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The Journal of Antimicrobial... Mar 2019Recent reports indicate the emergence of a new carbapenemase-producing Klebsiella pneumoniae clone, ST307. We sought to better understand the global epidemiology and...
OBJECTIVES
Recent reports indicate the emergence of a new carbapenemase-producing Klebsiella pneumoniae clone, ST307. We sought to better understand the global epidemiology and evolution of this clone and evaluate its association with antimicrobial resistance (AMR) genes.
METHODS
We collated information from the literature and public databases and performed a comparative analysis of 95 ST307 genomes (including 37 that were newly sequenced).
RESULTS
We show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the blaCTX-M-15 ESBL gene and several other AMR determinants.
CONCLUSIONS
Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance has occasionally emerged.
Topics: Carbapenem-Resistant Enterobacteriaceae; Drug Resistance, Bacterial; Genome, Bacterial; Genotype; Global Health; Humans; Klebsiella Infections; Klebsiella pneumoniae; Molecular Epidemiology; beta-Lactamases
PubMed: 30517666
DOI: 10.1093/jac/dky492 -
MicrobiologyOpen Apr 2019Resistance to colistin, mediated by chromosomal mutations and more recently, by plasmid-borne mcr genes, is increasingly being reported in bacterial isolates taken from...
Resistance to colistin, mediated by chromosomal mutations and more recently, by plasmid-borne mcr genes, is increasingly being reported in bacterial isolates taken from humans, animals, farms, foods, and the environment. To easily identify and contain this quickly spreading menace, efficient diagnostics that are cheaper, faster, simpler, sensitive, and specific have become indispensable and urgently necessary. A thorough and systematic review of the literature available at Pubmed, ScienceDirect and Web of Science was thus undertaken to identify articles describing novel and efficient colistin resistance- and mcr gene-detecting methods. From the final 23 studies included in this review, both phenotypic and molecular tests were found. The phenotypic tests consisted of novel culture media viz., SuperPolymyxin™, CHROMagar COL-APSE and LBJMR media, commercial automated MIC-determining instruments such as MICRONAUT-S, Vitek 2, BD Phoenix, Sensititre and MicroScan, and novel assays such as Colistin MAC test, Colispot, rapid polymxin NP test (RPNP), alteration of Zeta potential, modified RPNP test, MICRONAUT-MIC Strip, MIC Test Strip, UMIC System, and Sensitest™ Colistin. Molecular diagnostics consisted of the CT103XL microarray, eazyplex SuperBug kit, and Taqman /SYBR Green real-time PCR assays, with 100% sensitivity and specificity plus a shorter turnaround time (<3 hr). Based on the sensitivity, specificity, cost, required skill and turnaround time, the RPNP test and/or novel culture media is recommended for under-resourced laboratories while the Multiplex PCR or Taqman /SYBR Green real-time PCR assay alongside the RPNP or novel culture media is suggested for well-resourced ones.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Bacterial Infections; Bacterial Proteins; Colistin; Drug Resistance, Bacterial; Genetic Techniques; Humans; Microbial Sensitivity Tests
PubMed: 29974640
DOI: 10.1002/mbo3.682 -
PloS One 2018Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa.
METHODS
Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias. A random effects model was used to assess heterogeneity and estimate pooled proportions. Relative and cumulative frequencies were calculated to describe the overall preponderance of FQ-resistance determinants in quinolone resistant isolates.
RESULTS
The pooled proportion of gyrA mutants (Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Salmonella enterica serovar Enteritidis) was estimated at 5.7% (95% Confidence interval (CI) = 2.6, 9.8; Tau squared (T2) = 0.1105), and was higher in S. Typhi than in S. Typhimurium (odds ratio (OR) = 3.3, 95%CI = 2, 5.7). The proportions of each of gyrB and parC mutants, and strains with Plasmid Mediated Quinolone Resistance genes (qnrA, qnrB and qnrS) were low (≤ 0.3%). Overall, 23 mutant serotypes were identified, and most strains had mutations at codons encoding Ser83 and Asp87 of gyrA (82%, 95%CI = 78, 86).
CONCLUSIONS
Mutations at gyrA appear to account for ciprofloxacin non-susceptibility in most clinical Salmonella strains in Africa. The estimates could be harnessed to develop a mismatch-amplification mutation-assay for the detection of FQ-resistant strains in Africa.
Topics: Africa; Drug Resistance, Bacterial; Fluoroquinolones; Molecular Epidemiology; Mutation; Salmonella
PubMed: 29432492
DOI: 10.1371/journal.pone.0192575 -
Zoonoses and Public Health Feb 2018The emergence and spread of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-PE) are complex and of the public health concern across the globe. This... (Meta-Analysis)
Meta-Analysis Review
Preliminary insights into the occurrence of similar clones of extended-spectrum beta-lactamase-producing bacteria in humans, animals and the environment in Tanzania: A systematic review and meta-analysis between 2005 and 2016.
The emergence and spread of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-PE) are complex and of the public health concern across the globe. This review aimed at assessing the ESBL-PE clones circulating in humans, animals and the environment to provide evidence-based insights for combating ESBL-PE using One Health approach. Systematic search from Medline/PubMed, Google Scholar and African Journals Online was carried out and retrieved nine eligible articles (of 131) based on phenotypic and genotypic detection of ESBL-PE between 2005 and 2016 in Tanzania. Analysis was performed using STATA 11.0 software to delineate the prevalence of ESBL-PE, phenotypic resistance profiles and clones circulating in the three interfaces. The overall prevalence of ESBL-PE in the three interfaces was 22.6% (95% CI: 21.1-24.2) with the predominance of Escherichia coli (E. coli) strains (51.6%). The majority of ESBL-PE were resistant to the commonly used antimicrobials such as trimethoprim-sulfamethoxazole and tetracycline/doxycycline, 38%-55% were resistant to ciprofloxacin and all were sensitive to meropenem/imipenem. ESBL-PE infections were more associated with deaths compared to non-ESBL-PE infections. Strikingly, E. coli ST38, ST131 and ST2852 were found to intersect variably across the three interfaces. The predominant allele, bla was found mostly in the conjugative IncF plasmids connoting transmission potential. The high prevalence of ESBL-PE and shared clones across the three interfaces, including the global E. coli ST131 clone, indicates wide and inter-compartmental spread that calls for One Health genomic-driven studies to track the resistome flow.
Topics: Animals; Bacteria; Drug Resistance, Multiple, Bacterial; Environmental Microbiology; Humans; Tanzania; beta-Lactamases
PubMed: 28834351
DOI: 10.1111/zph.12387 -
The Cochrane Database of Systematic... Jun 2017Peripheral artery disease (PAD) is associated with a high clinical and socioeconomic burden. Treatments to alleviate the symptoms of PAD and decrease the risks of... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Peripheral artery disease (PAD) is associated with a high clinical and socioeconomic burden. Treatments to alleviate the symptoms of PAD and decrease the risks of amputation and death are a high societal priority. A number of growth factors have shown a potential to stimulate angiogenesis. Growth factors delivered directly (as recombinant proteins), or indirectly (e.g. by viral vectors or DNA plasmids encoding these factors), have emerged as a promising strategy to treat patients with PAD.
OBJECTIVES
To assess the effects of growth factors that promote angiogenesis for treating people with PAD of the lower extremities.
SEARCH METHODS
The Cochrane Vascular Information Specialist searched the Specialised Register (June 2016) and CENTRAL (2016, Issue 5). We searched trial registries for details of ongoing or unpublished studies. We also checked the reference lists of relevant publications and, if necessary, tried to contact the trialists for details of the studies.
SELECTION CRITERIA
We included randomised controlled trials comparing growth factors (delivered directly or indirectly) with no intervention, placebo or any other intervention not based on the growth factor's action in patients with PAD of the lower extremities. The primary outcomes were limb amputation, death and adverse events. The secondary outcomes comprised walking ability, haemodynamic measures, ulceration and rest pain.
DATA COLLECTION AND ANALYSIS
Two review authors independently selected trials and assessed the risk of bias. We used outcomes of the studies at low risk of bias for the main analysis and of all studies in the sensitivity analyses. We calculated odds ratios (OR) for dichotomous outcomes and mean differences for continuous outcomes with 95% confidence intervals (CI). We evaluated statistical heterogeneity using the I statistic and Cochrane's Q test. We conducted meta-analysis for the overall effect and for each growth factor as a subgroup analysis using OR in a fixed-effect model. We evaluated the robustness of the results in a sensitivity analysis using risk ratio (RR) and/or a random-effects model. We also assessed the quality of the evidence for each outcome.
MAIN RESULTS
We included 20 trials in the review and used 14 studies (on approximately 1400 participants) with published results in the analyses. Six published studies compared fibroblast growth factors (FGF), four studies hepatocyte growth factors (HGF) and another four studies vascular endothelial growth factors (VEGF), versus placebo or no therapy. Six of these studies exclusively or mainly investigated participants with intermittent claudication and eight studies exclusively participants with critical limb ischaemia. Follow-up generally ranged from three months to one year. Two small studies provided some data at 2 years and one of them also at 10 years.The direction and size of effects for growth factors on major limb amputations (OR 0.99, 95% CI 0.71 to 1.38; 10 studies, N = 1075) and death (OR 0.99, 95% CI 0.69 to 1.41; 12 studies, N = 1371) at up to two years are uncertain. The quality of the evidence is low due to risk of bias and imprecision (at one year, moderate-quality evidence due to imprecision). However, growth factors may decrease the rate of any limb amputations (OR 0.56, 95% CI 0.31 to 0.99; 6 studies, N = 415). The quality of the evidence is low due to risk of bias and selective reporting.The direction and size of effects for growth factors on serious adverse events (OR 1.09, 95% CI 0.79 to 1.50; 13 studies, N = 1411) and on any adverse events (OR 1.10, 95% CI 0.73 to 1.64; 4 studies, N = 709) at up to two years are also uncertain. The quality of the evidence is low due to risk of bias and imprecision (for serious adverse events at one year, moderate-quality evidence due to imprecision).Growth factors may improve haemodynamic measures (low-quality evidence), ulceration (very low-quality evidence) and rest pain (very low-quality evidence) up to one year, but they have little or no effect on walking ability (low-quality evidence). We did not identify any relevant differences in effects between growth factors (FGF, HGF and VEGF).
AUTHORS' CONCLUSIONS
The results of this review do not support the use of therapy with the growth factors FGF, HGF or VEGF in people with PAD of the lower extremities to prevent death or major limb amputation or to improve walking ability. However, the use of these growth factors may improve haemodynamic measures and decrease the rate of any limb amputations (probably due to preventing minor amputations) with an uncertain effect on adverse events; an improvement of ulceration and rest pain is very uncertain. New trials at low risk of bias are needed to generate evidence with more certainty.
Topics: Amputation, Surgical; Fibroblast Growth Factors; Hepatocyte Growth Factor; Humans; Intermittent Claudication; Leg; Leg Ulcer; Peripheral Arterial Disease; Randomized Controlled Trials as Topic; Vascular Endothelial Growth Factor A
PubMed: 28594443
DOI: 10.1002/14651858.CD011741.pub2 -
Antimicrobial Resistant Streptococcus pneumoniae: Prevalence, Mechanisms, and Clinical Implications.American Journal of Therapeutics May 2017Streptococcus pneumoniae is a major cause of pneumonia, meningitis, sepsis, bacteremia, and otitis media. S. pneumoniae has developed increased resistance to multiple... (Review)
Review
BACKGROUND
Streptococcus pneumoniae is a major cause of pneumonia, meningitis, sepsis, bacteremia, and otitis media. S. pneumoniae has developed increased resistance to multiple classes of antibiotics.
STUDY DESIGN
Systematic literature review of prevalence, mechanisms, and clinical implications in S. pneumoniae resistance.
AREAS OF UNCERTAINTY
Since S. pneumoniae resistance to penicillin was first reported with subsequent development of resistance to other classes of drugs, selection of appropriate antibiotic treatment is challenging.
DATA SOURCES
We searched PubMed (English language) for citations to antibiotic resistance in S. pneumoniae published before March 1, 2016.
RESULTS
We present a review of S. pneumoniae resistance to beta-lactams, macrolides, lincosamides, fluoroquinolones, tetracyclines, and trimethoprim-sulfamethoxazole (TMP-SMX). There has been a steady decline in susceptibility of S. pneumoniae to commonly used beta-lactams. Phenotypic expression of penicillin resistance occurs as a result of a genetic structural modification in penicillin-binding proteins. Between 20% and 40% of S. pneumoniae isolates are resistant to macrolides. Macrolide resistance mechanisms include ribosomal target site alteration, alteration in antibiotic transport, and modification of the antibiotic. Approximately 22% of S. pneumoniae isolates are resistant to clindamycin. Similar to macrolide resistance, clindamycin involves a target site alteration. The prevalence of fluoroquinolone resistance is low, although increasing. S. pneumoniae resistance to fluoroquinolones occurs by accumulated mutations within the bacterial genome, increased efflux, or acquisition of plasmid-encoded genes. S. pneumoniae resistance has also increased for the tetracyclines. The primary mechanism is mediated by 2 genes that confer ribosomal protection. The prevalence of TMP-SMX resistance is around 35%. As with fluoroquinolones, resistance to TMP-SMX is secondary to mutations in the bacterial genome.
CONCLUSIONS
Effective treatment of resistant S. pneumoniae is a growing concern. New classes of drugs, newer formulations of older drugs, combination antibiotic therapy, nonantibiotic modalities, better oversight of antibiotic usage, and enhanced preventive measures hold promise.
Topics: Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Genome, Bacterial; Humans; Mutation; Pneumococcal Infections; Prevalence; Streptococcus pneumoniae
PubMed: 28430673
DOI: 10.1097/MJT.0000000000000551 -
European Journal of Clinical... Mar 2017Quinolones are a family of synthetic broad-spectrum antimicrobial drugs. These molecules have been widely prescribed to treat various infectious diseases and have been... (Review)
Review
Quinolones are a family of synthetic broad-spectrum antimicrobial drugs. These molecules have been widely prescribed to treat various infectious diseases and have been classified into several generations based on their spectrum of activity. Quinolones inhibit bacterial DNA synthesis by interfering with the action of DNA gyrase and topoisomerase IV. Mutations in the genes encoding these targets are the most common mechanisms of high-level fluoroquinolone resistance. Moreover, three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998 and include Qnr proteins, the aminoglycoside acetyltransferase AAC(6')-Ib-cr, and plasmid-mediated efflux pumps QepA and OqxAB. Plasmids with these mechanisms often encode additional antimicrobial resistance (extended spectrum beta-lactamases [ESBLs] and plasmidic AmpC [pAmpC] ß-lactamases) and can transfer multidrug resistance. The PMQR determinants are disseminated in Mediterranean countries with prevalence relatively high depending on the sources and the regions, highlighting the necessity of long-term surveillance for the future monitoring of trends in the occurrence of PMQR genes.
Topics: Anti-Bacterial Agents; Drug Resistance, Bacterial; Enterobacteriaceae; Enterobacteriaceae Infections; Humans; Mediterranean Region; Plasmids; Prevalence; Quinolones
PubMed: 27889879
DOI: 10.1007/s10096-016-2847-x -
Infection Ecology & Epidemiology 2014Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBL) has been found all over the world, and risk factors for acquiring these bacteria involve hospital... (Review)
Review
INTRODUCTION
Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBL) has been found all over the world, and risk factors for acquiring these bacteria involve hospital care and antibiotic treatment. Surveillance studies are present in Europe, North America, and Asia, but there is no summarizing research published on the situation in Africa.
AIM
This review aims to describe the prevalence of ESBL-producing Enterobacteriaceae in hospital and community settings in Africa and the ESBL genes involved.
METHOD
A non-systematic literature search was performed in PubMed. All articles published between 2008 and 2012 were screened and read in full text. Relevant articles were assessed for quality of evidence and included in the review. Articles were divided into regional areas in Africa and tabulated.
RESULTS
ESBL-producing Enterobacteriaceae in hospitalized patients and in communities varies largely between countries and specimens but is common in Africa. ESBLs (class A and D) and plasmid-encoded AmpC (pAmpC) were regularly found, but carbapenemases were also present.
CONCLUSION
ESBL-producing Enterobacteriaceae in hospital and community settings in Africa is common. Surveillance of antimicrobial resistance needs to be implemented in Africa to tailor interventions targeted at stopping the dissemination of ESBL-producing Enterobacteriaceae.
PubMed: 24765249
DOI: 10.3402/iee.v4.20342 -
Beneficial Microbes Sep 2014Lactobacillus reuteri ATCC 55730 has been shown to provide a moderate clinical effect in the treatment of acute gastroenteritis (AGE) in children. However, as the L.... (Meta-Analysis)
Meta-Analysis Review
Lactobacillus reuteri ATCC 55730 has been shown to provide a moderate clinical effect in the treatment of acute gastroenteritis (AGE) in children. However, as the L. reuteri ATCC 55730 strain was found to carry potentially transferable resistance traits for tetracycline and lincomycin, it was replaced by a new strain, L. reuteri DSM 17938, without unwanted plasmid-borne antibiotic resistance. Bioequivalence of the two strains has been suggested. We aimed to systematically evaluate data on the effectiveness of L. reuteri DSM 17938 and the original strain, L. reuteri ATCC 55730, in the treatment of AGE in children. The Cochrane Library, MEDLINE, and EMBASE databases, reference lists, and abstract books of major scientific meetings were searched in August 2013, with no language restrictions, for relevant randomised controlled trials (RCTs). Two RCTs (n=196) that evaluated L. reuteri DSM 17938 and three RCTs (n=156) that evaluated L. reuteri ATCC 55730, which involved hospitalised children aged 3 to 60 months, met the inclusion criteria. Compared with placebo or no treatment, DSM 17938 significantly reduced the duration of diarrhoea (mean difference -32 h, 95% confidence interval (CI): -41 to -24) and increased the chance of cure on day 3 (relative risk: 3.5, 95% CI: 1.2 to 10.8, random effects model). Similar results were obtained with the original strain, L. reuteri ATCC 55730. In conclusion, in hospitalised children, use of both strains of L. reuteri reduced the duration of diarrhoea, and more children were cured within 3 days. Data from outpatients and countryspecific cost-effectiveness analyses are needed. Given the limited data and the methodological limitations of the included trials, the evidence should be viewed with caution.
Topics: Anti-Bacterial Agents; Child, Preschool; Diarrhea; Drug Resistance, Multiple, Bacterial; Feces; Gastroenteritis; Humans; Infant; Limosilactobacillus reuteri; Lincomycin; Probiotics; Tetracycline
PubMed: 24463209
DOI: 10.3920/BM2013.0056 -
VASA. Zeitschrift Fur Gefasskrankheiten Sep 2013Beyond pharmacological, endovascular and surgical treatment strategies for peripheral arterial disease (PAD), therapeutic angiogenesis has been advocated to relieve... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Beyond pharmacological, endovascular and surgical treatment strategies for peripheral arterial disease (PAD), therapeutic angiogenesis has been advocated to relieve symptoms and support limb salvage, in particular in patients with critical limb ischemia. We aimed to systematically review randomized controlled trials (RCTs) of gene therapy in PAD.
PATIENTS AND METHODS
A systematic search of electronic databases was performed to identify RCTs studying local administration of pro-angiogenic growth factors (VEGF, FGF, HGF, Del-1, HIF-1alpha) using plasmid or viral gene transfer by intra-arterial or intra-muscular injections. Outcomes of interest comprised all-cause mortality, amputations, ulcer healing, walking distance and ankle-brachial index. If feasible, standard meta-analysis should be performed with subgroup analysis for claudicants and patients with critical limb ischemia (CLI).
RESULTS
The systematic search yielded 12 RCTs for analysis from 1163 citations. In total, 1494 patients (29 % females) were included with the majority suffering from CLI (64 %). Various endpoints were improved by single studies, but none by a majority of studies. Meta-analysis showed neither a significant benefit nor harm for gene therapy when synthesizing data for all-cause mortality (OR 0.88, 95 % CI 0.62 - 1.26) amputations (OR 0.64, 95 % CI 0.31 - 1.31) or ulcer healing (OR 1.79, 95 % CI 0.8 - 4.01). No differences were seen between patients with intermittent claudication or CLI.
CONCLUSIONS
Despite promising results in single studies, no clear benefit could be identified for gene therapy in PAD patients, irrespective of disease severity.
Topics: Adult; Aged; Aged, 80 and over; Chi-Square Distribution; Critical Illness; Female; Genetic Therapy; Humans; Ischemia; Limb Salvage; Male; Middle Aged; Neovascularization, Physiologic; Odds Ratio; Peripheral Arterial Disease; Risk Factors; Treatment Outcome
PubMed: 23989068
DOI: 10.1024/0301-1526/a000298