Antimicrobial Susceptibility Data Research Articles

Multidrug-Resistant Infections Among Hospitalized Adults With Community-Acquired Pneumonia In An Indonesian Tertiary Referral Hospital.

ObjectivesTo evaluate the clinical and microbiological appearance among hospitalized pneumonia patients focusing on resistance and risk factors for mortality in a referral hospital.Patients and methodsThe study was an observational retrospective study on patients with CAP from 2014 to 2016 at Dr Soetomo referral hospital of Surabaya, Indonesia. All positive cultures with antimicrobial susceptibility results from blood and respiratory specimens were included. Patients infected with drug-susceptible pathogens and MDR organisms were also assessed in terms of clinical characteristics, day-3 clinical improvement, and 14-day mortality.ResultsOf 202 isolates, 181 possessed antimicrobial susceptibility data. S. pneumoniae was the most prevalent pathogen causing CAP (18.3%). Most patients were empirically treated with ceftriaxone (n=75; 41.4%). Among beta-lactam antibiotics, the susceptibility to the third-generation cephalosporins remained relatively high, between 67.4% and 82.3%, compared with the other beta-lactams such as amoxicillin/clavulanate and ampicillin/sulbactam (a sensitivity rate of 36.5% and 47.5, respectively). For carbapenem antibiotics, imipenem and meropenem susceptibility was 69.6% and 82.3% respectively. Approximately 22% of isolates were identified as MDR that showed significant differences in clinical outcomes of 14-day mortality rates (p<0.001). Notably, patients with day-3 improvement had a lower risk of mortality (OR= 0.06; 95% CI= 0.02–0.19).ConclusionOne-fifth of causative agents among hospitalized CAP cases were identified as MDR organisms. The pathogens of MDR and non-MDR CAP remain susceptible to the third-generation cephalosporins. Together with additional consideration of culture findings and Pneumonia Severity Index (PSI) assessment, a 3-day clinical assessment is essential to predict the prognosis of 14-day mortality.

Standardising the reporting of microbiology and antimicrobial susceptibility data

Standardising the reporting of microbiology and antimicrobial susceptibility data

2707. Non 13-Valent Pneumococcal Conjugate Vaccine Serotypes Predominate as Causes of Pneumococcal Otitis Media in Children

BackgroundPneumococcal acute otitis media (AOM) in children due to vaccine-related serotypes (ST) has declined after the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), although some serotypes, such has 3, 19A and 19F have persisted. Among non-vaccine serotypes, 35B has been shown to contribute substantially to both OM and invasive infections. This study describes the current epidemiology of pneumococcal OM isolates obtained from the U S Pediatric Multicenter Pneumococcal Surveillance Group (USPMPSG).MethodsFrom the USPMPSG database, we collected data from patients <18 years of age with pneumococcal OM isolates from 2014 to 2018. Analysis included demographics, immunization status, antimicrobial susceptibility data and serotype. Statistical comparisons included Fisher’s exact and Wilcoxon rank-sum tests.ResultsA total of 494 patients with isolates were identified within the time period from 5 children’s hospitals. Median age was 1.7 years (range 0–17.6) and 299 (60.5%) were male; 176 (35.7%) had an underlying condition. Thirty-two patients had received no dose of either PCV7 or PCV13. Thirty-five serotypes were identified (3 isolates were non-typeable), of which 6 serotypes [35B (16.8%), 3 (9.5%), 15A (7.9%), 15B (7.9%), 23B (7.9%) and 21 (6.1%)] caused more than half of the total OM infections (figure). Ninety (18.2%) isolates were of PCV13 serotypes. Twenty-five of 476 (5.3%) isolates had a penicillin MIC>2 µg/mL. These were of serotypes 11A, 15A/C, 19A/F, 35B and NT; 10/455 (2.2%) isolates had ceftriaxone MIC>1 µg/mL and were of ST 3, 15A, 19A/F and 35B.ConclusionMost pneumococcal OM were caused by non-PCV13 serotypes. Serotype 35B remained the most common serotype among pneumococcal isolates recovered from ear drainage or middle ear cultures. The low proportion of penicillin-resistant isolates along with the increasing proportion of AOM cases being due to non-pneumococcal isolates supports the consideration to switch routine antibiotic treatment for AOM to standard dose amoxicillin-clavulanate from high dose amoxicillin in PCV13 immunized children (Pediatr Infect Dis J 2018;37:1255–1257). Disclosures All authors: No reported disclosures.

628. Integrated Surveillance for Antimicrobial-Resistance in Salmonella From Clinical and Retail Meat Sources—Pennsylvania, 2015–2017

BackgroundAntimicrobial resistance (AMR) in foodborne pathogens of animal origin, including nontyphoidal Salmonella (NTS), is a public health concern. Pennsylvania conducts integrated surveillance for AMR in NTS from human and animal sources in collaboration with the FDA and CDC National Antimicrobial Resistant Monitoring System (NARMS).MethodsWe reviewed pulsed-field gel electrophoresis (PFGE), antimicrobial susceptibility (SST) and whole-genome sequencing (WGS) data for isolates from animal and food sources, including 96 NTS from 2,520 meat samples (poultry, ground beef and pork chops) purchased during 2015–2017 from randomly selected retail outlets in Pennsylvania. SST to 15 antimicrobial agents was done on 109 NTS clinical isolates that had similar PFGE patterns to meat isolates. SST and WGS were used to characterize all isolates from meat and two clinical isolates from 2017.Results28 (29.2%) and 17 (17.7%) NTS isolated from meat sources were resistant to ≥3 and ≥5 antibiotics classes, respectively. Resistance to ceftriaxone rose from 12% (3/25) in 2015 to 27% (10/37) in 2016 and resistance to amoxicillin/clavulanate also increased. Plasmid-mediated bla CMY-2 β-lactam resistance genes that hydrolyze extended-spectrum cephalosporins (ESC) increased from 12% in 2015 (3/25) to 18.9% (7/37) in 2016. Four blaCTX-M-65 genes that confer resistance to extended-spectrum β-lactamases (ESBLs) were identified in 2016 (n = 3) and 2017. Of the 109 clinical isolates, 25.7% demonstrated resistance to ≥3 and 11% to ≥5 antibiotics classes, respectively. No clinical isolates were resistant to ceftriaxone in 2015, 12.5% (6/48) and 24.3% (9/37) were resistant in 2016 and 2017, respectively. Resistance to amoxicillin/clavulanate was demonstrated in 8.3% (4/48) of isolates in 2016 (figure). Two clinical isolates carried blaCTX-M-65 ESB Ls genes and were resistant to eight antimicrobial agents (ACSSuTCxNalCot. Phenotype).ConclusionNTS (≥25%) from animal and human sources were multidrug-resistant and harbored CMY-2 and CTX-M-65 genes. Dissemination of genes that confer resistance to ESBLs and ESCs in NTS undermines recommended treatment for severe infections and underscores the need for One-Health surveillance and antimicrobial stewardship efforts. Disclosures All authors: No reported disclosures.

623. Antimicrobial Resistance in Non-Typhoidal Salmonella from Retail Poultry Meat by Antibiotic Usage-related Production Claims—Pennsylvania, 2008–2017

BackgroundAntimicrobial-resistant (AMR) nontyphoidal Salmonella infections are a public health concern. Injudicious use of antimicrobials fuels emergence of resistance. The National Antimicrobial Resistance Monitoring System (NARMS) tracks AMR in Salmonella from humans, animals and foods. There is limited evidence regarding antimicrobial use in food animals and AMR bacteria in retail meat.MethodsWe reviewed antimicrobial susceptibility and whole-genome sequencing data from 320 Salmonella isolated from poultry meat in Pennsylvania as part of NARMS activities. Salmonella strains were isolated from 3,481 samples purchased from randomly selected retail outlets during 2008–2017. Antibiotic usage claims on meat packages were used to compare AMR Salmonella from conventional and antibiotic-free/organic (Abx-free) samples. Genetic mechanisms for AMR were investigated in a subset of isolates.ResultsThe prevalence of Salmonella in conventional poultry meat 10.2% (280/2,733) was significantly higher than the prevalence in poultry meat labeled as Abx-free (5.3%, 40/748; P < 0.0001). Salmonella from conventional poultry meat was more likely to be resistant to 3 or more drugs (55.0%, 154/280) compared with poultry meat labeled as Abx-free (27.5%, 11/40; P = 0.0011). Salmonella from conventional poultry exhibited significantly higher resistance to 4 drug classes including β-lactams (P = 0.006) (figure). One hundred isolates from conventional poultry meat and 8 isolates from antibiotic-free/organic samples harbored a gene conferring resistance to the β-lactam class; 24.3% (68/280) of isolates from conventional and 7.5% (3/40) of isolates from Abx-free samples (P = 0.0145) contained the extended-spectrum β-lactamase (ESBL) gene blaCMY-2.ConclusionMeat samples from conventionally-raised poultry were more likely to be contaminated with AMR Salmonella strains and have genes that reduce the effectiveness of antimicrobial drugs recommended for treatment of severe infections. Contamination of poultry with AMR Salmonella strains is concerning as is the presence of genes that decrease the power of critical antibiotics such as β-lactams. These findings highlight the importance of judicious use of antibiotics in food-producing animals. Disclosures All authors: No reported disclosures.

New antimicrobial susceptibility data from monitoring of Mycoplasma bovis isolated in Europe

Mycoplasma bovis is an important respiratory pathogen of cattle across Europe and is included in the MycoPath pan-European antimicrobial susceptibility monitoring programme. M. bovis strains (232) were isolated from cattle, not recently treated with antimicrobials, at diverse geographical locations in France, Great Britain, Hungary, Italy and Spain during 2014 to 2016. Only one isolate per farm and per outbreak was retained. For each isolate, the MICs of ten antimicrobials were determined in a central laboratory using a broth microdilution method with modified Eaton’s medium and incubation at 35 °C ± 1 °C for 24 ± 6 h. MIC50/MIC90 (mg/L) values for the 232 strains were: danofloxacin 0.25/1; enrofloxacin 0.5/8; marbofloxacin 1/4; gamithromycin >64/>64; spiramycin 8/16; tilmicosin >64/>64; tulathromycin >64/>64; tylosin 64/>64; florfenicol 4/8; oxytetracycline 8/32. Minor between-country differences in the MIC90 values were observed for the fluoroquinolones, spiramycin and oxytetracycline, whilst the MIC values for the other compounds were similar. Spain and Italy had the higher MIC90 values for the fluoroquinolones. Compared with the 2010–2012 study (156 isolates) results are similar, with an overall MIC50 increase of at most one doubling dilution for enrofloxacin, spiramycin, tylosin, florfenicol and oxytetracycline. In contrast, the MIC90 value for oxytetracycline decreased from >64 to 32 mg/L. Standardized laboratory methods and interpretive criteria for MIC testing of veterinary mycoplasmas are clearly needed; there are currently no clinical breakpoints available to facilitate data interpretation and correlation of MICs with in vivo efficacy.

Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - Experiences from the first inter-laboratory ring trial in four German speaking countries

Clostridium (Clostridioides) difficile is a major cause of nosocomial diarrhoea. A first inter-laboratory ring trial was performed in four European countries to evaluate the genotyping and antibiotic susceptibility testing (AST) accuracy.Six C. difficile isolates representing the epidemiologic important ribotypes (RT), RT001, RT002, RT010, RT014, RT027, and RT078 were blinded and send to 21 participating laboratories. Participants tested the samples with their genotyping and AST methods in use for concordance with reference.A total of 21 genotyping- and 14 antimicrobial susceptibility data sets were obtained. Ribotyping (11 participants) correctly identified most RTs (median 91% concordance rate) except for RT002, which was misidentified in 4/11 reports. However, this isolate was correctly asserted to RT002 after an update of a publicly available ribotyping database. Multilocus sequence typing, surface layer sequence typing, DNA microarray based genotyping, and whole genome sequencing, which were used by 1–3 participants, identified all six isolates correctly. AST was done by epsilometry by the participants and compared to agar dilution data determined by the coordinating reference centre. Susceptibilities against metronidazole, moxifloxacin, and vancomycin were correctly identified in 235 of 237 cases and in accordance to agar dilution as the gold standard.Genotyping of the C. difficile test strains revealed a remarkable high concordance on the level of ribotypes with a wide variety of methods. Epsilometry appears to be a reliable method for AST of C. difficile isolates in routine clinical microbiology laboratories.

Using Genomics to Track Global Antimicrobial Resistance.

The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this. We conducted a scientific literature review and here we present a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and provide future perspectives and recommendations. At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder, and ResFinder. Bioinformatics resources differ for several parameters including type of accepted input data, presence/absence of software for search within a database of AMR determinants that can be specific to a tool or cloned from other resources, and for the search approach employed, which can be based on mapping or on alignment. As a consequence, each tool has strengths and limitations in sensitivity and specificity of detection of AMR determinants and in application, which for some of the tools have been highlighted in benchmarking exercises and scientific articles. The identified tools are either available at public genome data centers, from GitHub or can be run locally. NCBI and European Nucleotide Archive (ENA) provide possibilities for online submission of both sequencing and accompanying phenotypic antimicrobial susceptibility data, allowing for other researchers to further analyze data, and develop and test new tools. The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants are essential to identify control and prevention strategies to combat the increasing threat of AMR. Accessible tools and DNA sequence data are expanding, which will allow establishing global pathogen surveillance and AMR tracking based on genomics. There is however, a need for standardization of pipelines and databases as well as phenotypic predictions based on the data.

Introducing herd level antimicrobial susceptibility data into the veterinarian-dairy farmer relationship.

Australian Veterinary JournalVolume 97, Issue 8 p. 289-289 AVAMS2018 CONFERENCE Introducing herd level antimicrobial susceptibility data into the veterinarian–dairy farmer relationship R Castle, Corresponding Author R Castle ray.castle@bayer.com Bayer Animal Health, PO Box 76369, Manukau, 2241 New ZealandCorresponding author.Search for more papers by this authorS McDougall, S McDougall Cognosco, Anexa FVC, Morrinsville, NZSearch for more papers by this author R Castle, Corresponding Author R Castle ray.castle@bayer.com Bayer Animal Health, PO Box 76369, Manukau, 2241 New ZealandCorresponding author.Search for more papers by this authorS McDougall, S McDougall Cognosco, Anexa FVC, Morrinsville, NZSearch for more papers by this author First published: 30 July 2019 https://doi.org/10.1111/avj.12813Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume97, Issue8August 2019Pages 289-289 RelatedInformation

Methicillin-resistant Staphylococcus aureus (MRSA) in East Africa: red alert or red herring?

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is associated with significant morbidity and mortality and has resultant important economic and societal costs underscoring the need for accurate surveillance. In recent years, prevalence rates reported in East Africa have been inconsistent, sparking controversy and raising concern.MethodsWe described antimicrobial susceptibility patterns of Staphylococcus aureus isolates cultured from patients within the Internal Medicine department of the largest public healthcare facility in East and Central Africa- the Kenyatta National Hospital (KNH) in Nairobi, Kenya. Routine antimicrobial susceptibility data from non-duplicate Staphylococcus aureus isolates cultured between the years 2014–2016 from the medical wards in KNH were reviewed.ResultsAntimicrobial susceptibility data from a total of 187 Staphylococcus aureus isolates revealed an overall MRSA prevalence of 53.4%. Isolates remained highly susceptible to linezolid, tigecycline, teicoplanin and vancomycin.ConclusionsThe prevalence of MRSA was found to be much higher than that reported in private tertiary facilities in the same region. Careful interrogation of antimicrobial susceptibility results is important to uproot any red herrings and reserve genuine cause for alarm, as this has a critical bearing on health and economic outcomes for a population.

In vitro Susceptibility Pattern of Major Gram Negative Isolates to Selected Antimicrobial Agents

Background: The choice of choosing right anti-microbial therapy in hospitals depends on the knowledge of local anti-microbial susceptibility profile. This retrospective study was conducted to assess the in vitro susceptibility pattern of different pathogen isolates to various antibiotics including Cefepime-Amikacin-Antibiotic resistant breakers (ARBs)* in various hospitals across the Jaipur City.&#x0D; Methods: To characterize the antimicrobial susceptibility pattern of different isolates from various hospitals across the Jaipur City, a retrospective, observational analysis was done for antibiogram data. A total of 1201 Gram negative isolates collected during the period from January 2017 to December 2017 were included in the study. Antibiotic sensitivity testing was done in accordance with the recommendations of Clinical Laboratory Standard Institute (CLSI) guidelines.&#x0D; Results: Of the total 1201 Gram negative isolates included in this study, 51.6% were from wounds and pus specimens, 40.1% were from respiratory and 8.2% from blood. P. aeruginosa (49.7%) was the most frequently isolated pathogen distantly followed by A. baumannii (21.6%), K. pneumoniae (16.6%) and E. coli (12.1%). The highest susceptibility was reported to polymyxins (100%) including Colistin and Polymyxin B, among all the tested bacteria’s and system wise. Among all the antibiotic tested, (Cefepime-Amikacin-ARBs*) sensitivity ranged for 87.9% to 52% on pathogens (E. coli, K. pneumonia, P. aeruginosa) tested from samples of skin and soft tissue, respiratory tract, blood stream, followed by Meropenem ranged for 78.4% to 55% on pathogens (E. coli, K. pneumonia, P. aeruginosa), followed by ceftazidime-tazobactam ranged for 82.7% to 58% on pathogens (E. coli, K. pneumonia, P. aeruginosa) and 22.7% sensitive for A. baumannii to Cefoperazone sulbactam. Based on pathogen type, E. coli exhibited highest overall susceptibility and the lowest was reported by A. baumannii. The susceptibility of A. baumannii ranged from 1-26% to all the tested antibiotics except polymyxins with 100% susceptibility.&#x0D; Conclusions: This in vitro susceptibility data suggests that Cefepime-Amikacin-ARBs* can serve as important therapeutic option for the treatment of various resistant Gram-negative bacterial infections to relieve the excess pressure on last resort antibiotics, carbapenems and other drugs including Colistin and polymyxin B. Cefepime-Amikacin-ARBs*on the basis of antimicrobial susceptibility data can be considered as an effective therapeutic option for carbapenems in treating gram negative bacterial infections, and could be considered as a broad spectrum antibiotic sparer’s like carbapenem, colistin and Polymyxin B.

Comparison of antibiotic treatment guidelines for urinary tract infections in 15 European countries: Results of an online survey

Appropriate antibiotic use for urinary tract infections (UTIs) is important in order to provide effective and safe treatment while minimising the risk of antimicrobial resistance development. This survey was carried out to compare existing national guidelines for UTIs in Europe. Experts in 37 European countries were asked to participate. An electronic questionnaire was used to obtain information on treatment recommendations, factors considered important when setting guidelines, acceptable resistance rates for empirical therapy, evidence grading, and existing resistance surveillance for uropathogens. Treatment guidelines and antimicrobial susceptibility data were collected. In total, 22 experts (59%) responded to the survey. National guidelines were missing in four countries and data were incomplete in three cases. Fifteen national guidelines published between 2004 and 2017 were included in the analysis. Great variability was found between guidelines in the selection of antibiotics, dosing regimens and treatment duration. For example, 10 different antibiotics were recommended as first-line therapy for uncomplicated cystitis. National surveillance data on antimicrobial susceptibility of uropathogens were available in 13 of 15 countries. Resistance epidemiology could not explain the observed differences between guidelines, and comparison of resistance rates was hampered by variations in methods. This study revealed major differences in treatment guidelines for UTIs within Europe, indicating that there are opportunities for improvement. More clinical research and a more systematic and stratified approach to resistance surveillance, including also antibiotics that are currently not available in all countries, is needed.

Cumulative antimicrobial susceptibility data for a tertiary-level paediatric oncology unit in Johannesburg, South Africa

Background: There is global concern regarding the spread of antimicrobial resistance in bacteria and fungi. Oncology patients are at particular risk of infections with multidrug resistant organisms. These patients require urgent initiation of empiric antimicrobial therapy when presenting with neutropenic fever. Currently, piperacillin-tazobactam and amikacin with or without vancomycin is the treatment of choice in the unit.Aim: The purpose of this study was to develop a cumulative antibiogram for the paediatric oncology unit at Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) to guide empiric treatment recommendations for patients presenting with suspected bacterial or fungal infection.Setting: Tertiary-level paediatric oncology unit.Methods: A retrospective observational analysis was performed of bacterial and fungal antimicrobial susceptibility data extracted from the microbiology laboratory information system for clinical specimens submitted from the paediatric oncology unit at CMJAH. Data was analysed for the period January 2015 to May 2018. In addition, analysis and comparison of two 17-month time periods was performed in order to elicit any changes over time.Results: Klebsiella pneumoniae and Escherichia coli were the most common gram-negative organisms isolated. Twenty-one percent of Enterobacteriaceae showed resistance to third generation cephalosporins and 9% to carbapenems. Rates of carbapenem-resistant isolates decreased significantly over time. Adding amikacin to piperacillin-tazobactam significantly increased bacterial coverage. Coagulase-negative staphylococci and Candida parapsilosis were the most common gram-positive and fungal isolates recovered during the study.Conclusion: The results support the continued use of piperacillin-tazobactam and amikacin for paediatric oncology patients presenting with neutropenic fever in this unit. Antibiograms are an important component of antimicrobial stewardship in conjunction with efficient infection prevention and control measures.

Bacterial isolates, antimicrobial susceptibility and multidrug resistance in cultures from samples collected from beef and pre-production dairy cattle in New Zealand (2003–2016)

ABSTRACTAims: To describe the common species and the antimicrobial susceptibility of bacteria cultured from samples submitted to commercial veterinary diagnostic laboratories from beef and pre-production dairy cattle between 2003–2016, and to describe the proportion of isolates with multidrug resistance (MDR).Methods: Bacterial culture and antimicrobial susceptibility data from July 2003 to March 2016 were obtained from commercial veterinary diagnostic laboratories in New Zealand. Results were included from samples from beef cattle, irrespective of age or sex, dairy-breed females aged <2 years and dairy-breed males of any age. Submission information provided included the specimen description, the organisms cultured, and the antimicrobial susceptibilities of isolates, if tested. Antimicrobial resistance (AMR) was defined as any isolate not showing susceptibility to an antimicrobial compound and MDR as any isolate showing AMR to ≥3 antimicrobial classes.Results: There were 1,858 unique laboratory submissions, yielding 2,739 isolates. Of these submissions, most were from the Canterbury (389; 21.9%), Manawatu (388; 21.9%) Waikato (231; 12.4%) and Hawke’s Bay (136; 7.3%) regions. There were 163 unique species identifications for the 2,739 isolates; the most common were Yersinia pseudotuberculosis (452; 16.5%), Campylobacter jejuni (249; 9.1%), Escherichia coli (230; 8.4%) and Salmonella enterica serovar Typhimurium (143; 5.2%). Only 251/2,739 (9.2%) isolates from 122/1,858 (6.6%) submissions had antimicrobial susceptibility results. There were no sensitivity results for Yersinia spp., and only one each for Salmonella spp., and Campylobacter spp. Amongst the isolates tested, susceptibility to ampicillin was lowest (33/56; 58.9%). Overall, 57/251 (20.7%) isolates tested for antimicrobial susceptibility had MDR, and MDR was most common for Enterococcus spp. (12/17; 71%) and E. coli (13/30; 43%).Conclusions and Clinical Relevance: This is the first report on antimicrobial susceptibility and MDR in New Zealand beef and pre-production dairy cattle. Findings highlight the limited use of bacterial culture and sensitivity testing by veterinarians and deficits in the information accompanying submissions. A national antimicrobial resistance surveillance strategy that specifically includes this population is recommended.

Population-Level Antimicrobial Consumption Is Associated With Decreased Antimicrobial Susceptibility in Neisseria gonorrhoeae in 24 European Countries: An Ecological Analysis.

There are substantial variations between different populations in the susceptibility of Neisseria gonorrhoeae to antimicrobials, and the reasons for this are largely unexplored. We aimed to assess whether the population-level consumption of antimicrobials is a contributory factor. Using antimicrobial susceptibility data from 24 countries in the European Gonococcal Antimicrobial Surveillance Programme and antimicrobial consumption data from the IQVIA MIDAS database, we built mixed-effects linear/logistic regression models with country-level cephalosporin, fluoroquinolone, and macrolide consumption (standard doses/1000 population/year) as the explanatory variables (from 2009 to 2015) and 1-year-lagged ceftriaxone, cefixime, azithromycin, and ciprofloxacin geometric mean minimum inhibitory concentrations (MICs) as the outcome variables (from 2010 to 2016). Positive correlations were found between the consumption of cephalosporins and the geometric mean MICs of ceftriaxone and cefixime (P < .05 for both comparisons). Fluoroquinolone consumption was positively associated with the prevalence of resistance to ciprofloxacin (P < .05). Differences in the population-level consumption of particular antimicrobials may contribute to variations in the level of antimicrobial resistance in N. gonorrhoeae in different settings. Further interventions to reduce misuse and overuse of antimicrobials in high-consumption populations and core groups are required.

The 2018 Lebanese Society of Infectious Diseases and Clinical Microbiology Guidelines for the use of antimicrobial therapy in complicated intra-abdominal infections in the era of antimicrobial resistance

BackgroundThe Lebanese Society of Infectious Diseases and Clinical Microbiology (LSIDCM) is involved in antimicrobial stewardship. In an attempt at guiding clinicians across Lebanon in regards to the proper use of antimicrobial agents, members of this society are in the process of preparing national guidelines for common infectious diseases, among which are the guidelines for empiric and targeted antimicrobial therapy of complicated intra-abdominal infections (cIAI). The aims of these guidelines are optimizing patient care based on evidence-based literature and local antimicrobial susceptibility data, together with limiting the inappropriate use of antimicrobials thus decreasing the emergence of antimicrobial resistance (AMR) and curtailing on other adverse outcomes.MethodsRecommendations in these guidelines are adapted from other international guidelines but modeled based on locally derived susceptibility data and on the availability of pharmaceutical and other resources.ResultsThese guidelines propose antimicrobial therapy of cIAI in adults based on risk factors, site of acquisition of infection, and clinical severity of illness. We recommend using antibiotic therapy targeting third-generation cephalosporin (3GC)-resistant gram negative organisms, with carbapenem sparing as much as possible, for community-acquired infections when the following risk factors exist: prior (within 90 days) exposure to antibiotics, immunocompromised state, recent history of hospitalization or of surgery and invasive procedure all within the preceding 90 days. We also recommend antimicrobial de-escalation strategy after culture results. Prompt and adequate antimicrobial therapy for cIAI reduces morbidity and mortality; however, the duration of therapy should be limited to no more than 4 days when adequate source control is achieved and the patient is clinically stable. The management of acute pancreatitis is conservative, with a role for antibiotic therapy only in specific situations and after microbiological diagnosis. The use of broad-spectrum antimicrobial agents including systemic antifungals and newly approved antibiotics is preferably restricted to infectious diseases specialists.ConclusionThese guidelines represent a major step towards initiating a Lebanese national antimicrobial stewardship program. The LSIDCM emphasizes on development of a national AMR surveillance network, in addition to a national antibiogram for cIAI stratified based on the setting (community, hospital, unit-based) that should be frequently updated.

Antimicrobial Susceptibility Testing of Leptospira spp. in the Lao People's Democratic Republic Using Disk Diffusion.

.Leptospirosis is a global zoonotic disease caused by pathogenic bacteria of the Leptospira genus, which are fastidious, slow-growing organisms. Antimicrobial susceptibility data are limited; traditionally, the organisms have not been culturable on solid media. The recent development of Leptospira Vanaporn Wuthiekanun (LVW) agar, which facilitates rapid growth of Leptospira spp., provides the opportunity for antimicrobial susceptibility testing. Eighty-three Leptospira spp. clinical isolates originating from patients in Laos between 2006 and 2016 were tested against six antimicrobials (azithromycin, ceftriaxone, ciprofloxacin, doxycycline, gentamicin, and penicillin G) using disk diffusion on LVW agar. Quality control was undertaken using American Type Culture Collection (ATCC) reference strains with known susceptibilities on both standard media and LVW agar. All Leptospira spp. isolates produced large zones of inhibition around each of the six antimicrobials. All zones were greater than 25 mm: gentamicin produced the smallest zones (median 35 mm; interquartile range 30 mm–37 mm) and azithromycin produced the largest zones (median 85 mm; interquartile range 85 mm–85 mm). Zones produced by non-leptospiral ATCC reference strains on LVW agar were within 2 mm of accepted strain-specific quality control range on standard media. Antimicrobial activity on LVW agar appears to be similar to that on standard media. As there are no published susceptibility guidelines for the Leptospira genus, zone interpretation was subjective. Leptospira Vanaporn Wuthiekanun agar enabled antimicrobial susceptibility testing of multiple Leptospira isolates on solid media; the large zone sizes observed suggest that resistance has not emerged to these six antimicrobials in Lao Leptospira spp.

Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

BackgroundRecent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes.ResultsWe present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. Gen2Epi is a command-line tool integrating third-party software and tailored specifically for N. gonorrhoeae. For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. The assemblies were generated using raw as well as trimmed short reads. The median genome coverage of full-length scaffolds and “N” statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Molecular antimicrobial resistant (AMR) determinants identified by Gen2Epi reproduced information for the 1484 samples as previously reported, including NG-MLST, NG-MAST, and NG-STAR molecular sequence types.ConclusionsGen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. Gen2Epi is publicly available under “CC BY-NC 2.0 CA” Creative Commons licensing as a VirtualBox image containing the constituent software components running on the LINUX operating system (CentOS 7). The image and associated documentation are available via anonymous FTP at ftp://www.cs.usask.ca/pub/combi or ftp://ftp.cs.usask.ca/pub/combi

Nocardiosis: 7-year experience at an Australian tertiary hospital.

Nocardiosis has historically been reported in immunocompromised patients, but Australian epidemiological and antimicrobial susceptibility data are limited. To describe the epidemiology, diagnosis and initial treatment of nocardiosis in an Australian tertiary hospital over 7 years. In this retrospective study, all positive cultures for Nocardia species from any site isolated at the Alfred Hospital, Melbourne, between 1 January 2010 and 31 December 2016 were identified, and corresponding laboratory data and medical records reviewed. Sixty-eight non-duplicate isolates were identified from 67 patients. Common predisposing factors were chronic lung disease (38/67; 57%), organ, particularly lung, transplantation (13/67; 19%) and solid organ malignancy (6/67; 9%); 12% (8/67) of patients had no identifiable systemic risk factors. Seventy-nine percent (53/67) of patients had pulmonary nocardiosis only. Nocardia nova was the most commonly isolated species (20/68; 29%). In 48% (32/67) of patients, Nocardia species were isolated only on specific mycobacterial media. All tested species were susceptible to sulfamethoxazole-trimethoprim and amikacin, with the majority (58/63; 92%) susceptible to imipenem. All-cause mortality rates at 6 and 12 months where data were available were 15% (10/66 patients) and 22% (14/64 patients) respectively. In the largest Australian series in 25 years, nocardiosis predominantly affected patients with chronic lung disease or impaired cell-mediated immunity. A significant proportion of organisms from pulmonary sites were isolated on mycobacterial culture media only, suggesting that its use may improve yield. Isolates remain highly susceptible to sulfamethoxazole-trimethoprim, amikacin and imipenem, while other agents should be used only after confirmation of in vitro susceptibility.

A compilation of antimicrobial susceptibility data from a network of 13 Lebanese hospitals reflecting the national situation during 2015\u20132016

BackgroundThere is a lack of official national antimicrobial resistance (AMR) data in Lebanon. Individual hospitals generate their own antibiotic susceptibility data in the form of yearly pamphlets.MethodsIn this study, antibiotic susceptibility data from 13 hospitals distributed across different governorates of Lebanon were collected to conduct a compilation-based surveillance of AMR in Lebanon for the years 2015–2016. The findings were compared with those of a previous nationwide study in this country conducted between 2011 and 2013 as well as with similar data obtained from the 2015 and 2016 European surveillance reports of AMR. To provide a clear presentation of the AMR situation, mean percent susceptibility of different antibiotic–microbe combinations was calculated.ResultsDuring 2015–2016, the percent susceptibility of Enterobacteriaceae to third-generation cephalosporins and to carbapenems was 59 and 97%, respectively. Among Pseudomonas aeruginosa and Acinetobacter spp., carbapenem susceptibility reached 70 and 12%, respectively. Among Gram positive organisms, the percent susceptibility to methicillin in Staphylococcus aureus was 72%, that to vancomycin in Enterococcus spp. was 98% and that to penicillin in Streptococcus pneumoniae was 75%. Compared with results of 2011–2013, there was an overall trend of decreased susceptibility of bacteria to the tested antibiotics, with a variation of 5 to 10%. The antibiotic susceptibility data from Lebanon were found to be comparable with those from Eastern and South-eastern European countries.ConclusionThis study highlights the need to establish a robust national AMR surveillance system that enables data from Lebanon to be included in global AMR maps.