EUCAST expert rules in antimicrobial susceptibility testing

Evaluation of Resistance Mechanisms in Carbapenem-Resistant Enterobacteriaceae

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) is a major concern leading to morbidity and mortality in the world. CRE often is becoming a cause of therapeutic failure in both hospital and community-acquired infections.

AIM

This study aimed to investigate the resistance mechanisms of CRE by phenotypic and molecular methods.

MATERIALS AND METHODS

Sixty CRE (50 Klebsiella pneumoniae, 6 Escherichia coli, and 4 Enterobacter spp.) were isolated from October 2018 to June 2019. Antimicrobial susceptibility testing was carried out using phenotypic methods. The carbapenem resistance mechanisms including efflux pump hyperexpression, AmpC overproduction, carbapenemase genes, and deficiency in OmpK35 and OmpK36 were determined by phenotypic and molecular methods, respectively.

RESULTS

Sixty CRE (50 Klebsiella pneumoniae, 6 Escherichia coli, and 4 Enterobacter spp.) were isolated from October 2018 to June 2019. Amikacin was found to be the most effective drug against CRE isolates. All isolates were resistant to imipenem and meropenem by the micro-broth dilution. AmpC overproduction was observed in all Enterobacter spp. and three K. pneumoniae isolates. No efflux pump activity was found. Carba NP test and Modified Hodge Test could find carbapenemase in 59 (98%) isolates and 57 (95%) isolates, respectively. The most common carbapenemase gene was bla OXA-48-like (72.8%) followed by bla NDM (50.8%), bla IMP (18.6%), bla VIM (11.8%), and bla KPC (6.7%). The ompK35 and ompK36 genes were not detected in 10 and 7 K. pneumoniae isolates, respectively.

CONCLUSION

The amikacin is considered as a very efficient antibiotic for the treatment of CRE isolates in our region. Carbapenemase production and overproduction of AmpC are the main carbapenem resistance mechanisms in CRE isolates. Finally, Carba NP test is a rapid and reliable test for early detection of carbapenemase-producing isolates.

OXA-1 β-lactamase and non-susceptibility to penicillin/β-lactamase inhibitor combinations among ESBL-producing Escherichia coli

Background

ESBL-producing Escherichia coli have expanded globally since the turn of the century and present a major public health issue. Their in vitro susceptibility to penicillin/inhibitor combinations is variable, and clinical use of these combinations against ESBL producers remains controversial. We hypothesized that this variability related to co-production of OXA-1 penicillinase.

Methods

During a national study we collected 293 ESBL-producing E. coli from bacteraemias, determined MICs by BSAC agar dilution, and undertook genomic sequencing with Illumina methodology.

Results

The collection was dominated by ST131 (n = 188 isolates, 64.2%) and blaCTX-M-15 (present in 229 isolates, 78.2%); over half the isolates (159/293, 54.3%) were ST131 with blaCTX-M-15. blaOXA-1 was found in 149 ESBL producers (50.9%) and blaTEM-1/191 in 137 (46.8%). Irrespective of whether all isolates were considered, or ST131 alone, there were strong associations (P < 0.001) between co-carriage of blaOXA-1 and reduced susceptibility to penicillin/inhibitor combinations, whereas there was no significant association with co-carriage of blaTEM-1/191. For piperacillin/tazobactam the modal MIC rose from 2 mg/L in the absence of blaOXA-1 to 8 or 16 mg/L in its presence; for co-amoxiclav the shift was smaller, from 4 or 8 to 16 mg/L, but crossed the breakpoint. blaOXA-1 was strongly associated with co-carriage also of aac(6')-Ib-cr, which compromises amikacin and tobramycin.

Conclusions

Co-carriage of OXA-1, a penicillinase with weak affinity for inhibitors, is a major correlate of resistance to piperacillin/tazobactam and co-amoxiclav in E. coli and is commonly associated with co-carriage of aac(6')-Ib-cr, which narrows aminoglycoside options.

Diagnostic and medical needs for therapeutic drug monitoring of antibiotics

Therapeutic drug monitoring (TDM) of antibiotics has been practiced for more than half a century, but it is still not widely applied for infected patients. It has a traditional focus on limiting toxicity of specific classes of antibiotics such as aminoglycosides and vancomycin. With more patients in critical care with higher levels of sickness severity and immunosuppression as well as an increasingly obese and ageing population, an increasing risk of suboptimal antibiotic exposure continues to escalate. As such, the value of TDM continues to expand, especially for beta-lactams which constitute the most frequently used antibiotic class. To date, the minimum inhibitory concentration (MIC) of infectious microbes rather than classification in terms of susceptible and resistant can be reported. In parallel, increasingly sophisticated TDM technology is becoming available ensuring that TDM is feasible and can deliver personalized antibiotic dosing schemes. There is an obvious need for extensive studies that will quantify the improvements in clinical outcome of individual TDM-guided dosing. We suggest that a broad diagnostic and medical investigation of the TDM arena, including market analyses and analytical technology assessment, is a current priority.

A 10-year single-center experience on Stenotrophomonas maltophilia resistotyping in Szeged, Hungary

Stenotrophomonas maltophilia is an aerobic, oxidase-negative and catalase-positive bacillus. S. maltophilia is a recognized opportunistic pathogen. Due to the advancements in invasive medical procedures, organ transplantation and chemotherapy of malignant illnesses, the relevance of this pathogen increased significantly. The therapy of S. maltophilia infections is challenging, as these bacteria show intrinsic resistance to multiple classes of antibiotics, the first-choice drug is sulfamethoxazole/trimethoprim. Our aim was to assess the epidemiology of S. maltophilia from various clinical samples and the characterization of resistance-levels and resistotyping of these samples over a long surveillance period. The study included S. maltophilia bacterial isolates from blood culture samples, respiratory samples and urine samples and the data for the samples, received between January 2008 until December 2017, a total of 817 S. maltophilia isolates were identified (respiratory samples n = 579, 70.9%, blood culture samples n = 175, 21.4% and urine samples n = 63, 7.7%). Levofloxacin and colistin-susceptibility rates were the highest (92.2%; n = 753), followed by tigecycline (90.5%, n = 739), the first-line agent sulfamethoxazole/trimethoprim (87.4%, n = 714), while phenotypic resistance rate was highest for amikacin (72.5% of isolates were resistant, n = 592). The clinical problem of sulfamethoxazole/trimethoprim-resistance is a complex issue, because there is no guideline available for the therapy of these infections.

Antibiotic resistant Klebsiella spp. from a hospital, hospital effluents and wastewater treatment plants in the uMgungundlovu District, KwaZulu-Natal, South Africa

Hospital effluents are crucial hotspots for the dissemination of antibiotic resistant microorganisms. This study analysed hospital effluent and proximate wastewater treatment plants for the presence of antibiotic resistant Klebsiella spp. Water samples were obtained twice over a three-month period from an urban and rural hospital at three effluent points each, and from two proximate wastewater treatment plants (WWTPs) comprising influent and effluent and river water samples up/downstream the WWTPs. Presumptive Klebsiella spp. were enumerated, isolated, and phenotypically confirmed using a well-established commercial test system for Enterobacteriaceae (API20E). Clinical Klebsiella pneumoniae isolates were provided by a hospital for comparison. The antibiotic resistance profiles of Klebsiella spp. isolates to 16 selected antibiotics were established according to EUCAST (European Committee on Antimicrobial Susceptibility Testing). In addition, extended spectrum β-lactamase (ESBL) and carbapenemase production was analysed. A total of 93 confirmed Klebsiella spp. isolates from hospital effluents and 37 from WWTPs were obtained, comprising K. pneumoniae and K. oxytoca. The viable counts for confirmed Klebsiella spp. for hospital effluents ranged from 1.38 × 10² to 1.03 × 10⁴, while those for WWTP influent were in a range of 1.76 × 10³ to 5.10 × 10³ CFU/ml. A higher proportion of Klebsiella spp. from urban hospital effluent was categorized as multidrug-resistant (MDR) (23%) compared to rural hospital effluent (9%). Resistance was observed to all antibiotic classes tested. Several clinical isolates presented resistance to four carbapenem antibiotics, while certain isolates from hospital effluent and WWTPs exhibited ertapenem and doripenem resistance. Fifteen Klebsiella spp. isolates (clinical and from urban hospital effluent) produced carbapenemases. Hospital effluents in South Africa contain antibiotic resistant Klebsiella spp. and may pose a risk to proximate informal communities if inadequately treated. Moreover, common phenotypic resistance profiles among isolates from the clinical-hospital effluent-wastewater works continuum suggest a need for further treatment of such effluent.

Recommendations of the Spanish Antibiogram Committee (COESANT) for selecting antimicrobial agents and concentrations for in vitro susceptibility studies using automated systems

Automated antimicrobial susceptibility testing devices are widely implemented in clinical microbiology laboratories in Spain, mainly using EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints. In 2007, a group of experts published recommendations for including antimicrobial agents and selecting concentrations in these systems. Under the patronage of the Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) and the Study Group on Mechanisms of Action and Resistance to Antimicrobial Agents (GEMARA) from the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), and aligned with the Spanish National Plan against Antimicrobial Resistance (PRAN), a group of experts have updated this document. The main modifications from the previous version comprise the inclusion of new antimicrobial agents, adaptation of the ranges of concentrations to cover the EUCAST breakpoints and epidemiological cut-off values (ECOFFs), and the inference of new resistance mechanisms. This proposal should be considered by different manufacturers and users when designing new panels or cards. In addition, recommendations for selective reporting are also included. With this approach, the implementation of EUCAST breakpoints will be easier, increasing the quality of antimicrobial susceptibility testing data and their microbiological interpretation. It will also benefit epidemiological surveillance studies as well as the clinical use of antimicrobials aligned with antimicrobial stewardship programs.

Combined Molecular and Phenotypic Antimicrobial Susceptibility Testing Is Beneficial in Detection of ESBL and AmpC Beta-Lactamase Producing Isolates of Enterobacteriaceae in Pediatric Patients with Bloodstream Infections

Objectives: The aim was to assess the potential advantage of combined genotypic testing with phenotypic antimicrobial susceptibility testing (AST) to detect AmpC β-lactamases (AmpC) and extended-spectrum β-lactamases (ESBL) producing Enterobacteriaceae isolated from blood cultures in a pediatric population. Materials and Methods: All first-time Enterobacteriaceae isolates recovered from blood cultures of pediatric patients at the Cincinnati Children's Hospital Medical Center between January 2017 and December 2018 were evaluated. The Check-MDR CT103XL β-lactamase assay was used to determine the presence of AmpC and ESBL, while AST was performed using the VITEK 2 platform. Phenotypic ESBL resistance was defined by resistance to either ceftriaxone or ceftazidime using Clinical and Laboratory Standards Institute breakpoints, while combined cefoxitin resistance with ceftriaxone or ceftazidime resistance was used to detect AmpCs (as per European Committee on Antimicrobial Susceptibility Testing standards). Results: Overall, there were 170 isolates. Genotypically, 21 (12.4%) had AmpC and 18 (10.6%) had ESBL genes detected. Phenotypically, 11 (6.5%) isolates were AmpC and 26 (15.3%) were ESBL producing organisms. Genotypic testing identified an additional 14 AmpC and two ESBL isolates that failed to meet phenotypic criteria. Conclusions: Using combined genotypic and phenotypic methods to detect AmpC and ESBL producing organisms increased the identification of resistant organism and provided potentially clinical relevant data to guide the treatment of resistant organisms.

Experimental concepts for linking the biological activities of antimicrobial peptides to their molecular modes of action

The search for novel compounds to combat multi-resistant bacterial infections includes exploring the potency of antimicrobial peptides and derivatives thereof. Complementary to high-throughput screening techniques, biophysical and biochemical studies of the biological activity of these compounds enable deep insight, which can be exploited in designing antimicrobial peptides with improved efficacy. This approach requires the combination of several techniques to study the effect of such peptides on both bacterial cells and simple mimics of their cell envelope, such as lipid-only vesicles. These efforts carry the challenge of bridging results across techniques and sample systems, including the proper choice of membrane mimics. This review describes some important concepts toward the development of potent antimicrobial peptides and how they translate to frequently applied experimental techniques, along with an outline of the biophysics pertaining to the killing mechanism of antimicrobial peptides.

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.

Epidemiological linkage of vancomycin-resistant Enterococcus faecium from different sources in Ahwaz, Iran

This study was set to determine the genetic linkage and the clonal relationship between vancomycin-resistant Enterococcusfaecium (VREfm) isolates in three hospitals of Ahwaz city. In this study, 1050 samples were collected from various rectal swabs, hands of health care workers, environmental surfaces, medical equipment and 146 enterococci isolates from clinical sources of three hospitals from March to September 2015. Antimicrobial resistance patterns in VREfm were detected by disk diffusion method. Genetic linkages of VREfm strains were investigated by pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Out of 366 enterococcal isolates, 163 Enterococcus faecium isolates were found to be resistant to vancomycin. PFGE and MLST analysis showed the presence of 79 pulsotypes and 11 sequence types (ST), respectively. In total, 90% of the isolates belonged to clonal complex 17 (CC17). Three new STs were reported for the first time in this study and ST80 was the predominant ST. We found a high prevalence of diverse VREfm with threatening antibiotic resistance patterns in all the studied sources with the dominance of CC17 VREfm strains in Ahwaz hospitals. Also, the results of typing method showed inter- and intra-hospital circulation of VREfm and similar pulsotypes and STs among different sources.

Staphylococcus aureus Specific FRET Probe-Based Antibacterial Susceptibility Testing (SF-AST) by Detection of Micrococcal Nuclease Activity

In this study, we describe a simple and rapid antibacterial susceptibility testing (AST) method for Staphylococcus aureus called S. aureus specific fluorescence resonance energy transfer (FRET) probe-based AST (SF-AST), which is based on an S. aureus specific FRET probe (SF probe) that detects micrococcal nuclease (MNase) activity secreted from S. aureus. The SF-AST was tested with an S. aureus quality control (QC) strain against six relevant antibiotics, and the minimum inhibitory concentration (MIC) values obtained with the broth microdilution (BMD) method were compared, as a gold standard AST. Results were obtained with high accuracy in 4-6 h. The MIC for the methicillin resistance using 20 clinical S. aureus isolates of SF-AST showed 100% sensitivity, specificity, positive predictive value, and negative predictive value, as compared to BMD. Thus, the SF-AST method is a simple, rapid, and useful antibiotic resistance test for S. aureus, and it provides a basis for clinical treatment in a short time.

Characterization of Resistance in Gram-Negative Urinary Isolates Using Existing and Novel Indicators of Clinical Relevance: A 10-Year Data Analysis

Classical resistance classifications (multidrug resistance [MDR], extensive drug resistance [XDR], pan-drug resistance [PDR]) are very useful for epidemiological purposes, however, they may not correlate well with clinical outcomes, therefore, several novel classification criteria (e.g., usual drug resistance [UDR], difficult-to-treat resistance [DTR]) were introduced for Gram-negative bacteria in recent years. Microbiological and resistance data was collected for urinary tract infections (UTIs) retrospectively, corresponding to the 2008.01.01–2017.12.31. period. Isolates were classified into various resistance categories (wild type/susceptible, UDR, MDR, XDR, DTR and PDR), in addition, two new indicators (modified DTR; mDTR and mcDTR) and a predictive composite score (pMAR) were introduced. Results: n = 16,240 (76.8%) outpatient and n = 13,386 (69.3%) inpatient UTI isolates were relevant to our analysis. Citrobacter-Enterobacter-Serratia had the highest level of UDR isolates (88.9%), the Proteus-Providencia-Morganella group had the highest mDTR levels. MDR levels were highest in Acinetobacter spp. (9.7%) and Proteus-Providencia-Morganella (9.1%). XDR- and DTR-levels were higher in non-fermenters (XDR: 1.7%–4.7%. DTR: 7.3%–7.9%) than in Enterobacterales isolates (XDR: 0%–0.1%. DTR: 0.02%–1.5%). Conclusions: The introduction of DTR (and its’ modifications detailed in this study) to the bedside and in clinical practice will definitely lead to substantial benefits in the assessment of the significance of bacterial resistance in human therapeutics.

Evaluation of the Coverage of 3 Antibiotic Regimens for Neonatal Sepsis in the Hospital Setting Across Asian Countries

IMPORTANCE

High levels of antimicrobial resistance in neonatal bloodstream isolates are being reported globally, including in Asia. Local hospital antibiogram data may include too few isolates to meaningfully examine the expected coverage of antibiotic regimens.

OBJECTIVE

To assess the coverage offered by 3 antibiotic regimens for empirical treatment of neonatal sepsis in Asian countries.

DESIGN, SETTING, AND PARTICIPANTS

A decision analytical model was used to estimate coverage of 3 prespecified antibiotic regimens according to a weighted-incidence syndromic combination antibiogram. Relevant data to parameterize the models were identified from a systematic search of Ovid MEDLINE and Embase. Data from Asian countries published from 2014 onward were of interest. Only data on blood culture isolates from neonates with sepsis, bloodstream infection, or bacteremia reported from the relevant setting were included. Data analysis was performed from April 2019 to July 2019.

EXPOSURES

The prespecified regimens of interest were aminopenicillin-gentamicin, third-generation cephalosporins (cefotaxime or ceftriaxone), and meropenem. The relative incidence of different bacteria and their antimicrobial susceptibility to antibiotics relevant for determining expected concordance with these regimens were extracted.

MAIN OUTCOMES AND MEASURES

Coverage was calculated on the basis of a decision-tree model incorporating relative bacterial incidence and antimicrobial susceptibility of relevant isolates. Data on 7 bacteria most commonly reported in the included studies were used for estimating coverage, which was reported at the country level.

RESULTS

Data from 48 studies reporting on 10 countries and 8376 isolates were used. Individual countries reported 51 (Vietnam) to 6284 (India) isolates. Coverage varied considerably between countries. Meropenem was generally estimated to provide the highest coverage, ranging from 64.0% (95% credible interval [CrI], 62.6%-65.4%) in India to 90.6% (95% CrI, 86.2%-94.4%) in Cambodia, followed by aminopenicillin-gentamicin (from 35.9% [95% CrI, 27.7%-44.0%] in Indonesia to 81.0% [95% CrI, 71.1%-89.7%] in Laos) and cefotaxime or ceftriaxone (from 17.9% [95% CrI, 11.7%-24.7%] in Indonesia to 75.0% [95% CrI, 64.8%-84.1%] in Laos). Aminopenicillin-gentamicin coverage was lower than that of meropenem in all countries except Laos (81.0%; 95% CrI, 71.1%-89.7%) and Nepal (74.3%; 95% CrI, 70.3%-78.2%), where 95% CrIs for aminopenicillin-gentamicin and meropenem were overlapping. Third-generation cephalosporin coverage was lowest of the 3 regimens in all countries. The coverage difference between aminopenicillin-gentamicin and meropenem for countries with nonoverlapping 95% CrIs ranged from -15.9% in China to -52.9% in Indonesia.

CONCLUSIONS AND RELEVANCE

This study's findings suggest that noncarbapenem antibiotic regimens may provide limited coverage for empirical treatment of neonatal sepsis in many Asian countries. Alternative regimens must be studied to limit carbapenem consumption.

Patients with cirrhosis and SBP: Increase in multidrug-resistant organisms and complications

BACKGROUND

Spontaneous bacterial peritonitis (SBP) is a serious complication in patients with liver cirrhosis. In recent years, it has been postulated that the rate of multidrug-resistant organisms (MDROs) is increasing, especially in nosocomial SBP patients. Aim of the present work was to investigate this hypothesis and its possible clinical consequences.

MATERIALS AND METHODS

One hundred and three culture-positive patients between 2007 and 2014 were compared with 81 patients between 2015 and 2017, to study the change of microbiological profiles and their clinical consequences. The cirrhosis patients with bacterascites requiring treatment were included as well.

RESULTS

The most prevalent Gram-negative bacteria isolated from ascites were Enterobacterales (31.6%) and in Gram-positive pathogens Staphylococci (22.8%). There was a significant increase in MDROs (22.3% ICU 40.7%, P = .048), accompanied by an increased incidence of sepsis (from 21.4% to 37.0%, P = .021), hepatorenal syndrome (from 40.8% to 58.0%, P = .007) and the need of catecholamine therapy (from 21.4% to 38.8%, P = .036). Nosocomial origin correlated with higher MDRO proportion, more complications and lower antimicrobial susceptibility rates in 12 commonly used antibiotics. MDROs were confirmed as an isolated predictor for inpatient mortality and complications in multivariable logistic regression.

CONCLUSIONS

The feeling in clinical practice that MDROs have increased in the last 11 years could be confirmed in our study in Munich, Germany. Nosocomial SBP correlated with significantly higher MDRO rates (nearly 50%) and complication rates. In our opinion, an antibiotic combination with comprehensive effect should be taken into account in nosocomial SBP patients in this region.

From CLSI to EUCAST, a necessary step in Spanish laboratories

The Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) presents in this document a simple "roadmap" or decalogue of recommendations, with a view to facilitating the transition from the Clinical and Laboratory Standards Institute (CLSI) to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) antimicrobial susceptibility testing regulations to the Clinical Microbiology Spanish laboratories that still use the CLSI guidelines. The objectives are to adapt the closer European regulations to the Spanish clinical and epidemiological reality and to fully implement the EUCAST recommendations in all microbiology laboratories in Spain.

A comprehensive overview of the cystic fibrosis on the island of São Miguel (Azores, Portugal)

BACKGROUND

Early diagnosis and treatment are improving significantly the quality of life of patients with cystic fibrosis (CF). This recessive disease is caused by a great variability of mutations in the CF transmembrane conductance (CFTR) gene, whose spectrum and frequency can be different across populations.

METHODS

We performed a retrospective cross-sectional study of CF patients from the island of São Miguel (Azores, Portugal) through a clinical, genealogical, genetic and epidemiological investigation. The clinical course of patients was analyzed as a whole and according to their genotype.

RESULTS

We identified 14 CF patients within a 23-year period, corresponding to a cumulative incidence of 1:3012 births, being three of them born from consanguineous unions. Genetic analysis revealed three CFTR genotypes: p.[Ser4Ter];[Gln1100Pro] was present in one patient with a less severe phenotype (1/14); c.[120del23];p.[Phe508del], a very rare one (2/14); and p.[Phe508del];[Phe508del] in the remaining patients (11/14). Clinically, respiratory infections (8/14) and growth failure (6/14) were the most common initial manifestations. All patients presented pancreatic dysfunction, with 21.4 and 100% of them showing endocrine and exocrine insufficiency, respectively. As expected, patients with severe phenotype were homozygous for p.Phe508del and had the lowest value of body mass index.

CONCLUSIONS

The present study demonstrated that São Miguel Island has an increased incidence of CF when compared to recent Portuguese data (1:7500 live births). It also allowed a comprehensive overview of CF in São Miguel, improving medical practice along with genetic counselling and creating opportunities for genotype-targeted therapies.

Antibacterial activity of Mn(I) and Re(I) tricarbonyl complexes conjugated to a bile acid carrier molecule

A bifunctional cholic acid-bis(2-pyridylmethyl)amine (bpa) ligand featuring an amide linker was coordinated to a manganese(i) or rhenium(i) tricarbonyl moiety to give [M(bpacholamide)(CO)3] with M = Mn, Re in good yield and very high purity. Strong antibacterial activity was observed against four strains of methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) Staphylococcus aureus, with minimum inhibitory concentrations (MICs) in the range of 2-3.5 μM. No difference in response was observed for the MSSA vs. MRSA strains. Activity was also independent of the nature of the metal center, as the Mn and Re complexes showed essentially identical MIC values. In contrast to some other metal carbonyl complexes, the activity seems to be unrelated to the release of carbon monoxide, as photoactivation of the Mn complex reduced the potency by a factor of 2-8. Both metal complexes were non-toxic in Galleria mellonella larvae at concentrations of up to 100× the MIC value. In vivo testing in Galleria larvae infected with MRSA/MSSA demonstrated a significant increase in overall survival rates from 46% in the control to 88% in the group treated with the metal complexes. ICP-MS analysis showed that the Mn and Re cholamide complexes are efficiently internalized by E. coli cells and do not interfere with membrane integrity, as evident from a lack of release of intracellular ATP. An increased sensitivity was observed in acrB, acrD, and mdt mutants that are defective in multidrug exporters, indicating that the compounds have an intracellular mechanism of action. Furthermore, E. coli mntP mutants defective in the gene encoding an Mn exporter were more sensitive than the wildtype, while inactivation of the regulator that controls expression of the Mn uptake proteins MntP and MntH slightly increased sensitivity to the compound. Single knockout mutants defective in genes linked to bile salt and oxidative stress response (dinF, yiaH, sodA, katE, and soxS) did not show increased sensitivity relative to the wild type. Overall, neither the cholic acid moiety nor the metal-carbonyl fragment alone appear to be responsible for the biological activity observed and thus the search for the primary intracellular target continues.

Changes in pathogen spectrum and antimicrobial resistance development in the time-course of acute necrotizing pancreatitis

BACKGROUND AND AIM

In contrast to the first peak of multi-organ failure in acute pancreatitis, the second peak is mostly triggered by septic complications. Our aim was to analyze the spectrum of pathogens and antimicrobial resistance development in relation to the time-course of the disease and its clinical outcome.

METHODS

One hundred twenty-two patients with acute necrotizing pancreatitis undergoing pancreas puncture at two tertiary academic medical centers in Germany were retrospectively analyzed.

RESULTS

At species level, there was a change in spectrum from Enterococcus faecalis (∆d150 - d1 = 14.6% - 16.7% = -2.1%) to Enterococcus faecium (∆d150 - d1 = 93.1% - 16.3% = 76.8%) (P < 0.001) and from Candida albicans (∆d150 - d1 = 39.7% - 23.6% = 16.1%) to non-albicans Candida spp. (∆d150 - d1 = 43.5% - 6.4% = 37.1%) (P = 0.005). Time-to-event analysis of acquired antimicrobial resistance showed that the overall number of patients with Enterobacteriaceae presented an antimicrobial susceptibility decrease by 59.7% (∆d1 - d100 = 87.0% - 27.3% = 59.7%). The cumulative incidence of multi-resistant bacteria increased with length of hospital stay (∆d150 - d1 = 49.1% - 3.1% = 46.0%) (P = 0.004). Multivariable logistic regression analysis in relation to the pathogen spectrum and antimicrobial resistance development showed a significantly higher mortality for non-albicans Candida spp. (P = 0.039, odds ratio [OR] = 3.32 [95% confidence interval [CI]: 1.07-10.35]), E. faecium (P = 0.009, OR = 3.73 [95% CI: 1.38-10.05]), and multi-resistant bacteria (P = 0.007, OR = 5.08 [95% CI: 1.55-16.66]).

CONCLUSIONS

Antimicrobial treatment of infected pancreatic necrosis becomes more challenging over time, owing to a change in spectrum favoring difficult-to-treat pathogens and an increase in multi-resistant bacteria associated with worse clinical outcomes (World Health Organization trial registration number: DRKS00014785).

Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon

The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911^T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.

Combination of mass spectrometry and DNA sequencing for detection of antibiotic resistance in diagnostic laboratories

In the last two decades, microbiology laboratories have radically changed by the introduction of novel technologies, like Next-Generation Sequencing (NGS) and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Nevertheless, emergence of antibiotic-resistant microorganisms represents a global threat of current medicine, being responsible for increasing mortality and health-care direct and indirect costs. In addition, the identification of antibiotic-resistant microorganisms, like OXA-48 carbapenemase-producing Enterobacteriaceae, has been changeling for clinical microbiology laboratories. Even the cost of NGS technology and MALDI-TOF MS equipment is relatively high, both technologies are increasingly used in diagnostic and research protocols. Therefore, the aim of this review is to present applications of these technologies used in clinical microbiology, especially in detection of antibiotic resistance and its surveillance, and to propose a combinatory approach of MALDI-TOF MS and NGS for the investigation of microbial associated infections.

Betaproteobacteria are predominant in drinking water: are there reasons for concern?

Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that can be found in drinking water, including mineral water. The combination of physiology and ecology traits place some Betaproteobacteria in the list of potential, yet sometimes neglected, opportunistic pathogens that can be transmitted by water or aqueous solutions. Indeed, some drinking water Betaproteobacteria with intrinsic and sometimes acquired antibiotic resistance, harbouring virulence factors and often found in biofilm structures, can persist after water disinfection and reach the consumer. This literature review summarises and discusses the current knowledge about the occurrence and implications of Betaproteobacteria in drinking water. Although the sparse knowledge on the ecology and physiology of Betaproteobacteria thriving in tap or bottled natural mineral/spring drinking water (DW) is an evidence of this review, it is demonstrated that DW holds a high diversity of Betaproteobacteria, whose presence may not be innocuous. Frequently belonging to genera also found in humans, DW Betaproteobacteria are ubiquitous in different habitats, have the potential to resist antibiotics either due to intrinsic or acquired mechanisms, and hold different virulence factors. The combination of these factors places DW Betaproteobacteria in the list of candidates of emerging opportunistic pathogens. Improved bacterial identification of clinical isolates associated with opportunistic infections and additional genomic and physiological studies may contribute to elucidate the potential impact of these bacteria.

Ventilator-associated pneumonia due to Stenotrophomonas maltophilia: Risk factors and outcome

BACKGROUND

Stenotrophomonas maltophilia (SM) is increasingly identified in intensive care unit (ICU). This study aim to identify risk factors for SM ventilator-associated pneumonia (VAP) and whether it affects ICU mortality METHODS: Two nested matched case-control studies were performed based in OUTCOMEREA database. The first episodes of SM-VAP patients were matched with two different control groups: VAP due to other micro-organisms (VAP-other) and Pseudomonas aeruginosa VAP (Pyo-VAP). Matching criteria were the hospital, the SAPS II, and the previous duration of mechanical ventilation (MV).

RESULTS

Of the 102 SM-VAP patients (6.2% of all VAP patients), 92 were matched with 375 controls for the SM-VAP/other-VAP matching and 84 with 237 controls for the SM-VAP/Pyo-VAP matching. SM-VAP risk factors were an exposition to ureido/carboxypenicillin or carbapenem during the week before VAP, and respiratory and coagulation components of SOFA score upper to 2 before VAP. SM-VAP received early adequate therapy in 70 cases (68.6%). Risk factors for Day-30 were age (OR = 1.03; p < 0.01) and Chronic heart failure (OR = 3.15; p < 0.01). Adequate treatment, either monotherapy or combination of antimicrobials, did not modify mortality. There was no difference in 30-day mortality, but 60-day mortality was higher in patients with SM-VAP compared to Other-VAP (P = 0.056).

CONCLUSIONS

In a large series, independent risk factors for the SM-VAP were ureido/carboxypenicillin or carbapenem exposure the week before VAP, and respiratory and coagulation components of the SOFA score > 2 before VAP. Mortality risk factors of SM-VAP were age and chronic heart failure. Adequate treatment did not improve SM-VAP prognosis.

The BACH classification of long bone osteomyelitis

Objectives

The aim of this study was to assess the clinical application of, and optimize the variables used in, the BACH classification of long-bone osteomyelitis.

Methods

A total of 30 clinicians from a variety of specialities classified 20 anonymized cases of long-bone osteomyelitis using BACH. Cases were derived from patients who presented to specialist centres in the United Kingdom between October 2016 and April 2017. Accuracy and Fleiss’ kappa (Fκ) were calculated for each variable. Bone involvement (B-variable) was assessed further by nine clinicians who classified ten additional cases of long bone osteomyelitis using a 3D clinical imaging package. Thresholds for defining multidrug-resistant (MDR) isolates were optimized using results from a further analysis of 253 long bone osteomyelitis cases.

Results

The B-variable had a classification accuracy of 77.0%, which improved to 95.7% when using a 3D clinical imaging package (p < 0.01). The A-variable demonstrated difficulty in the accuracy of classification for increasingly resistant isolates (A1 (non-resistant), 94.4%; A2 (MDR), 46.7%; A3 (extensively or pan-drug-resistant), 10.0%). Further analysis demonstrated that isolates with four or more resistant test results or less than 80% sensitive susceptibility test results had a 98.1% (95% confidence interval (CI) 96.6 to 99.6) and 98.8% (95% CI 98.1 to 100.0) correlation with MDR status, respectively. The coverage of the soft tissues (C-variable) and the host status (H-variable) both had a substantial agreement between users and a classification accuracy of 92.5% and 91.2%, respectively.

Conclusions

The BACH classification system can be applied accurately by users with a variety of clinical backgrounds. Accuracy of B-classification was improved using 3D imaging. The use of the A-variable has been optimized based on susceptibility testing results.

Cite this article: A. J. Hotchen, M. Dudareva, J. Y. Ferguson, P. Sendi, M. A. McNally. The BACH classification of long bone osteomyelitis. Bone Joint Res 2019;8:459–468. DOI: 10.1302/2046-3758.810.BJR-2019-0050.R1

Prevalence of Livestock-Associated Methicillin-Resistant Staphylococcus Aureus (LA-MRSA) Among Farm and Slaughterhouse Workers in Italy

OBJECTIVE

We measured the prevalence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in swine livestock workers, examined LA-MRSA resistance profile, and associated carriage with the working activities.

METHODS

Information was collected on demographics and occupational history. Swabs were collected and tested for the isolation of S. aureus, examined for antimicrobial susceptibility, and all MRSA underwent ST398qPCR assay.

RESULTS

LA-MRSA was isolated in 7.3% of the 396 enrolled workers. LA-MRSA colonization was more likely in farmers than in slaughterhouse workers (Fisher exact P = 0.001). Carriage was associated with herd size, being less frequent in small/medium farms (odds ratio = 0.20; 95% confidence interval = 0.07 to 0.53), and with the number of working days per week (OR = 2.11; 95% confidence interval = 1.07 to 4.19).

CONCLUSIONS

LA-MRSA carriage is strongly animal-exposure related, and educational intervention informing about the risks related to the activity with livestock is needed.

On the Etiological Relevance of Escherichia coli and Staphylococcus aureus in Superficial and Deep Infections - A Hypothesis-Forming, Retrospective Assessment

Introduction

Escherichia coli and Staphylococcus aureus are important causes of severe diseases like blood stream infections. This study comparatively assessed potential differences in their impact on disease severity in local and systemic infections.

Methods

Over a 5-year interval, patients in whom either E. coli or S. aureus was detected in superficial or primary sterile compartments were assessed for the primary endpoint death during hospital stay and the secondary endpoints duration of hospital stay and infectious disease as the main diagnosis.

Results

Significance was achieved for the impacts as follows: Superficial infection with S. aureus was associated with an odds ratio of 0.27 regarding the risk of death and of 1.42 regarding infectious disease as main diagnosis. Superficial infection with E. coli was associated with a reduced duration of hospital stay by –2.46 days and a reduced odds ratio of infectious diseases as main diagnosis of 0.04. The hospital stay of patients with E. coli was increased due to third-generation cephalosporin and ciprofloxacin resistance, and in the case of patients with S. aureus due to tetracycline and fusidic acid resistance.

Conclusions

Reduced disease severity of superficial infections due to both E. coli and S. aureus and resistance-driven prolonged stays in hospital were confirmed, while other outcome parameters were comparable.

Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains

Three human clinical isolates of bacteria (designated strains Em1, Em2 and Em3) had high average nucleotide identity (ANI) to Elizabethkingia meningoseptica. Their genome sizes (3.89, 4.04 and 4.04 Mb) were comparable to those of other Elizabethkingia species and strains, and exhibited open pan-genome characteristics, with two strains being nearly identical and the third divergent. These strains were susceptible only to trimethoprim/sulfamethoxazole and ciprofloxacin amongst 16 antibiotics in minimum inhibitory tests. The resistome exhibited a high diversity of resistance genes, including 5 different lactamase- and 18 efflux protein- encoding genes. Forty-four genes encoding virulence factors were conserved among the strains. Sialic acid transporters and curli synthesis genes were well conserved in E. meningoseptica but absent in E. anophelis and E. miricola. E. meningoseptica carried several genes contributing to biofilm formation. 58 glycoside hydrolases (GH) and 25 putative polysaccharide utilization loci (PULs) were found. The strains carried numerous genes encoding two-component system proteins (56), transcription factor proteins (187~191), and DNA-binding proteins (6~7). Several prophages and CRISPR/Cas elements were uniquely present in the genomes.

From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective

OBJECTIVES

Predicting the antibiotic susceptibility phenotype from genomic data is challenging, especially for some specific antibiotics in the order Enterobacterales. Here we aimed to assess the performance of whole genomic sequencing (WGS) for predicting the antibiotic susceptibility in various Enterobacterales species using the detection of antibiotic resistance genes (ARGs), specific mutations and a knowledge-based decision algorithm.

METHODS

We sequenced (Illumina MiSeq, 2×250 bp) 187 clinical isolates from species possessing (n = 98) or not (n = 89) an intrinsic AmpC-type cephalosporinase. Phenotypic antibiotic susceptibility was performed by the disc diffusion method. Reads were assembled by A5-miseq and ARGs were identified from the ResFinder database using Diamond. Mutations on GyrA and ParC topoisomerases were studied. Piperacillin, piperacillin-tazobactam, ceftazidime, cefepime, meropenem, amikacin, gentamicin and ciprofloxacin were considered for prediction.

RESULTS

A total of 1496 isolate/antibiotic combinations (187 isolates × 8 antibiotics) were considered. In 230 cases (15.4%), no attempt of prediction was made because it could not be supported by current knowledge. Among the 1266 attempts, 1220 (96.4%) were correct (963 for predicting susceptibility and 257 for predicting resistance), 24 (1.9%) were major errors (MEs) and 22 (1.7%) were very major errors (VMEs). Concordance were similar between non-AmpC and AmpC-producing Enterobacterales (754/784 (96.2%) vs 466/482 (96.7%), chi-square test p 0.15), but more VMEs were observed in non-AmpC producing strains than in those producing an AmpC (19/784 (2.4%) vs 3/466 (0.6%), chi-square test p 0.02). The majority of VMEs were putatively due to the overexpression of chromosomal genes.

CONCLUSIONS

In conclusion, the inference of antibiotic susceptibility from genomic data showed good performances for non-AmpC and AmpC-producing Enterobacterales species. However, more knowledge about the mechanisms underlying the derepression of AmpC are needed.

Optimization of the empirical antibiotic choice during the treatment of acute prosthetic joint infections: a retrospective analysis of 91 patients

Background and purpose - The preferred treatment of an acute prosthetic joint infection (PJI) is debridement, antibiotics, irrigation and retention of the prosthesis (DAIR). The antibiotic treatment consists of an empirical and targeted phase. In the empirical phase, intravenous antibiotics are started after surgery before micro-organisms are determined in microbiological cultures. Which empirical antibiotic is used differs between hospitals, partly reflecting geographic differences in susceptibility spectrums. We investigated whether flucloxacillin should remain the antibiotic of choice in our hospital for empiric treatment of acute PJI with DAIR. Patients and methods - We retrospectively analyzed 91 patients treated for PJI with DAIR between 2012 and 2016. The susceptibility of micro-organisms was determined in multiple cultures of periprosthetic tissue and synovial fluid for 3 antibiotics: amoxicillin/clavulanic acid, cefazolin, and flucloxacillin. Results - Positive microbiological cultures from 68 patients were analyzed. Staphylococcus aureus was the predominant pathogen, cultured in half of the patients. In one-third of patients more than 1 micro-organism was found. On a patient level, the data showed that 65% were responsive to flucloxacillin, 76% to amoxicillin/clavulanic acid, and 79% to cefazolin. Interpretation - Flucloxacillin appeared to be a suboptimal choice in our patient population treated with DAIR. We therefore changed our practice to cefazolin as the preferred antibiotic in the empirical treatment of acute PJI with DAIR.

Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp

The evolution of multidrug resistant bacteria to the most diverse antimicrobials known so far pose a serious problem to global public health. Currently, microorganisms that develop resistant phenotypes to multiple drugs are associated with high morbidity and mortality. This resistance is encoded by a group of genes termed ‘bacterial resistome’, divided in intrinsic and extrinsic resistome. The first one refers to the resistance displayed on an organism without previous exposure to an antibiotic not involving horizontal genetic transfer, and it can be acquired via mutations. The latter, on the contrary, is acquired exclusively via horizontal genetic transfer involving mobile genetic elements that constitute the ‘bacterial mobilome’. This transfer is mediated by three different mechanisms: transduction, transformation, and conjugation. Recently, a problem of public health due to implications in the emergence of multi-drug resistance in Aeromonas spp. strains in water environments has been described. This is derived from the genetic material transfer via conjugation events. This is important, since bacteria that have acquired antibiotic resistance in natural environments can cause infections derived from their ingestion or direct contact with open wounds or mucosal tissue, which in turn, by their resistant nature, makes their eradication complex. Implications of the emergence of resistance in Aeromonas spp. by horizontal gene transfer on public health are discussed.

Species-specific mutation rates for ampC derepression in Enterobacterales with chromosomally encoded inducible AmpC β-lactamase

Background

AmpC β-lactamases are encoded on the chromosomes of certain Enterobacterales and lead to clinical resistance to various β-lactams in case of high-level expression. In WT bacteria with inducible AmpC, the expression is low, but selection of stably ampC-derepressed mutants may occur during β-lactam therapy. Thus, for Enterobacter spp., Citrobacter freundii complex, Serratia spp. and Morganella morganii that test susceptible in vitro to oxyimino-cephalosporins, the EUCAST expert rules recommend suppressing susceptibility testing results for these agents or noting that their use in monotherapy should be discouraged, owing to the risk of selecting resistance. However, clinical observations suggest that emergence of resistance is not equally common in all species with inducible AmpC.

Objectives

To determine species-specific mutation rates, which are more accurate and reproducible than previously described mutant frequencies, for ampC derepression in Enterobacterales with inducible AmpC.

Methods

Mutation rates were determined using a protocol based on Luria-Delbrück fluctuation analyses. Overall, 237 isolates were analysed.

Results

Mutation rates were high in Enterobacter cloacae complex, Enterobacter aerogenes, C. freundii complex and Hafnia alvei isolates, with a mean mutation rate of 3 × 10-8. In contrast, mean mutation rates were considerably lower in Providencia spp., Serratia spp. and especially M. morganii isolates. Furthermore, we observed species-specific variations in the resistance patterns of ampC-derepressed mutants.

Conclusions

Our data might help to predict the risk of treatment failure with oxyimino-cephalosporins in infections by different Enterobacterales with inducible AmpC. Moreover, we make a proposal for optimization of the current EUCAST expert rule.

Resistance Levels and Epidemiology of Non-Fermenting Gram-Negative Bacteria in Urinary Tract Infections of Inpatients and Outpatients (RENFUTI): A 10-Year Epidemiological Snapshot

Background: Urinary tract infections (UTIs) are one of the most common infections in the human medicine, both among outpatients and inpatients. There is an increasing appreciation for the pathogenic role of non-fermenting Gram-negative bacteria (NFGNBs) in UTIs, particularly in the presence of underlying illnesses. Methods: The study was carried out using data regarding a 10-year period (2008-2017). The antimicrobial susceptibility testing was performed using the disk diffusion method, E-tests, and broth microdilution. Results: NFGNB represented 3.46% ± 0.93% for the outpatients, while 6.43% ± 0.81% of all positive urine samples for the inpatients (p < 0.001). In both groups, Pseudomonas spp. (78.7% compared to 85.1%) and Acinetobacter spp. (19.6% compared to 10.9%), were the most prevalent. The Acinetobacter resistance levels were significantly higher in inpatients isolates (p values ranging between 0.046 and <0.001), while the differences in the resistance levels of Pseudomonas was not as pronounced. The β-lactam-resistance levels were between 15-25% and 12-28% for the Acinetobacter and Pseudomonas spp., respectively. 4.71% of Acinetobacter and 1.67% of Pseudomonas were extensively drug resistant (XDR); no colistin-resistant isolates were recovered. Conclusions: Increasing resistance levels of the Acinetobacter spp. from 2013 onward, but not in the case of the Pseudomonas spp. Although rare, the drug resistant NFGNB in UTIs present a concerning therapeutic challenge to clinicians with few therapeutic options left.

Space Station conditions are selective but do not alter microbial characteristics relevant to human health

The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.

The International Space Station is a unique habitat for humans and microbes. Here, Mora et al. analyze microbial communities from several areas aboard, finding similarities with those of ground-based indoor environments, as well as adaptations towards biofilm formation but not necessarily relevant to human health.

Antibacterial resistance in ophthalmic infections: a multi-centre analysis across UK care settings

BACKGROUND

Bacterial ophthalmic infections are common. Empirical treatment with topical broad-spectrum antibiotics is recommended for severe cases. Antimicrobial resistance (AMR) to agents used for bacterial ophthalmic infections make it increasingly important to consider changing resistance patterns when prescribing, however UK data in this area are lacking. We evaluate the epidemiology and antimicrobial susceptibilities of ophthalmic pathogens across care settings and compare these with local and national antimicrobial prescribing guidelines.

METHODS

A retrospective, multi-centre observational analysis was undertaken of ophthalmic microbiology isolates between 2009 and 2015 at a centralised North-West London laboratory (incorporating data from primary care and five London teaching hospitals). Data were analysed using descriptive statistics with respect to patient demographics, pathogen distribution (across age-groups and care setting), seasonality, and susceptibility to topical chloramphenicol, moxifloxacin, and fusidic acid.

RESULTS

Two thousand six hundred eighty-one isolates (n = 2168 patients) were identified. The commonest pathogen in adults was Staphylococcus spp. across primary, secondary, and tertiary care (51.7%; 43.4%; 33.6% respectively) and in children was Haemophilus spp. (34.6%;28.2%;36.6%). AMR was high and increased across care settings for chloramphenicol (11.8%;15.1%;33.8%); moxifloxacin (5.5%;7.6%;25.5%); and fusidic acid (49.6%;53.4%; 58.7%). Pseudomonas spp. was the commonest chloramphenicol-resistant pathogen across all care settings, whilst Haemophilus spp. was the commonest fusidic acid-resistant pathogen across primary and secondary care. More isolates were recorded in spring (31.6%) than any other season, mostly due to a significant rise in Haemophilus spp.

CONCLUSIONS

We find UK national and local antimicrobial prescribing policies for ophthalmic infections may not be concordant with the organisms and antimicrobial susceptibilities found in clinical samples. We also find variations in microbial incidence related to patient age, clinical setting, and season. Such variations may have further important implications for prescribing practices and modification of antimicrobial guidelines.

Evaluating the best empirical antibiotic therapy in patients with acute-on-chronic liver failure and spontaneous bacterial peritonitis

BACKGROUND/AIMS

Spontaneous bacterial peritonitis (SBP) is a life-threatening complication of advanced cirrhosis. By studying the susceptibility of isolated organisms and analyzing empirical antibiotic therapy combined with clinical outcomes, we aimed to find an improved empirical antibiotic therapy by considering the individual acute-on-chronic liver failure (ACLF) grade for patients with or without sepsis.

METHODS

Clinical outcomes of 182 patients were assessed retrospectively with multivariable regression analysis. Each of the 223 isolates was individually evaluated regarding susceptibility results and intrinsic resistances.

RESULTS

Piperacillin/tazobactam had the highest antimicrobial susceptibility among monotherapies/fixed combinations, which was significantly lower than combination therapies such as meropenem-linezolid (75.3% vs. 98.5%, P < 0.001). The sensitivity of pathogens to empirical antibiotic therapy correlated with significantly lower inpatient mortality (18.9% vs. 37.0%, P = 0.018), shorter inpatient stay (16.3 ± 10.2 vs. 26.4 ± 21.0 days, P = 0.053) and shorter intensive care treatment (2.1 ± 4.5 vs. 7.9 ± 15.4 days, P = 0.016). The largest difference of mortality was observed in patients with ACLF grade 3 (54.5% vs. 73.1% [sensitive vs. non-sensitive]).

CONCLUSION

All SBP patients benefited from efficient empirical antibiotic therapy, regarding the reduced inpatient mortality and complications. For SBP patients with ACLF grade 3 without sepsis, the combination therapy with meropenem-linezolid may be suitable considering the susceptibility results and the concentration in the peritoneal cavity.

Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage and pattern of antibiotic resistance among sheep farmers from Southern Italy

PURPOSE

We conducted a cross-sectional study to measure the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization, with a particular focus on livestock associated (LA)-MRSA in farmers working in contact with livestock (sheep) in one Italian region. Furthermore, we have assessed the antimicrobial resistance pattern of isolates and the association of carriage with specific characteristic of farms and working tasks.

PATIENTS AND METHODS

Demographic data, occupational history, and contact with animals information was collected. Nasal and oropharyngeal swabs were collected and all samples were tested for the isolation and identification of S. aureus. Isolates were examined for antimicrobial susceptibility and all MRSA strains underwent molecular analyses through multiple-locus variable number of tandem repeat analysis (MLVA).

RESULTS

A total of 115 sheep farms and 275 sheep farmers were enrolled. MRSA colonized workers were found in three farms; S. aureus was isolated in 97 workers (35.5%), whereas MRSA was isolated in 3 (1.1%) workers. All MRSA isolates were classified as multidrug resistant. Two of the MRSA isolates were resistant to quinupristin/dalfopristin (QDA), mupirocin, erythromycin, and tetracycline. Among methicillin-susceptible S. aureus (MSSA), 32 (34%) were resistant to tetracycline, 31 (33%) to erythromycin, 26 (27.6%) to QDA, and 22 (23.4%) to linezolid and clindamycin. One MRSA belonged to MLVA complex (MC) 001, found to colonize both humans and animals.

CONCLUSION

The picture of MRSA transmission among sheep farmers does not seem to be critical, although there is the need to improve adequate control measures to prevent and minimize any biological risk in sheep farms for both animal and human health. Specific monitoring/surveillance programs would help in better understanding the epidemiology of resistant strains.

[Urosepsis]

Urosepsis is defined as a severe disease due to organ failure caused by a urinary tract infection. An empirical antibiotic therapy should be instigated within the first hour after diagnosis. Urine cultures and blood cultures should be performed before antibiotic treatment. Further diagnostics should be carried out at an early stage to enable an interventional focus control in the case of urinary tract obstruction or abscess formation, if necessary. Gram-negative pathogens are most frequently isolated. Extended spectrum beta-lactamase (ESBL) forming bacteria as a cause of urosepsis are increasing. Carbapenemase-forming Enterobacteriaceae, on the other hand, are still rare. The empirical treatment consists of a broad spectrum beta-lactam antibiotic. While piperacillin/tazobactam, carbapenems and the new cephalosporin/beta-lactamase inhibitor (BLI) combinations are given as monotherapy, cephalosporins should be combined with aminoglycosides (preferred) or fluoroquinolones. If a combination therapy is given, it should be de-escalated to a monotherapy after 48-72 h.

The accuracy of extended-spectrum beta-lactamase detection in Escherichia coli and Klebsiella pneumoniae in South African laboratories using the Vitek 2 Gram-negative susceptibility card AST-N255

Background

Phenotypic detection of extended-spectrum beta-lactamases (ESBLs) is based on the inhibition of ESBL enzymes by β-lactamase inhibitors and on the comparison of cephalosporin activity with or without a β-lactamase inhibitor. Many South African diagnostic laboratories rely on the Vitek 2 for automated susceptibility testing and for ESBL detection. However, the Gram-negative susceptibility card currently used locally (AST-N255) has been modified and its accuracy for ESBL detection is not known.

Methods

We randomly selected 50 isolates of Klebsiella pneumoniae and Escherichia coli from a collection of clinical bloodstream isolates from Groote Schuur Hospital from 2015 to 2016, including ESBL-producing and non-ESBL-producing strains. We used standardised phenotypic (disc diffusion and broth microdilution) and genotypic (conventional polymerase chain reaction (PCR) for bla_CTX-M, bla_SHV and bla_TEM) methods for detection of ESBLs. We compared ESBL detection by Vitek 2 to a composite reference standard comprising ESBL detection either by both phenotypic methods or by one phenotypic method together with genotypic detection.

Results

The sensitivity of Vitek 2 system for detection of ESBLs was 33/36 or 92% (78% – 97%) for E. coli, and 40/40 or 100% (91% – 100%) for K. pneumoniae, whilst specificity was 10/10 or 100% (72% – 100%) and 9/10 or 90% (60% – 98%), respectively. This is comparable with previous studies.

Conclusion

Using a composite reference standard of the phenotypic and genotypic methods employed in this study, no Vitek-categorised ESBL E. coli or K. pneumoniae was found to be a non-ESBL with the exception of possible misinterpretation with K. pneumoniae SHV-hyper-producing isolates.

Strong correlation between the rates of intrinsically antibiotic-resistant species and the rates of acquired resistance in Gram-negative species causing bacteraemia, EU/EEA, 2016

BackgroundAntibiotic resistance, either intrinsic or acquired, is a major obstacle for treating bacterial infections.AimOur objective was to compare the country-specific species distribution of the four Gram-negative species Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter species and the proportions of selected acquired resistance traits within these species.MethodWe used data reported for 2016 to the European Antimicrobial Resistance Surveillance Network (EARS-Net) by 30 countries in the European Union and European Economic Area.ResultsThe country-specific species distribution varied considerably. While E. coli accounted for 31.9% to 81.0% (median: 69.0%) of all reported isolates, the two most common intrinsically resistant species P. aeruginosa and Acinetobacter spp. combined (PSEACI) accounted for 5.5% to 39.2% of isolates (median: 10.1%). Similarly, large national differences were noted for the percentages of acquired non-susceptibility to third-generation cephalosporins, carbapenems and fluoroquinolones. There was a strong positive rank correlation between the country-specific percentages of PSEACI and the percentages of non-susceptibility to the above antibiotics in all four species (rho > 0.75 for 10 of the 11 pairs of variables tested).ConclusionCountries with the highest proportion of P. aeruginosa and Acinetobacter spp. were also those where the rates of acquired non-susceptibility in all four studied species were highest. The differences are probably related to national differences in antibiotic consumption and infection prevention and control routines.

Antimicrobial resistance in nephrology

The prevalence of antimicrobial resistance among many common bacterial pathogens is increasing. The emergence and global dissemination of these antibiotic-resistant bacteria (ARB) is fuelled by antibiotic selection pressure, inter-organism transmission of resistance determinants, suboptimal infection prevention practices and increasing ease and frequency of international travel, among other factors. Patients with chronic kidney disease, particularly those with end-stage renal disease who require dialysis and/or kidney transplantation, have some of the highest rates of colonization and infection with ARB worldwide. These ARB include methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus spp. and several multidrug-resistant Gram-negative organisms. Antimicrobial resistance limits treatment options and increases the risk of infection-related morbidity and mortality. Several new antibiotic agents with activity against some of the most common ARB have been developed, but resistance to these agents is already emerging and highlights the dire need for new treatment options as well as consistent implementation and improvement of basic infection prevention practices. Clinicians involved in the care of patients with renal disease must be familiar with the local epidemiology of ARB, remain vigilant for the emergence of novel resistance patterns and adhere strictly to practices proven to prevent transmission of ARB and other pathogens.

Amino Acid Biosynthetic Pathways Are Required for Klebsiella pneumoniae Growth in Immunocompromised Lungs and Are Druggable Targets during Infection

The emergence of multidrug-resistant Klebsiella pneumoniae has rendered a large array of infections difficult to treat. In a high-throughput genetic screen of factors required for K. pneumoniae survival in the lung, amino acid biosynthesis genes were critical for infection in both immunosuppressed and wild-type (WT) mice. The limited pool of amino acids in the lung did not change during infection and was insufficient for K. pneumoniae to overcome attenuating mutations in aroA, hisA, leuA, leuB, serA, serB, trpE, and tyrA in WT and immunosuppressed mice. Deletion of aroA, which encodes 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase class I, resulted in the most severe attenuation. Treatment with the EPSP synthase-specific competitive inhibitor glyphosate decreased K. pneumoniae growth in the lungs. K. pneumoniae expressing two previously identified glyphosate-resistant mutations in EPSP synthase had significant colonization defects in lung infection. Selection and characterization of six spontaneously glyphosate-resistant mutants in K. pneumoniae yielded no mutations in aroA Strikingly, glyphosate treatment of mice lowered the bacterial burden of two of three spontaneous glyphosate-resistant mutants and further lowered the burden of the less-attenuated EPSP synthase catalytic mutant. Of 39 clinical isolate strains, 9 were resistant to glyphosate at levels comparable to those of selected resistant strains, and none appeared to be more highly resistant. These findings demonstrate amino acid biosynthetic pathways essential for K. pneumoniae infection are promising novel therapeutic targets.

Evaluating the antimicrobial resistance patterns among major bacterial pathogens isolated from clinical specimens taken from patients in Mofid Children's Hospital, Tehran, Iran: 2013-2018

BACKGROUND

This study evaluates the epidemiology and antimicrobial resistance profile of Gram-negative bacteria (GNB) and Gram-positive bacteria (GPB) isolated from clinical specimens in children admitted to Mofid Children's Hospital.

METHODS

This was a retrospective study of the patients' clinical specimens collected from January 2013 until the end of December 2018. All specimens were evaluated to determine the presence of infection-causing agents using a BACTEC 9120 blood culture. Isolation and identification of bacterial strains were performed using conventional biochemical tests. Antibiotic resistance was determined using Kirby-Bauer disk diffusion and broth microdilution methods. Results were interpreted according to CLSI and EUCAST.

RESULTS

A total of 1130 different pathogenic bacteria were detected from 14,690 different clinical specimens and the overall detection rate was 7.7% (1130/14,690). Among bacterial pathogen isolated from clinical specimens, 55% (n=622) were GNB and 45% (n=508) were GPB. The predominant GNB isolates were Pseudomonas aeruginosa, Klebsiella spp., Acinetobacter baumannii, Escherichia coli, Enterobacter spp., Citrobacter spp., respectively. Among GPB, CoNS was the most frequent and Enterococcus spp. was found to have low levels of resistance to linezolid. In GNB, most A. baumannii and P. aeruginosa were ceftriaxone resistant. P. aeruginosa was found to have low levels of resistance to levofloxacin and ciprofloxacin.

CONCLUSIONS

Our findings revealed that the resistance rate among GNB and GPB associated with different infections in children is very high. These results suggest a constant screening and follow-up programs for the detection of antibiotic resistance, and it also suggests to develop antimicrobial stewardship programs in Tehran, Iran.

The microbiology of chronic osteomyelitis: Changes over ten years

AIM

This study quantified changes in the microbiology of osteomyelitis over a ten year period from a single centre within the UK with regard to infection with multi-drug resistant (MDR) bacteria and susceptibility of antimicrobial regimens.

METHOD

Patients with chronic osteomyelitis undergoing definitive surgery from 2013-2017 were inluded (n = 223). Microbiology was compared to patients in a cohort from 2001-2004, using the same diagnostic criteria, and same deep tissue sampling technique (n = 157). Clinical features associated with MDR bacterial infection were analysed using logistic regression.

RESULTS

Both cohorts had similar baseline characteristics. Despite a similar proportion of Staphylococcus aureus in both cohorts, the rate of methicillin resistant Staphylococcus aureus (MRSA) infection was lower in 2013-2017 compared to 2001-2004 (11.4% vs 30.8% of Staphylococcus aureus, p = 0.007). However, the proportion of MDR infections was similar in both cohorts (15.2% versus 17.2%). Metalwork was associated with MDR infection (unadjusted OR 5.0; 95% CI: 1.15 to 22.0). There was no change in resistance to glycopeptide / meropenem combination treatment (2.2% vs 2.5%, p > 0.9).

CONCLUSIONS

In this centre, rates of MRSA osteomyelitis have fallen by two thirds, over the past 10 years, in line with the reducing rate of MRSA bacteraemia nationally. A history of metalwork may predict MDR infection. A glycopeptide with an anti-pseudomonal carbapenem remains the post-operative empiric systemic regimen of choice. Resistance patterns support the use of a glycopeptide with an aminoglycoside in local antibiotic therapy.

Comparative Epidemiology and Resistance Trends of Common Urinary Pathogens in a Tertiary-Care Hospital: A 10-Year Surveillance Study

Background and Objective: Urinary tract infections (UTIs) are common in human medicine, affecting large patient populations worldwide. The principal cause of UTIs is uropathogenic Escherichia coli (UPEC) and Klebsiella, both in community and nosocomial settings. The assessment of local data on prevalence and resistance is essential to evaluate trends over time and to reflect on the national situation, compared to international data, using the methods of analytical epidemiology. Materials and Methods: The aim of this study was to assess resistance trends and epidemiology of UTIs caused by E. coli and Klebsiella species in inpatients and outpatients at a tertiary-care hospital in Hungary, using microbiological data. To evaluate resistance trends, several antibiotics were chosen as indicator drugs, based on local utilization data. Results: E. coli was the most prevalent isolate, representing 56.75 ± 4.86% for outpatients and 42.29 ± 2.94% for inpatients. For E. coli, the ratio of resistant strains for several antibiotics was significantly higher in the inpatient group, while in Klebsiella, similar trends were only observed for gentamicin. Extended-spectrum β-lactamase (ESBL)-producing isolates were detected in 4.33-9.15% and 23.22-34.22% from outpatient, 8.85-38.97% and 10.89-36.06% from inpatient samples for E. coli and Klebsiella, respectively. Conclusions: Resistance developments in common UTI pathogens (especially to fosfomycin, sulfamethoxazole-trimethoprim, fluoroquinolones, and 3rd generation cephalosporins), seriously curb therapeutic options, especially in outpatient settings.

Resistance Trends and Epidemiology of Citrobacter-Enterobacter-Serratia in Urinary Tract Infections of Inpatients and Outpatients (RECESUTI): A 10-Year Survey

Background and objectives: Urinary tract infections (UTIs) are the third most common infections in humans, representing a significant factor of morbidity, both among outpatients and inpatients. The pathogenic role of Citrobacter, Enterobacter, and Serratia species (CES bacteria) has been described in UTIs. CES bacteria present a therapeutic challenge due to the various intrinsic and acquired resistance mechanisms they possess. Materials and Methods: The aim of this study was to assess and compare the resistance trends and epidemiology of CES pathogens in UTIs (RECESUTI) in inpatients and outpatients during a 10-year study period. To evaluate the resistance trends of isolated strains, several antibiotics were chosen as indicator drugs based on local utilization data. 578 CES isolates were obtained from inpatients and 554 from outpatients, representing 2.57 ± 0.41% of all positive urine samples for outpatients and 3.02 ± 0.40% for inpatients. E. cloacae was the most prevalent species. Results: The ratio of resistant strains to most of the indicator drugs was higher in the inpatient group and lower in the second half of the study period. ESBL-producing isolates were detected in 0-9.75% from outpatient and 0-29.09% from inpatient samples. Conclusions: Resistance developments of CES bacteria, coupled with their intrinsic non-susceptibility to several antibiotics, severely limits the number of therapeutic alternatives, especially for outpatients.

Antibiotic stewardship: ripartiamo dalla pratica clinica

Antibiotic stewardship: a milestone in everyday clinical practice Infectious diseases caused by multi-resistant pathogens are increasing worldwide and are challenging for clinicians, also in urological setting. The alarming situation is worsened by the limited perspective of new antibiotic developments. Several authors demonstrated that in Italy we have alarming data about resistance rates: in Campania about 58% of Escherichia coli are resistant to fluroquinolones, as 46% to sulfamethoxazole-trimethoprim. On the other hand, the resistance rate against fosfomycin is still low less than 5%. More alarming data are reported about Klebsiella pneumoniae: resistance rate to flurquinolones 65% and 58% to sulfamethoxazole-trimethoprim. A continuing uncritical, non-guideline-conform and overuse of antibiotics leads to selection of multidrug-resistant pathogens, which can colonize patients and make the treatment a real challenge. A revision of our approach to urinary tract infections at the light of antibiotic stewardiship principles are urgently required, in particular starting from the everyday clinical practice.

New Delhi Metallo-β-lactamase and other mechanisms of carbapenemases among Enterobacteriaceae in rural South India

OBJECTIVES

The emergence and dissemination of carbapenem-resistant Enterobacteriaceae (CRE) is an important public health problem. This study aimed to understand the prevalence and mechanisms of carbapenem resistance in clinically important members of Enterobacteriaceae in rural South India.

METHODS

Routine clinical isolates of Escherichia coli and Klebsiella spp. were tested for Ertapenem (ETP) non-susceptibility by the disk diffusion method over a 3-year period (2012-2014). The ETP non-susceptible isolates were preserved, and tested for the MIC of carbapenems and the carriage of major carbapenemase-encoding genes. Representative genes were sequenced and selective isolates were tested for the production of carbapenemase by carbapenem inactivation method.

RESULTS

A total of 444 ETP non-susceptible isolates were identified in increasing incidence over the study period. Among them, MIC₅₀ and MIC₉₀ of carbapenems (excluding ETP) were 0.25-0.5μg/mL and 8-16μg/mL, respectively, and the prevalence of non-ETP carbapenem resistance was estimated as 3%. Among the 177 tested isolates, 65 (37%) had one or more carbapenemase-encoding genes with a predominance of New Delhi Metallo-β-lactamase (NDM; 32 of 65; 49.2%).

CONCLUSIONS

This study documented the MIC range for carbapenems, prevalence and mechanisms of carbapenem resistance among Enterobacteriaceae in rural South India. It substantiated NDM as a leading mechanism of carbapenem resistance and highlighted the importance of MIC testing in patient management.