosa exhibit antibiotic-resistance and it is the main cause of hospital infections. Objectives: The current study aimed at evaluating the diversity of genes coding for antibiotic resistance in clinical and environmental isolates of P. aeruginosa in Hamadan, West of Iran. Methods: In the current cross sectional study, 100 clinical and 50 environmental isolates of P. aeruginosa were collected from October 2013 to May 2014. The standard disk diffusion method (SDD) was performed to test antibiotic susceptibility. All isolates were evaluated by the polymerase chain reaction (PCR) for the presence of class 1 integrons and genes encoding resistance to aminoglycoside antibiotics. The relationship between antibiotic resistance and integrons was tested by the 2-tailed chi-square (χ 2 ) or the Fisher exact tests. P values ≤ 0.05 were considered statistically significant. Results: The most common antibiotic resistance was to cotrimoxazole (61.3%). The least observed resistance was to meropenem (9.3%) and piperacillin /tazobactam (12%). The result of minimum inhibitory concentration (MIC) for amikacin showed that 20% of the strains were resistant, 15% had intermediate resistance, and 65% were sensitive. Class 1 integrons were found in 57% of the isolates. The aminoglycoside-resistance cassette included aadA (confers resistance to streptomycin and spectinomycin) and aphA1 (encoded aminoglycoside 3’-phosphotransferase) genes were the most prevalent in the isolates. Conclusions: Antibiotic resistance had a high prevalence in clinical isolates of P. aeruginosa and was commonly associated with class 1 integrons. The knowledge of drug resistance patterns helps to apply effective antibiotic treatments and appropriate infection control measures to prevent the spread of infection in hospitals.

Characterisation of a novel integrative and conjugative element ICESsD9 carrying erm(B) and tet(O) resistance determinants in Streptococcus suis, and the distribution of ICESsD9-like elements in clinical isolates

This study identified a novel integrative and conjugative element (ICESsD9) carrying erm(B) and tet(O) resistance determinants in Streptococcus suis D9 and determined its prevalence in clinical isolates. Comparative genome analysis was performed using Mauve and Artemis Comparison Tool visualisation programs. Inverse PCR was utilised to detect its circular intermediate. The transfer capacity of ICESsD9 was evaluated by mating assays using S. suis A7 and Enterococcus faecalis JH2-2 as recipients. A genome walking approach was employed to analyse the characteristics of integration sites in transconjugants. A total of 118 clinical S. suis isolates were tested by PCR mapping assays to detect ICESsD9-like elements. MLST was performed on isolates containing ICESsD9 variants to determine their clonal relatedness. This 55 683-bp element can actively excise from the chromosome. Additionally, it was capable of transferring both into S. suis and E. faecalis with frequencies of 1.2×10-4 and 5.8×10-6 per donor, respectively. When investigating integration site features, it was found that ICESsD9 can enter S. suis and E. faecalis chromosomes by different sites, generating 15-bp and 3-bp direct repeat sequences, respectively. Twelve isolates mainly belonging to sequence types ST1, ST7 and ST28 were confirmed to harbour ICESsD9-like elements. In conclusion, this study provides the first description of an ICE in S. suis that is capable of transferring both into S. suis and E. faecalis. The presence of different ICESsD9 variants in clinical isolates suggests already wide dissemination of this family element in S. suis in China.

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution.

CRISPRs offer adaptive immunity in prokaryotes by acquiring genomic fragments from infecting phage and subsequently exploiting them for phage restriction via an RNAi-like mechanism. Here, we develop and analyze a dynamical model of CRISPR-mediated prokaryote-phage coevolution that incorporates classical CRISPR kinetics along with the recently discovered infection-induced activation and autoimmunity side effects. Our analyses reveal two striking characteristics of the CRISPR defense strategy: that both restriction and abortive infections operate during coevolution with phages, driving phages to much lower densities than possible with restriction alone, and that CRISPR maintenance is determined by a key dimensionless combination of parameters, which upper bounds the activation level of CRISPRs in uninfected populations. We contrast these qualitative observations with experimental data on CRISPR kinetics, which offer insight into the spacer deletion mechanism and the observed low CRISPR prevalence in clinical isolates. More generally, we exploit numerical simulations to delineate four regimes of CRISPR dynamics in terms of its host, kinetic, and regulatory parameters.

Prediction of the origin of French Legionella pneumophila strains using a mixed-genome microarray

BackgroundLegionella is a water and soil bacterium that can infect humans, causing a pneumonia known as Legionnaires’ disease. The pneumonia is almost exclusively caused by the species L. pneumophila, of which serogroup 1 is responsible for 90% of patients. Within serogroup 1, large differences in prevalence in clinical isolates have been described. A recent study, using a Dutch Legionella strain collection, identified five virulence associated markers. In our study, we verify whether these five Dutch markers can predict the patient or environmental origin of a French Legionella strain collection. In addition, we identify new potential virulence markers and verify whether these can predict better. A total of 219 French patient isolates and environmental strains were compared using a mixed-genome micro-array. The micro-array data were analysed to identify predictive markers, using a Random Forest algorithm combined with a logistic regression model. The sequences of the identified markers were compared with eleven known Legionella genomes, using BlastN and BlastX; the functionality for each of the predictive markers was checked in the literature.ResultsThe five Dutch markers insufficiently predicted the patient or environmental origin of the French Legionella strains. Subsequent analyses identified four predictive markers for the French collection that were used for the logistic regression model. This model showed a negative predictive value of 91%. Three of the French markers differed from the Dutch markers, one showed considerable overlap and was found in one of the Legionella genomes (Lorraine strain). This marker encodes for a structural toxin protein RtxA, described for L. pneumophila as a factor involved in virulence and entry in both human cells and amoebae.ConclusionsThe combination of a mixed-genome micro-array and statistical analysis using a Random Forest algorithm has identified virulence markers in a consistent way. The Lorraine strain and related Dutch and French Legionella strains contain a marker that encodes a RtxA protein which probably is involved in the increased prevalence in clinical isolates. The current set of predictive markers is insufficient to justify its use as a reliable test in the public health field in France. Our results suggest that genetic differences in Legionella strains exist between geographically distinct entities. It may be necessary to develop region-specific mixed-genome microarrays that are constantly adapted and updated.

Evolutionary Changes in Antimicrobial Resistance of Invasive Neisseria meningitidis Isolates in Belgium from 2000 to 2010: Increasing Prevalence of Penicillin Nonsusceptibility

This study was conducted to evaluate the evolution of the antimicrobial susceptibility of Neisseria meningitidis causing invasive diseases in Belgium in the period of January 2000 to December 2010. A total of 1,933 cases of N. meningitidis from invasive infections were analyzed by antimicrobial susceptibility testing at the Belgian Meningococcal Reference Centre. The majority of strains were susceptible to antibiotics that are currently used for the treatment and prophylaxis of meningococcal disease, but the prevalence of clinical isolates with reduced susceptibility to penicillin increased over the years. The phenotyping, genotyping, and determination of MICs of penicillin G were performed. The systematic shift of the curves toward higher penicillin MICs in the susceptible population indicated that this population became less sensitive to penicillin in this period. A 402-bp DNA fragment in the 3' end of penA was sequenced for the 296 nonsusceptible meningococcal strains isolated between 2000 and 2010 to examine the genetic diversity and evolution of their penA gene. In conclusion, the data obtained in our study support the statement that the position of penicillin G as a first choice in the treatment of invasive meningococcal diseases in Belgium should be reexamined. Despite an important number of isolates displaying a reduced susceptibility to penicillin, at present the expanded-spectrum cephalosporins, such as ceftriaxone, are not affected. The follow-up of the evolutionary changes in antimicrobial resistance has also proved to be essential for the recommendation of an appropriate antimicrobial treatment for invasive meningococcal diseases.

Detection of the Smqnr quinolone protection gene and its prevalence in clinical isolates of Stenotrophomonas maltophilia in China

The aim of this study was to detect novel variants of the Stenotrophomonas maltophilia Smqnr gene family and analyse the prevalence of Smqnr genes in clinical isolates of S. maltophilia in China. In total, 442 clinical isolates of S. maltophilia were collected from nine hospitals in four provinces in China. Antimicrobial susceptibility testing against six commonly used antibiotics was performed on these isolates. The sequences of the Smqnr genes amplified by PCR were aligned with those of known Smqnr genes in GenBank and an Smqnr database. The resistance rate against co-trimoxazole was highest at 48.6 %, followed by resistance rates against ceftazidime, chloramphenicol, ticarcillin/clavulanate and tigecycline at 28.7, 21.3, 19.0 and 16.1 %, respectively. The highest susceptibility was shown to levofloxacin, with a resistance rate of just 6.1 %. Smqnr genes were detected in 114 isolates, and comprised 11 previously identified genes and 20 new variants, bringing the total number of known Smqnr genes to 47. The 20 novel Smqnr genes were designated Smqnr28-47 and the encoded proteins showed only 1-12 amino acid differences among each other. The most common Smqnr genes in China were Smqnr8 and its variant Smqnr35 with prevalences of 17.5 % (20/114) and 13.2 % (15/114), respectively. Both the known and the novel Smqnr genes were discovered in both quinolone non-sensitive and sensitive isolates with similar frequency, suggesting that the Smqnr gene makes little contribution to quinolone resistance in this organism.

The prevalence of the duodenal ulcer promoting gene (dupA) in Helicobacter pylori isolates varies by ethnic group and is not universally associated with disease development: a case-control study

BackgroundThe putative H. pylori pathogenicity-associated factor dupA has been associated with IL-8 induction in vitro, and duodenal ulcer (DU) and gastric cancer (GC) development in certain populations, but this association is inconsistent between studies. We aimed to investigate dupA prevalence in clinical isolates from Sweden, Australia and from ethnic Chinese, Indians and Malays resident in Malaysia and Singapore and to examine the association with DU and GC. In addition we investigated the sequence diversity between isolates from these diverse groups and compared the level of IL-8 secretion in isolates possessing and lacking dupA.MethodsPCR primers were designed to amplify over the C/T insertion denoting a continuous dupA. PCR products from 29 clinical isolates were sequenced and compared with sequences from three additional strains obtained from GenBank. Clinical isolates from 21 Malaysian patients (8 dupA-positive, 14 dupA-negative) were assessed for their ability to induce IL-8 in AGS cells in vitro. Statistical analysis was performed using Fisher's exact test.ResultsThe prevalence of dupA in isolates from Swedish functional dyspepsia (FD) control patients (65%, 13/20) was higher and in isolates from Indian FD patients (7.1%, 3/42) was lower as compared with isolates from Chinese (28.9%, 13/49, P = 0.005, P = 0.025), Malay (35.7%, 5/14, P = 0.16, P = 0.018) and Australian (37.8%, 17/45, P = 0.060, P < 0.001) FD patients. dupA was associated with DU and GC development in Chinese with 62.5% (10/16) and 54.6% (12/22) of isolates possessing dupA respectively as compared with FD controls (28.9%) (P = 0.015, P = 0.032). No significant difference in prevalence of dupA between FD controls, DU (63.6%, 7/11) and GC (61.9%, 13/21) cases (P = 1.000) was observed in the Swedish population. Sequence analysis revealed a pairwise variation of 1.9% and all isolates possessed the C/T insertion. The average IL-8 induction was 1330 pg/mL for dupA-positive isolates and 1378 pg/mL for dupA-negative isolates.ConclusionAlthough dupA is highly conserved when present, we identified no consistent association between dupA and DU or GC development across the ethnic groups investigated, with the dupA prevalence in control groups varying significantly. Our results would suggest that in the clinical isolates investigated dupA is not associated with IL-8 induction in vitro.

Burkholderia cepacia Complex Bacteria from Clinical and Environmental Sources in Italy: Genomovar Status and Distribution of Traits Related to Virulence and Transmissibility

Sixty-eight Burkholderia cepacia complex isolates recovered from the sputum of 53 cystic fibrosis patients and 75 isolates collected from the maize rhizosphere were compared to each other to assess their genomovar status as well as some traits related to virulence such as antibiotic susceptibility, proteolytic and hemolytic activities, and transmissibility, in which transmissibility is determined by detection of the esmR and cblA genes. Among the clinical isolates, B. cepacia genomovar III comprised the majority of isolates examined and only a very few isolates were assigned to B. cepacia genomovar I, B. stabilis, and B. pyrrocinia; among the environmental isolates a prevalence of B. cepacia genomovar III and B. ambifaria was observed, whereas few environmental isolates belonging to B. cepacia genomovar I and B. pyrrocinia were found. Antibiotic resistance analysis revealed a certain degree of differentiation between clinical and environmental isolates. Proteolytic activity and onion tissue maceration ability were found to be spread equally among both clinical and environmental isolates, whereas larger percentages of environmental isolates than clinical isolates had hemolytic activity. The esmR gene was found exclusively among isolates belonging to B. cepacia genomovar III, with a marked prevalence in clinical isolates, whereas only one clinical isolate belonging to B. cepacia genomovar III was found to bear the cblA gene. In conclusion, the results of the present study show that the species compositions of the clinical and environmental B. cepacia complex populations examined are quite different and that some of the candidate determinants related to virulence and transmissibility are not confined solely to clinical isolates but are also spread among environmental isolates belonging to different species of the B. cepacia complex.

Missense mutations that alter the DNA-binding domain of the MtrR protein occur frequently in rectal isolates of Neisseria gonorrhoeae that are resistant to faecal lipids.

Resistance of Neisseria gonorrhoeae to structurally diverse hydrophobic agents (HAs) has been associated with missense or deletion mutations in the mtrR (multiple transferable resistance Regulator) gene of laboratory-derived strains but their prevalence in clinical isolates was heretofore unknown. Since faecal lipids provide strong selective pressure for the emergence of variants resistant to HAs (HAR), the nucleotide sequence of the mtrR gene from rectal isolates of N. gonorrhoeae, which displayed different levels of HAR, was determined. Compared to the mtrR gene possessed by the HA-sensitive strain FA19, each clinical isolate contained mutations in the coding and/or promoter regions of their mtrR gene. A missense mutation in codon 45 (Gly-45 to Asp) was the most common mutation found in the strains studied and impacted the structure of the helix-turn-helix domain of the MtrR protein thought to be important in DNA-binding activity. Two clinical isolates bearing a missense mutation in codon 45 also contained a single basepair deletion in a 13 bp inverted sequence positioned within the mtrR promoter region. Introduction of mtrR sequences amplified from the clinical isolates into strain FA19 revealed that acquisition of the single basepair deletion was correlated with high level HAR while mutations in the mtrR-coding region provided for an intermediate level of HAR.

Focused microbiological surveillance by specific hospital unit as a sensitive means of defining antimicrobial resistance problems

An annual summary of susceptibility patterns for the predominant clinical isolates from hospitalized patients can be of considerable assistance in selecting antimicrobial agents for sepsis of unclear etiology, as well as for guiding empiric therapy for other serious infections. Yearly summaries of the susceptibility patterns of the predominant clinical isolates from all patients hospitalized at Vanderbilt University Hospital (VUH) from July 1987 through June 1991 revealed only minor differences over time in susceptibility patterns. However, the clinical impression of physicians treating patients in various intensive care units (ICUs) was that there were serious resistance problems in some units. To better define the prevalence of clinical isolates and their susceptibility patterns for patients within ICUs at VUH, we utilized a "focused microbiologic surveillance" technique that addressed each unit separately. Both the predominant clinical isolates and their susceptibility patterns were determined and compared with those from the hospital as a whole. Because susceptibility patterns of clinical isolates by site of infection within these units were considered important, we also reviewed the summaries of susceptibility patterns for blood, sputum, and urine isolates from patients in ICUs and compared these with the summaries from each ICU and from the hospital. No major resistance problems were identified on a hospital-wide basis. In contrast, focused microbiologic surveillance by specific hospital ICU revealed important differences in the prevalence of pathogens among units and at different times. In 1987, Pseudomonas aeruginosa was the single most common Gram-negative organism isolated in the neonatal unit, while Acinetobacter spp. were rarely isolated. By 1991, this trend was completely reversed.(ABSTRACT TRUNCATED AT 250 WORDS)