Antimicrobial Susceptibility Testing Results Research Articles

Rapid diagnostic testing in the management of urinary tract infection: Potentials and limitations

Urine culture and sensitivity (C&S) remains the gold standard diagnostic for urinary tract infections (UTI). To reduce the use of inaccurate or broad-spectrum empiric antimicrobials, rapid identification and quantification (IDQ) and antimicrobial susceptibility testing (AST) with results within 30 and 150 min, respectively, are under development. To assess the impact of rapid diagnostics, five UTI vignettes were constructed, and ninety-one United States physicians were surveyed regarding their diagnostic, management, and antimicrobial choices before and after IDQ and AST results. Rapid diagnostics increased the postponement of antimicrobial therapy pending AST results from 16% to 38% and 5% to 54% in Vignettes 1 and 2 and reduced the use of ineffective antibiotics from 41% to 0% and 69% to 0% in Vignettes 2 and 4. Rapid diagnostics increased the use of narrow spectrum agents in the five vignettes, indicating its potential to revitalize physician responsibility in antimicrobial stewardship.

Risk factors of rescue bismuth quadruple therapy failure for Helicobacter pylori eradication.

Failure of bismuth quadruple therapy for Helicobacter pylori eradication is frequently observed. To increase the eradication rate, comprehensive analyses need to be performed regarding risk factors of bismuth quadruple therapy failure based on complete standard culture and antimicrobial susceptibility testing results. Patients with history of failed first therapy who had H.pylori colonies isolated from culture and successful minimum inhibitory concentration (MIC) test were enrolled. Esomeprazole, bismuth, metronidazole, and tetracycline (quadruple) therapies for 7 or 14days were given. Eradication rate, treatment compliance, adverse events, and risk factors for the failure of bismuth quadruple therapy were analyzed. A total 54 patients were enrolled. Overall eradication rate in the present study was 88.8%. The eradication rate for cases with metronidazole resistance such as MIC 8-16μg/mL or 16-32μg/mL was 92.8% (13/14). For cases with high level metronidazole resistance (MIC >32μg/mL), the eradication rate was only 60% (6/10). Multivariate analysis regarding compliance, treatment duration, age>60, three kinds of metronidazole MICs, tetracycline MIC >4μg/mL, adverse events and any other parameters, "metronidazole resistance, high level (MIC>32μg/mL)" was the only independent risk factor for eradication failure (P=0.007). For cases with metronidazole resistance at MIC>32μg/mL, rescue therapy other than bismuth-containing quadruple therapy is needed.

Risk factors of clinical mastitis and antimicrobial susceptibility test results of mastitis milk from dairy cattle in western Thailand: Bayesian network analysis

Using Bayesian network analysis, this cross-sectional study aimed to identify the conditional probability among dairy farm practices, cow characteristics, bacteriological culture results, and antimicrobial susceptibility test results of milk from dairy cows with clinical mastitis in western Thailand. Data associated with risk factors and clinical signs were collected using a structured questionnaire that was administered to 34 small dairy holders. In total, 100 quarters of milk samples from 100 cows were used for Bayesian network analysis. Conditional probability results showed that the following variables had the highest probabilities relevant to the occurrence of clinical mastitis pathogens: parity, concrete and rubber floor, hand stripping after using machine milking, dry cow therapy, and routine cleaning of milking machines. These variables were associated with the first four highest posterior probabilities of the occurrence of Streptococcus spp. (16.68%; reachable range or the minimum and maximum posterior probability values for the occurrence of Streptococcus spp., 15.45%–17.91%), Staphylococcus spp. (11.87%; reachable range, 11.06%–12.67%), Escherichia coli (7.53%; reachable range, 6.95%–8.17%), and Streptococcus dysgalactiae (7.28%; reachable range, 6.73%–7.83%), which were the most frequently isolated pathogens. Conditional probability results indicated these pathogens were most sensitive to amoxicillin/clavulanic acid (80.58%) and cloxacillin (64.28%). Most pathogens were resistant to penicillin G (40.37%). In this study, Bayesian network analysis revealed several clinically significant risk factors of mastitis associated with various pathogens and farming characteristics. Simple statistics could not provide sufficient information for the successful control of mastitis. In contrast, through in-depth data analysis, Bayesian networks could identify risk factors in various situations, hence providing information that will be crucial to help farmers reduce the cost of farming.

Antimicrobial susceptibility testing (AST) and associated clinical outcomes in individuals with cystic fibrosis: A systematic review

BackgroundAntimicrobial susceptibility testing (AST) is a cornerstone of infection management. Cystic fibrosis (CF) treatment guidelines recommend AST to select antimicrobial treatments for CF airway infection but its utility in this setting has never been objectively demonstrated. MethodsWe conducted a systematic review of primary published articles designed to address two PICO (patient, intervention, comparator, outcome) questions: 1) “For individuals with CF, is clinical response to antimicrobial treatment of bacterial airways infection predictable from AST results available at treatment initiation?” and 2) “For individuals with CF, is clinical response to antimicrobial treatment of bacterial airways infection affected by the method used to guide antimicrobial selection?” Relationships between AST results and clinical response (changes in pulmonary function, weight, signs and symptoms of respiratory tract infection, and time to next event) were assessed for each article and results were compared across articles when possible. ResultsTwenty-five articles describing the results of 20 separate studies, most of which described Pseudomonas aeruginosa treatment, were identified. Thirteen studies described pulmonary exacerbation (PEx) treatment and seven described ‘maintenance’ of chronic bacterial airways infection. In only three of 16 studies addressing PICO question #1 was there a suggestion that baseline bacterial isolate antimicrobial susceptibility was associated with clinical response to treatment. None of the four studies addressing PICO question #2 suggested that antimicrobial selection methods influenced clinical outcomes. ConclusionsThere is little evidence that AST predicts the clinical outcome of CF antimicrobial treatment, suggesting a need for careful consideration of current AST use by the CF community.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets.

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Prevalence and associated factors of urinary tract infections among diabetic patients in Arba Minch Hospital, Arba Minch province, South Ethiopia.

Urinary tract infection (UTI) is a common and grave health problem in the world. In fact, patients with diabetes mellitus have an immense risk for developing UTI. The development of resistance among uropathogens to antibiotics is a major crisis which limits the use of drug of choice for the treatment of UTI. On this view point, the aim of the present study is to elucidate the prevalence of UTI, associated factors, causative agents and their antimicrobial susceptibility amongst diabetic patients attending Arba Minch Hospital, Arba Minch, Ethiopia. A facility based cross-sectional study was carried out in diabetic patients visiting the Internal Medicine Unit of Arba Minch Hospital (AMH) during the study period (March to May 2016). Pre-tested structured questionnaire was used for collecting the data pertaining to socio-demographic characteristics and possible risk factors. In order to quantify the uropathogens, midstream urine samples were collected in sterile leak proof culture bottles and streaked onto diverse bacteriological media. All the positive urine cultures showing significant bacteriuria as per the Kass count (>105 organisms/mL) were further subjected to biochemical tests. The antimicrobial susceptibility test was performed to determine the resistance/susceptibility pattern of isolated uropathogens. Data entry and analysis were done using Statistical Package for Social Services, version 20. In total, 239 diabetic patients were included in the study of which 60.2% (n=144) were females. A total of 81 (33.8%) diabetic patients had positive urine cultures. Sixty-eight (83.9%) female diabetic patients had significant bacteriuria (p=0.000). Fifty-two (64.1%) participants had drinking habit and 79 (97.5%) of respondents had higher glucose levels (≥126 mg/dL) (p=0.004 and p=0.003), respectively. According to the biochemical tests, in a total of 90 isolates from patients with significant bacteriuria, eight species of uropathogens such as Escherichia coli, Klebsiella sp., Proteus sp., Citrobacter spp., Staphylococcus aureus, Coagulase negative Staphylococcus (CNS), Enterococcus faecalis and yeast isolates were identified. The antibiogram evidenced that 79.6% (n=51) of Gram-negative bacteria were invariably resistant to amoxicillin and penicillin whereas 73.4% (n=47) and 65.6 % (n=42) of them were resistant to trimethoprim, erythromycin and chloramphenicol, respectively. Regarding the Gram-positive bacteria, high degree of resistance was exhibited towards penicillin and trimethoprim (100%, n=24) followed by amoxicillin (83.3%, n=20) and gentamicin (62.5%, n=15). Invariably, all the Gram-positive cocci and Gram-negative bacilli were susceptible (100%) to amikacin, doxycycline, ceftriaxone and nitrofurantoin. The prevalence of UTI is higher in diabetic patients. Results revealed that the predominant pathogens of UTI were Gram-negative bacilli (Enterobacteriaceae), particularly E. coli. Significant bacteriuria had an association with the consumption of alcohol, gender and glucose level. Based on the results of antimicrobial susceptibility tests, it might be inferred that the antibiotics such as amikacin, doxycycline, ceftriaxone and nitrofurantoin are the drugs of choice for the management of both Gram-negative and Gram-positive uropathogenic bacteria in the study area.

Distribution of ExPEC Virulence Factors, bla CTX-M, fosA3, and mcr-1 in Escherichia coli Isolated From Commercialized Chicken Carcasses.

Pathogenic Escherichia coli found in humans and poultry carcasses harbor similar virulence and resistance genes. The present study aimed to analyze the distribution of extraintestinal pathogenic E. coli (ExPEC) virulence factors (VF), blaCTX−M groups, fosA3, and mcr-1 genes in E. coli isolated from commercialized chicken carcasses in southern Brazil and to evaluate their pathogenic risk. A total of 409 E. coli strains were isolated and characterized for genes encoding virulence factors described in ExPEC. Results of antimicrobial susceptibility testing confirmed that the strains were resistant to β-lactams, fosfomycin, colistin, and others resistance groups. The highest prevalence of VFs was observed in isolates belonging to the CTX-M groups, especially the CTX-M-2 group, when compared to those in other susceptible strains or strains with different mechanisms of resistance. Furthermore, ESBL strains were found to be 1.40 times more likely to contain three to five ExPEC virulence genes than non-ESBL strains. Our findings revealed the successful conjugation between ESBL-producing E. coli isolated from chicken carcass and the E. coli recipient strain J53, which suggested that genetic determinants encoding CTX-M enzymes may have originated from animals and could be transmitted to humans via food chain. In summary, chicken meat is a potential reservoir of MDR E. coli strains harboring resistance and virulence genes that could pose serious risks to human public health.

English

A cross-sectional study was conducted from December 2016 to May 2017 in and around Sebeta town with the aim of assessing the prevalence of mastitis, isolation of aerobic bacterial and fungal causal agents and assessing antimicrobial resistance pattern of isolated Staphylococcus species in dairy cows. From a total of 383 dairy cows, 220 (57.4%) were found to be positive for mastitis of which 10.4% were affected by clinical mastitis and 47% by subclinical mastitis. Mastitis was more likely to occur in cows above 8 years of age (OR = 16.9, 95% CI = 7.8 - 36.00) and in those cows washed by hand before milking (OR =7.8, 95% CI = 4.2-14.6) as compared to those subjected to udder washing and drying using towels. Staphylococcus aureus was the most frequently isolated bacterial species (25%) followed by Streptococcus agalactiae (12.3%) and coagulase negative Staphylococcus species (10.5%). Yarrowia lipolytica (10.9%) and Candida etchellsii (7.3%) were the major yeast species isolated, while Aspergillus (6.8%), Mucor (5.9%), Penicillium (3.6%) and Fusarium (3.6%) were the major filamentous fungi species identified from the cultured milk samples. The results of antimicrobial susceptibility testing revealed that the isolated Staphylococcus species were highly resistant to penicillin G (93.1%) and oxytetracycline (79.3%) but were susceptible to vancomycin (100%), sulphamethoxazole/trimethoprim (96.6%), ampicillin (89.7%) and erythromycin (86.2%). It could be concluded that bovine mastitis is a major challenge to the dairy producers in and around Sebeta towns. Appropriate control and preventative measures must be instituted and dairy farmers and workers must be trained on proper milking and hygiene practices in order to reduce the prevalence of mastitis in this region. The penicillin resistant S. aureus could be a source of serious infection in humans as well and hence comprehensive studies including molecular characteristics of drug resistance gene of S. aureus especially of methicillin-resistant should be conducted as farm animals, primarily dairy cattle might serves as a reservoir of infection for humans. In 2% of the cases, only fungal species were identified as causes of mastitis, hence further investigation regarding their pathogenicity and contribution to bovine mastitis is needed. Key words: Antimicrobial resistance, bovine mastitis, bacteria, Ethiopia, fungus, prevalence, Sebeta.

Occurrence, Molecular Characterization and Antimicrobial Resistance of Pathogenic Aeromonas Hydrophila from Retail Fish

A total of 150 fish samples, including 75 samples each of Tilapia nilotica and Mugil cephalus collected from different fish markets distributed in Mansoura city, Egypt were examined bacteriologically to determine the prevalence, antimicrobial susceptibility and the virulence of Aeromonas hydrophila regarding to aerolysin and haemolysin toxins using PCR technique. Phenotypically, presumptive A. hydrophila could be detected in 43/75 (57.33%) and 38/75 (50.67%) of the examined Tilapia nilotica and Mugil cephalus, respectively, with an overall incidence of 81/150 (54%). The results of PCR test based on using A. hydrophila 16S rRNA gene demonstrated that 32/75 (42.67%) and 29/75 (38.67%) of the examined Tilapia nilotica and Mugil cephalus, respectively were contaminated with A. hydrophila, with an overall incidence of 61/150 (40.67%). The aerA gene was detected in all (61) A. hydrophila strains, while hlyA gene couldn't detected in any of the identified strains. The results of antimicrobial susceptibility test showed that all (100%) isolated A. hydrophila strain were resistant to both ampicillin and carbenicillin, while chloramphenicol and amikacin showed the same percentage but account for sensitivity, whereas higher percentage of sensitivity was detected against ciprofloxacin (92.59%), followed by cefoxitin (87.65%), cefotaxime (80.24%), trimethoprim/sulfamethoxazole (79%), tetracycline (74%). The result declared that examined fish samples were markedly contaminated with virulent and multidrug strains of A. hydrophila which may be of a potential health risk.

Patterns of Drug-Resistant Bacteria in a General Hospital, China, 2011-2016.

Drug-resistant bacteria has been a threat to public life and property. We described the trends and changes in antibiotic resistance of important pathogens in a general hospital in Zhengzhou, China from 2011 to 2016, to control antimicrobial-resistant bacteria in hospital and provide support to clinicians and decision-making departments.Five dominant bacteria were enrolled based on the data from the general hospital during 6 years. The results of antimicrobial susceptibility testing were interpreted according to Clinical and Laboratory Standards Institute (CLSI). From 2011 to 2016, a total of 19,260 strains of bacteria were isolated, of which Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Acinetobacter baumannii accounted for 51.98%. The resistance rate of K. pneumoniae and E. coli to carbapenem was less than 15%, but resistance of K. pneumoniae to carbapenems increased with time and resistance of E. coli to meropenem increased. The rate of extended-spectrum beta-lactamase (ESBL) production among K. pneumoniae and E. coli was decreasing. For most antibiotics, the resistance rate of ESBL-positive isolates was higher than that of ESBL-negative isolates, excluding carbapenems and cefoxitin. For S. aureus, the rate of methicillin-resistant S. aureus (MRSA) was stable. Resistance of S. aureus to mostly antibiotics decreased with time. Besides polymyxin B, P. aeruginosa and A. baumannii showed high resistance to other antibiotics. For A. baumannii, the resistance rate to mostly antibiotics was increasing. The bacteria showed high levels of resistance and multiple drug resistance. Continuous surveillance and optimizing the use of antibiotics are essential.

The hypothetical impact of Accelerate Pheno™ system on time to effective therapy and time to definitive therapy in an institution with an established antimicrobial stewardship programme currently utilizing rapid genotypic organism/resistance marker identification.

BackgroundRapid organism identification and antimicrobial susceptibility testing (AST) can optimize antimicrobial therapy in patients with bacteraemia. The Accelerate Pheno™ system (ACC) can provide identification and AST results within 7 h of a positive culture.ObjectivesTo assess the hypothetical impact of ACC on time to effective therapy (TTET), time to definitive therapy (TTDT) and antimicrobial usage at the Detroit Medical Center (DMC).MethodsPatients with positive blood cultures from 29 March to 24 June 2016 were included. ACC was performed in parallel with normal laboratory procedures, but results were not made available to the clinicians. The potential benefit of having ACC results was determined if clinicians modified therapy based on actual AST results. Potential changes in TTET, TTDT and antibiotic usage were calculated.ResultsOne hundred and sixty-seven patients were included. The median TTET was 2.4 h (IQR 0.5, 15.1). Had ACC results been available, TTET could have been improved in four patients (2.4%), by a median decrease of 18.9 h (IQR 11.3, 20.4). The median TTDT was 41.4 h (IQR 21.7, 73.3) and ACC results could have improved TTDT among 51 patients (30.5%), by a median decrease of 25.4 h (IQR 18.7, 37.5). ACC implementation could have led to decreases in usage of cefepime (16% reduction), aminoglycosides (23%), piperacillin/tazobactam (8%) and vancomycin (4%).ConclusionsACC results could potentially improve time to de-escalation and reduce use of antimicrobials. The impact of ACC on TTET was small, likely related to the availability of other rapid diagnostic tests at DMC.

Clinical efficacy of marbofloxacin in dogs and cats diagnosed with lower urinary tract disorders

Marbofloxacin is one of the fluoroquinolones developed exclusively for veterinary medicine. The primary aim of the present study is to identify and assess evidence for marbofloxacin’s clinical efficacy in the treatment of urinary tract infections in small animal practice. The study included 118 dogs and 123 cats that were referred to the Internal Medicine Department with lower urinary tract symptoms. We excluded animals that had received antimicrobial or anti-inflammatory therapy in the previous 15 days. Diagnosis was confirmed by clinical findings, urinalysis, and imaging. Rectal temperature, appetite, urinary signs, and abdominal pain were monitored during two visits (day 0 and 14). The timetable depended on the diagnosis of the following: two urinalyses, two bacterial examinations, and antibacterial susceptibility testing were performed for each case. Bacterial UTI were confirmed in 36 dogs and 28 cats. Urine samples were collected on day 0, which demonstrated the presence of various bacteria, with a marked predominance of P. mirabilis and coagulase-positive Staphylococci in canine and feline urine samples, respectively. Antimicrobial susceptibility test results revealed 25 (65.7%) of dog isolates and 24 (85.7%) of cat isolates were susceptible to marbofloxacin. Treatment of UTIs is generally challenging for the small animal practitioner. Because of the need for long-term antimicrobials, bacterial culture and susceptibility tests are especially important for successful treatment. Marbofloxacin can be part of an effective treatment of UTIs in dogs and cats.

AMRcloud: новая парадигма мониторинга антибиотикорезистентности

Antimicrobial resistance is a growing threat to global public health and requires closer attention from the medical community. Antibiotic resistance monitoring systems play a key role in observing the antimicrobial susceptibility changes for rational prescribing antimicrobial therapy. Most current systems use data on a global scale; however, local data evaluation is more important for practical application. Unique AMRcloud online platform (http://amrcloud.net) was developed to process user data on antimicrobial resistance. Structural modules are modified to address the needs of researchers. The application has powerful graphic capabilities, data analysis system with automated interpretation of the antimicrobial susceptibility testing results. Geocoding is performed in a double way, and information exchange of results is adjusted by user. The use of AMRcloud allows researchers to create their own methodology for organizing primary data and their evaluation.

DETECTION OF SOME BIOFILM GENES RELATED WITH MULTIDRUG-RESISTANT IN ACINOBACTER BAUMANNII ISOLATED FROM CLINICAL ISOLATES

Background: Acinetobacter baumannii (A. baumanii) has recently emerged as a major pathogen causing nosocomial infections in patients admitted to intensive care units with a surprisingly rapid acquisition of antibiotic resistance. Objective: To study the rate of occurrence of A. baumanii in different clinical samples and to investigate the association between biofilm formation and presence of ompA and bap genes in multi-drug resistance isolates. Methods: A total of 150 clinical samples were collected from (blood, sputum, urine, wound swab) during a period from the first of October 2017 to the end of March 2018 from Al-Imamein Al-Kadhimein City, Central Teaching Hospital of Pediatrics, Welfare Children Protection in Medical City and Al-Yarmouk Teaching Hospital and tested against 14 antibiotics by disc diffusion method. Quantitative microtiter plate assay was done for detection of biofilm formation. Polymerase chain reaction (PCR) was performed to detect ompA and bap genes. Results: There were 75 A. baumanii isolated from different clinical samples as follows: 41 from blood, 13 from wound, 12 from sputum and 9 from urine. The results of antimicrobial susceptibility test showed, high rate of resistance to Aztronem (94.7%) followed by Cefotaxime (89.3%), Cefepim (86.7%), Meropinem (86.7%), Ceftriaxone (86.7%), Ceftazidime (85%), Gentamicin (85%), and Piperacillin (82.7%) respectively. Moderate - to - low rate of resistance to Ciprofloxacin (78%), Impenim (46.7%), Levofloxacin (46%), Amikacin (44%), Tigacycline (42.3%) and Colistin (44%). The detection of biofilm formation showed that (52%) of isolate produce biofilm and the prevalence of ompA gene was 86.7% while the prevalence of Bap-gene was 34.7%. Conclusion: High frequency of A. baumannii infection was observed in different hospitals in Baghdad. More than half of the isolates were biofilm producer and there is highly significant association between the presence of bap gene and the biofilm formation but not with ompA gene. Keywords: Acinetobacter baumannii, ompA, Bap, MD Citation: Talib SS, Abdulrahman TR, Ali SH. Detection of some biofilm genes related with multidrug-resistant in Acinobacter baumannii isolated from clinical isolates. Iraqi JMS. 2018; 16(4): 430-438. doi: 10.22578/IJMS.16.4.11

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates.

Standard antimicrobial susceptibility testing (AST) approaches lead to delays in the selection of optimal antimicrobial therapy. Here, we sought to determine the accuracy of antimicrobial resistance (AMR) determinants identified by Nanopore whole-genome sequencing in predicting AST results. Using a cohort of 40 clinical isolates (21 carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae, 10 non-carbapenemase-producing carbapenem-resistant K. pneumoniae, and 9 carbapenem-susceptible K. pneumoniae isolates), three separate sequencing and analysis pipelines were performed, as follows: (i) a real-time Nanopore analysis approach identifying acquired AMR genes, (ii) an assembly-based Nanopore approach identifying acquired AMR genes and chromosomal mutations, and (iii) an approach using short-read correction of Nanopore assemblies. The short-read correction of Nanopore assemblies served as the reference standard to determine the accuracy of Nanopore sequencing results. With the real-time analysis approach, full annotation of acquired AMR genes occurred within 8 h from subcultured isolates. Assemblies sufficient for full resistance gene and single-nucleotide polymorphism annotation were available within 14 h from subcultured isolates. The overall agreement of genotypic results and anticipated AST results for the 40 K. pneumoniae isolates was 77% (range, 30% to 100%) and 92% (range, 80% to 100%) for the real-time approach and the assembly approach, respectively. Evaluating the patients contributing the 40 isolates, the real-time approach and assembly approach could shorten the median time to effective antibiotic therapy by 20 h and 26 h, respectively, compared to standard AST. Nanopore sequencing offers a rapid approach to both accurately identify resistance mechanisms and to predict AST results for K. pneumoniae isolates. Bioinformatics improvements enabling real-time alignment, coupled with rapid extraction and library preparation, will further enhance the accuracy and workflow of the Nanopore real-time approach.

Direct antimicrobial susceptibility tests of bacteria and yeasts from positive blood cultures by using serum separator gel tubes and MALDI–TOF MS

Early and appropriate antimicrobial treatment can effectively reduce the mortality rate caused by bloodstream infections (BSIs) and is critical for favorable patient outcomes. In general, >90% of positive blood cultures will show positive results within 48 h after incubation in the BACTECTM FX system. However, an additional 6–8 h are required to obtain clones of the bacterium and another 10–24 h to obtain antimicrobial susceptibility test (AST) results. In this study, direct ASTs of bacteria and yeasts from positive blood cultures were performed by using serum separator gel tubes and matrix-assisted laser desorption ionization–time of flight mass spectrometry(MALDI-TOF MS). 153 BSI cases were caused by a single pathogen. The coincidence rates of genus and species identification between the direct method (from positive blood cultures) and reference method (from subcultured clones) were 86.9% and 83%, respectively. On average, 98.6% of the direct ASTs in 88 Gram-negative bacteria tested had an accurate result compared to the reference method. In Gram- positive bacteria and yeasts, the accuracy rates were 99.2% and 100%, respectively. MALDI-TOF MS combined with serum separator gel tubes can be used for rapidly identifying and performing ASTs on positive blood cultures.

Analysis on clinical distribution and drug resistance of Klebsiella pneumoniae isolated for 5 consecutive years

Objective: To analyze the clinical distribution and drug resistance of Klebsiella pneumoniae isolated from patients in a certain hospital and provide a basis for the rational use of antibiotics in the clinical treatment for the infection of Klebsiella pneumoniae . Methods: 1,192 strains of Klebsiella pneumoniae isolated from clinical specimens from 2012 to 2016 were collected. The strains were identified by VITEK-2 Compact Microbiological Identification System, and the corresponding results of the antimicrobial susceptibility test were interpreted in accordance with the standards recommended by Clinical and Laboratory Standards Institute (CLSI). Results: 1,192 strains of Klebsiella pneumoniae were mainly isolated from sputum (65.6%), and most of them were from Respiratory Medicine Department and Medical Intensive Care Unit of Respiratory Medicine Department (MICU), accounting for 41.4%. Out of 1,192 strains, 448 strains were detected to produce extended-spectrum beta-lactamases (ESBLs), accounting for 37.6%. In addition, the detection rates of ESBL-producing Klebsiella pneumoniae for 5 consecutive years showed an increasing trend year by year, and they were higher than the national average values published by China Antimicrobial Resistance Surveillance System (CARSS) in the corresponding period. The drug resistance rate of ESBL-producing Klebsiella pneumoniae was significantly higher than that of non ESBL-producing strains. Conclusions: The infection caused by Klebsiella pneumoniae mainly occurs in the lower respiratory tract, and the drug resistance rates of Klebsiella pneumoniae to antibiotics in the drug susceptibility spectrum are maintained at a high level. Therefore, the rational selection of antibiotics for the clinical treatment of lower respiratory tract infection caused by Klebsiella pneumoniae must be based on the production of ESBLs and the results of antimicrobial susceptibility test.

Analysis on clinical distribution and drug resistance of Klebsiella pneumoniae isolated for 5 consecutive years

Objective: To analyze the clinical distribution and drug resistance of Klebsiella pneumoniae isolated from patients in a certain hospital and provide a basis for the rational use of antibiotics in the clinical treatment for the infection of Klebsiella pneumoniae . Methods: 1,192 strains of Klebsiella pneumoniae isolated from clinical specimens from 2012 to 2016 were collected. The strains were identified by VITEK-2 Compact Microbiological Identification System, and the corresponding results of the antimicrobial susceptibility test were interpreted in accordance with the standards recommended by Clinical and Laboratory Standards Institute (CLSI). Results: 1,192 strains of Klebsiella pneumoniae were mainly isolated from sputum (65.6%), and most of them were from Respiratory Medicine Department and Medical Intensive Care Unit of Respiratory Medicine Department (MICU), accounting for 41.4%. Out of 1,192 strains, 448 strains were detected to produce extended-spectrum beta-lactamases (ESBLs), accounting for 37.6%. In addition, the detection rates of ESBL-producing Klebsiella pneumoniae for 5 consecutive years showed an increasing trend year by year, and they were higher than the national average values published by China Antimicrobial Resistance Surveillance System (CARSS) in the corresponding period. The drug resistance rate of ESBL-producing Klebsiella pneumoniae was significantly higher than that of non ESBL-producing strains. Conclusions: The infection caused by Klebsiella pneumoniae mainly occurs in the lower respiratory tract, and the drug resistance rates of Klebsiella pneumoniae to antibiotics in the drug susceptibility spectrum are maintained at a high level. Therefore, the rational selection of antibiotics for the clinical treatment of lower respiratory tract infection caused by Klebsiella pneumoniae must be based on the production of ESBLs and the results of antimicrobial susceptibility test.

Validation of a novel molecular diagnostic panel for pediatric musculoskeletal infections: Integration of the Cepheid Xpert MRSA/SA SSTI and laboratory-developed real-time PCR assays for clindamycin resistance genes and Kingella kingae detection

BackgroundPathogen detection in pediatric patients with musculoskeletal infections relies on conventional bacterial culture, which is slow and can delay antimicrobial optimization. The ability to rapidly identify causative agents and antimicrobial resistance genes in these infections may improve clinical care. MethodsConvenience specimens from bone and joint samples submitted for culture to Children's Hospital Colorado (CHCO) from June 2012 to October 2016 were evaluated using a “Musculoskeletal Diagnostic Panel” (MDP) consisting of the Xpert MRSA/SA SSTI real-time PCR (qPCR, Cepheid) and laboratory-developed qPCRs for Kingella kingae detection and erm genes A, B, and C which confer clindamycin resistance. Results from the MDP were compared to culture and antimicrobial susceptibility testing (AST) results. ResultsA total of 184 source specimens from 125 patients were tested. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert MRSA/SA SSTI compared to culture and AST results were 85%, 98%, 93%, and 95% respectively for MSSA and 82%, 100%, 100%, and 99% for MRSA. Compared to phenotypic clindamycin resistance in S. aureus isolates, the erm A, B, and C gene PCRs collectively demonstrated a sensitivity, specificity, PPV, and NPV of 80%, 96%, 67%, and 98%. In comparison to clinical truth, Kingella PCR had a sensitivity, specificity, PPV, and NPV of 100%, 99.5%, 100%, and 100%. ConclusionsThis novel MDP offers a rapid, sensitive, and specific option for pathogen detection in pediatric patients with musculoskeletal infections.

Antimicrobial resistance changes of carbapenem-resistant Enterobacteriaceae strains isolated from children

Objective: To investigate the prevalence and resistance changes of carbapenem-resistant Enterobacteriaceae (CRE) strains isolated from children patients of Chinese Bacterial Resistance Surveillance Network (CHINET) from 2005 to 2017. Methods: Antimicrobial susceptibility testing was carried out by disk diffusion method (KB method) and automated systems. Results were analyzed according to the Clinical and Laboratory Standards Institute (CLSI) 2017 edition standards. Results: Among the 4 481 CRE clinical strains, the overall prevalence of CRE in children was 6.4%, including 8.8% in neonatal period, 7.3% in infancy, 3.8% in early childhood, 4.0% in preschool, 4.7% at school age and 7.4% of puberty. The CRE prevalence of citrobacter spp. remained stable in 2005-2017, whereas other bacteria showed an upward trend, which was higher than that of the adult group (P<0.01). Among the 4 481 CRE strains, there were 2 905 strains of Klebsiella spp. (64.8%), 813 strains of Escherichia coli (18.1%), 549 strains of Enterobacter spp.(12.3%), and 65 strains of Citrobacter spp.(1.5%). Among the 4 481 CRE strains, 20.7%, 13.3%, and 11.8% were from the intensive care unit (ICU), neonatal department and internal medicine wards, respectively. Specimens were distributed as respiratory (42.8%), urine (26.3%), and blood (14.9%). The results of antimicrobial susceptibility testing exhibited that the CRE strains were highly resistant to most commonly used antimicrobial agents in clinical practice, such as imipenem, meropenem and ertapenem, as well as penicillins and cephalosporins, etc. Conclusion: The prevalence of CRE strains in children is increasing year by year, and their antimicrobial resistance to common antibacterial agents in clinical practice is extremely serious, to which serious attention needs to be paid. According to the results of antimicrobial susceptibility testings, the antibacterial agents should be rationally selected to effectively control the spread of CRE.