The scheme for validation of clinical metagenomics sequencing assay / 中华检验医学杂志

Clinical metagenomic next-generation sequencing (mNGS) entails unbiased shotgun sequencing of all microbial and host nucleic acids present in a clinical sample. By analyzing the microbiota diversity, taxonomic, and phylogenetic relationships of clinical specimens, metagenomics related analysis provides an opportunity to investigate substantial biological significance of different microbes. According to the published paper, most studies on mNGS mainly focused on the clinical impact evaluation. However, the studies focused on the analytical performance validation of mNGS before clinical application were rare. Here, a scheme, included intended use, method establishment, assay validation and standard operating protocol, for the laboratory validation of clinical metagenomics sequencing assay was provided by summarizing experiences of clinical laboratory department of Peking Union Medical College Hospital protocol and relevant research. In this scheme, we discussed important topics of mNGS laboratory validation as below: specimen type and pathogen list, bioinformatics pipeline setup, dry lab standard preparation and performance validation, mNGS workflow setup, background nucleotide acid evaluation, wet lab standard preparation and performance validation.

Epidemiologic Features, Radiological Findings andClinical Outcomes of 19 Patients with COVID-19in a Single Center in Beijing, China / 中国医学科学杂志(英文版)

ObjectiveTo describe the epidemiologic, clinical, laboratory, and radiological characteristics and prognoses of COVID-19 confirmed patients in a single center in Beijing, China. Methods The study retrospectively included 19 patients with nucleic acid-confirmed SARS-CoV-2 infection at our hospital from January 20 to March 5, 2020. The final follow-up date was March 14, 2020. The epidemiologic and clinical information was obtained through direct communication with the patients or their family members. Laboratory results retrieved from medical records and radiological images were analyzed both qualitatively by two senior chest radiologists as well as quantitatively via an artificial intelligence software. Results We identified 5 family clusters (13/19, 68.4%) from the study cohort. All cases had good clinical prognoses and were either mild (3/19) or moderate (16/19) clinical types. Fever (15/19, 78.9%) and dry cough (11/19, 57.9%) were common symptoms. Two patients received negative results for more than three consecutive viral nucleic acid tests. The longest interval between an initial CT abnormal finding and a confirmed diagnosis was 30 days. One patient's nucleic acid test turned positive on the follow-up examination after discharge. The presence of radiological abnormalities was non-specific for the diagnosis of COVID-19. Conclusions COVID-19 patients with mild or no clinical symptoms are common in Beijing, China. Radiological abnormalities are mostly non-specific and massive CT examinations for COVID-19 screening should be avoided. Analyses of the contact histories of diagnosed cases in combination with clinical, radiological and laboratory findings are crucial for the early detection of COVID-19. Close monitoring after discharge is also recommended.

Preliminary Study on Clinical Features and CT Findings of Common-type Coronavirus Disease 2019 Patients in Peking Union Medical College Hospital / 中国医学科学院学报

To summarize the clinical characteristics and chest CT findings of coronavirus disease 2019(COVID-19)patients in Peking Union Medical College Hospital(PUMCH). A total of 13 patients with COVID-19 confirmed at PUMCH from January 20 to February 6,2020 were selected as the research subjects.Their epidemiological histories,clinical characteristics,laboratory tests,and chest CT findings were analyzed retrospectively.The location,distribution,density,and other accompanying signs of abnormal lung CT lesions were recorded,and the clinical types of these patients were assessed. The clinical type was "common type" in all these 13 patients aged(46.8±14.7)years(range:27-68 years).Ten patients had a travel history to Wuhan or direct contact with patients from Wuhan,2 cases had recent travel histories,and 1 case had a travel history to Beijing suburb.The white blood cell(WBC)count was normal or decreased in 92.3% of the patients and the lymphocyte count decreased in 15.4% of the patients.Twelve patients(92.3%)had a fever,among whom 11 patients were admitted due to fever and 2 patients(15.4%)had low fever.Eight patients(61.5%)had dry cough.The CT findings in these 13 patients were all abnormal.The lesions were mainly distributed along the bronchi and under the pleura.The lesions were relatively limited in 8 patients(affecting 1-3 lobes,predominantly in the right or left lower lobe),and diffuse multiple lesions of bilateral lungs were seen in 5 patients.The CT findings mainly included ground glass opacities(GGOs)(=10,76.9%),focal consolidation within GGOs(=7,53.8%),thickened vascular bundle passing through the lesions(=10,76.9%),bronchial wall thickening(=12,92.3%),air bronchogram(=10,76.9%),vacuole signs in the lesions(=7,53.8%),fine reticulation and interlobular septal thickening(=3,23.1%),reversed halo-sign(=2,15.4%),crazy-paving pattern(=2,15.4%),and pleural effusion(=2,15.4%). Most of our patients diagnosed with COVID-19 at PUMCH had a travel history to Wuhan or direct contact with patients from Wuhan.The first symptoms of COVID-19 mainly include fever and dry cough,along with normal or reduced counts of WBC and lymphocytes.CT may reveal that the lesions distribute along the bronchi and under the pleura;they are typically localized GGOs in the early stage but can become multiple GGOs and infiltrative consolidation in both lungs in the advanced stage.Scattered vacuole signs may be visible inside the lesions in some patients.

Surveillance of antimicrobial resistance in Peking Union Medical College Hospital in 2017 / 中国感染与化疗杂志

Objective To investigate the antimicrobial resistance of clinical bacterial isolates in Peking Union Medical College Hospital (PUMCH) in 2017. Methods A total of 9 515 non-duplicate clinical isolates were collected from January 1 to December 31, 2017. Disc diffusion test (Kirby-Bauer method) and E-test method were employed to determine antimicrobial susceptibility. Results Gram-negative bacilli and gram-positive cocci accounted for 68.2％ and 31.8％, respectively among the 9 515 clinical isolates. Methicillin-resistant strains in S. aureus (MRSA) and coagulase-negative Staphylococcus (MRCNS) accounted for 25.6％ and 73.3％, respectively. Extended-spectrum β-lactamases (ESBLs) -producing strains accounted for 47.6％ (877/1 842), 27.6％ (335/1 213) and 33.0％ (59/179) in E. coli, Klebsiella spp (K. pneumoniae and K. oxytoca) and P. mirabilis, respectively. Enterbacteriaceae strains were still highly susceptible to carbapenems, with an overall resistance rate of ≤ 3.8％. The resistance rates of K. pneumoniae to imipenem and meropenem were 8.5％ and 8.2％, respectively. About 72.7％ and 70.4％ of A. baumannii isolateswere resistant to imipenem and meropenem. The resistance rate of P. aeruginosa to imipenem and meropenem was 14.8％ and 10.0％, respectively. The prevalence of extensively drug-resistant strains in A. baumannii, P. aeruginosa and K. pneumoniae was 31.7％ (239/753), 1.0％ (10/1 035), and 3.0％ (33/1 117), respectively. Conclusions The common bacterialisolates show various level of resistance to antimicrobial agents. Laboratory staff should improve communication with clinicians to prevent the spread of resistant strains.

Surveillance of bacterial resistance in Peking Union Medical College Hospital during 2014 / 中国感染与化疗杂志

Objective To investigate the antimicrobial resistance proifle in the clinical bacterial strains isolated from Peking Union Medical College Hospital during 2014.Methods A total of 8 295 nonduplicate clinical isolates were collected. Disc diffusion test (Kirby-Bauer method) and automated systems were employed to study the antimicrobial susceptibility. The data were analyzed by using WHONET 5.6 software according to CLSI 2014 breakpoints.Results Of the 8 295 isolates, 67.4% were gram-negative, and 32.6% were gram-positive. The top 10 most frequently isolated bacteria were:E. coli(18.1%),P. aeruginosa (10.8%),K. pneumoniae (10.2%),S. aureus (9.8%), A. baumannii(9.2%),E. faecalis (6.3%),E. faecium (4.1%), coagulase-negativeStaphylococcus (4.1%),E. cloacae (3.1%) andS. maltophilia (2.9%). Methicillin resistant strains inS. aureus (MRSA) and coagulase negativeStaphylococcus (MRCNS) accounted for average of 28.4% and 66.5%, respectively. The resistance rates of MR strains to β-lactams and other antimicrobial agents were much higher than those MS strains. Overall, 81.3% of MRSA strains were still susceptible to trimethoprim-sulfamethoxazole, while 81.1% of MRCNS strains were susceptible to rifampin. No staphylococcal strains were resistant to vancomycin, teicoplanin or linezolid. The resistance rate ofE. faecalis strains to most of the drugs tested (except chloramphenicol) was much lower than those ofE. faecium. Several strains of bothE. faecium andE. faecalis were found resistant to vancomycin and teicoplanin, which were Van-A and Van-B types based on their phenotype. No linezolid resistant enterococcal strains were found. Data showed that 90.8% ofβ-hemolyticStreptococcus strains were susceptible to penicillin. ESBLs-producing strains accounted for 54.2%, 31.0% and 28.9% inE. coli,Klebsiella spp (K. pneumoniae andK. oxytoca) andP. mirabilis, respectively.Enterobacteriaceae isolates were still highly susceptible to carbapenems. Overall, no more than 3.3% of these strains were resistant to carbapenems. A few extensively drug-resistant strains ofK. pneumoniae (1.3%, 11/842) were identiifed. The resistance rates ofP. aeruginosa to imipenem and meropenem were 17.5% and 11.8%, respectively.P. aeruginosa isolates showed the lowest resistance rate (5.9%) to amikacin. And 69.0% and 67.4% ofA. baumanniiisolates were resistant to imipenem and meropenem.A. baumannii isolates showed the lowest resistance rates to cefoperazone-sulbactam and minocycline (47.8% and 28.7%), respectively. The prevalence of extensively drug-resistant strains was 32.3% inA. baumannii and 1.8% inP. aeruginosa. The prevalence of β-lactamase inH. inlfuenzae was 33.7%. More than 93.0% ofS. pneumoniae strains were resistant to erythromycin and clindamycin.Conelusions Bacterial resistance is still increasing in this hospital, especially carbapenem resistantEnterobacteriaceae. It is necessary to take effective hospital infection control measures and use antibiotics rationally.

Evaluation of PREVI Isola Automated Plate Streaker / 现代检验医学杂志

Objective To evaluate the characteristics of the PREVI Isola automated plate streaker (bioMérieux,SA).Methods 80 respiratory tract specimens,70 sterile fluids,52 stools,69 swabs,12 cerebrospinal fluids and 80 urines were collected in Peking Union Medicd College Hospital.Specimens were processed with manual streaking and PREVI Isola system.PREVI Isola system were evaluated comparing to the manual streaking.The quality of results were analyzed by SPSS 16.0, doing Wilcoxon’s Sign Rank Test for the results of finally isolated species,overall numbers of isolated colonies and semi-quantita-tive of the species were both isolated by the two methods.Results PREVI Isola system was highly automatic,which could select the right plates and stake the bar code on the back of the plate indicating the type of the agar and inoculation time, PREVI Isola system could accurately absorb the liquid specimen and use a novel comb streaking procedure for processing of fluid specimens on standard agar plates,like 17 inoculating loops work together.It also had a good reproducibility.The quali-ty of PREVI Isola system results:As to the finally isolated species,there was significant statistical difference between PREVI Isola system and manual streaking method in respiratory tract and stools specimen,there were more species isolated by manual streaking method than PREVI Isola system.There were no differences between the two methods for the other of specimen types.As to the amount of pure clones of the species were both isolated by the two methods,there were significant statistical differences between the two methods for respiratory tract,sterile fluid and stool specimens.The amount of clones isolated by PREVI Isola system was more than manual streaking method.In semi-quantitative results,there were significant statistical differences between the two methods for respiratory tract and urine specimen,Species had wider distribution of PREVI Isola system than manual streaking method.Inoculation efficiency:if the batch of specimen type was simple (mainly the urine and so on),using the same plates,PREVI Isola system was more efficient than manual streaking method.Howev-er,if the batch of specimen type was complicated,manual method was high-performance.Besides,not all specimen type could be inoculated by PREVI Isola system,such as cerebrospinal fluid,catheter and tissues.Conclusion If the lab had simple specimen type,or utilize the specimen type using the same agar plates to be inoculated together,PREVI Isola system belongs to a good performance automated plate streaker.

Evaluation of the capabilities of disc diffusion and Vitek2-compact GN13 methods for testing antimi-crobial susceptibility and screening of ESBLs Enterobacteriaceae clinical isolates / 中华微生物学和免疫学杂志

Objective To evaluate the capabilities of disc diffusion and Vitek2-compact GN13 methods for testing antimicrobial susceptibility of screening ESBLs ( extended-spectrumβ-lactamase) in En-terobacteriaceae clinical isolates.Methods A total of 93 Enterobacteriaceae strains were isolated from pa-tients with intra-abdominal infections in 21 hospitals during 2011 to 2012.The in vitro minimum inhibition concentration ( MIC ) values of ampicillin-sulbactam, piperacillin-tazobactam, ertapenem, ceftazidime, ceftriaxone, cefepime, imipenem, amikacin, ciprofloxacin and levofloxacin were determined by disc diffu-sion, Vitek2-compact GN13 and broth microdilution methods, respectively.Categorical agreement ( CA ) rates of disc diffusion and Vitek2-compact GN13 methods were determined by using broth microdilution meth-od as the reference method.The genes encoding ESBLs were screened in Escherichia coli (E.coli), Kleb-siella pneumoniae (K.pneumonia), Klebsiella oxytoca (K.oxytoca) and Proteus mirabilis (P.mirabilis) strains by using PCR analysis and gene sequencing.Disc diffusion and Vitek2-compact GN13 methods were used for the phenotypic confirmatory test of ESBLs and the sensitivity, specificity, positive predictive value and negative predictive value of the two tests were evaluated.Results The CA values of disc diffusion and Vitek2-compact GN13 methods for the 10 antibiotics were all >90% as compared with broth microdilution method.The major error (ME) rate for ertapenem was 3.2%and the very major error (VME) rates for am- picillin-sulbactam, ceftazidime and cefepime tests were all 2.2% by using Vitek2-compact GN13 method. The sensitivity, specificity, positive predictive value and negative predictive value of disc diffusion and Vitek2-compact GN13 methods in the phenotypic confirmatory test of ESBLs were 96.7%(29/30), 100%(20/20), 100%(30/30) and 95%(19/20), respectively.Conclusion Both disc diffusion and Vitek2-compact GN13 methods could be used for testing the antimicrobial susceptibility and the detection of ESBLs in Enterobacteriaceae clinical isolates with the advantage of accuarcy.Attention should be paid to the posibil-lity of oaurance of ME and VME when testing ertapenem, ampicillin-sulbactam, ceftazidime and cefepime by using Vitek2-compact GN13 method.

Surveillance of bacterial resistance in Peking Union Medical College Hospital during 2012 / 中国感染与化疗杂志

Objective To investigate the profile of antimicrobial resistance in clinical isolates from the patients in Peking Union Medical College Hospital during 2012.Methods A total of 6 662 nonduplicate clinical isolates were collected.Disc diffusion test or Kirby-Bauer method and automated systems were employed to study the antimicrobial resistance.The data were analyzed by WHONET 5.6 software according to CLSI 2012 breakpoints.Results Of the 6 662 bacterial strains included in this analysis, gram negative organisms and gram positive cocci accounted for 66.7% (4 446/6 662)and 33.3% (2 216/6 662),respectively. The top 10 most frequently isolated microorganisms were E.coli (17%),P .aeruginosa (11.4%),A.baumannii (11.4%), S.aureus (11.2%),K.pneumoniae (9.2%),E.faecalis (8.4%),E.faecium (4.1%),coagulase negative Staphylococcus (3.3%),E.cloacae (3.1%)and S.maltophilia (3.1%).About 39.9% of the S.aureus strains and 73.4% of the coagulase negative Staphylococcus were methicillin-resistant.No staphylococcal strains were found resistant to vancomycin,teicoplanin or linezolid.A few of vancomycin-or teicoplanin-resistant strains were identified in both E.faecium and E.faecalis.No lin-ezolid resistant strains were found.ESBLs-producing strains accounted for 53.0%,25.7% and 27.0% in E.coli,Klebsiella spp.(K.pneumoniae and K.oxytoca)and P .mirabilis, respectively.The Enterobacteriaceae strains were still highly susceptible to carbapenems. Overall, less than 2.6% of these strains were resistant to carbapenems.A few pan-re-sistant strains of K.pneumoniae (0.7%,4/615)were iden-tified.About 20.3% and 13.6% of the P .aeruginosa isolates were resistant to imipenem and meropenem,respectively.P . aeruginosa isolates showed the lowest resistance rate (7.2%)to amikacin.And 72.8% and 75.2% of A.baumannii strains were resistant to imipenem and meropenem.A.baumannii isolates showed relatively low resistance rate to cefoperazone-sulbac-tam (51.2%)and minocycline (30.2%).The prevalence of pan-resistant strains was 43.5% in A.baumannii and 1.4% in P . aeruginosa.Conclusions Bacterial resistance is still increasing,especially pan-resistant A.baumannii strains.It is mandatory to take effective measures to control hospital infections and improve rational antibiotic use.

Antimicrobial susceptibility of Gram-negative bacteria causing intra-abdominal infections in China: SMART China 2011 / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>The Study for Monitoring Antimicrobial Resistance Trends program monitors the activity of antibiotics against aerobic and facultative Gram-negative bacilli (GNBs) from intra-abdominal infections (IAIs) in patients worldwide.</p><p><b>METHODS</b>In 2011, 1 929 aerobic and facultative GNBs from 21 hospitals in 16 cities in China were collected. All isolates were tested using a panel of 12 antimicrobial agents, and susceptibility was determined following the Clinical Laboratory Standards Institute guidelines.</p><p><b>RESULTS</b>Among the Gram-negative pathogens causing IAIs, Escherichia coli (47.3%) was the most commonly isolated, followed by Klebsiella pneumoniae (17.2%), Pseudomonas aeruginosa (10.1%), and Acinetobacter baumannii (8.3%). Enterobacteriaceae comprised 78.8% (1521/1929) of the total isolates. Among the antimicrobial agents tested, ertapenem and imipenem were the most active agents against Enterobacteriaceae, with susceptibility rates of 95.1% and 94.4%, followed by amikacin (93.9%) and piperacillin/tazobactam (87.7%). Susceptibility rates of ceftriaxone, cefotaxime, ceftazidime, and cefepime against Enterobacteriaceae were 38.3%, 38.3%, 61.1%, and 50.8%, respectively. The leastactive agent against Enterobacteriaceae was ampicillin/sulbactam (25.9%). The extended-spectrum β-lactamase (ESBL) rates among E. coli, K. pneumoniae, Klebsiella oxytoca, and Proteus mirabilis were 68.8%, 38.1%, 41.2%, and 57.7%, respectively.</p><p><b>CONCLUSIONS</b>Enterobacteriaceae were the major pathogens causing IAIs, and the most active agents against the study isolates (including those producing ESBLs) were ertapenem, imipenem, and amikacin. Including the carbapenems, most agents exhibited reduced susceptibility against ESBL-positive and multidrug-resistant isolates.</p>

Non-cultural methods for the laboratory diagnosis of invasive fungal diseases / 中华检验医学杂志

Non-cultural laboratory diagnostic methods include fungal antigen detection, anti-fungal antibody detection and molecular methods. Fungal antigen detection aim at ( 1, 3 )-β-D-glucan, galactomannan, cryptococcal capsular polysaccharide antigen and candida mannan antigen.Different antigen is used to diagnose different fungal infection.Antifungal antibody include antibody against Histoplasma capsulatum, Coccidioides immitis/Paracoccidiodes and Blastomyces dermatitidis.Molecular methods include non-amplification nucleic acid detection, nucleic acid amplification test, direct sequencing and matrix-assisted laser desorption/ionization time of flight mass spectrometry ( MALDI-TOF MS ) technology.Even though molecular methods are limited because of no standardization, the future of its usage is promising.

Interpretation and application of antimicrobial susceptibility testing / 中华检验医学杂志

Antimicrobial susceptibility testing is an important tool for guiding rational use of antimicrobial agents in clinical settings.Proper use of antimicrobial susceptibility testing results requires clinicians and clinical microbiologists to have the knowledge of antimicrobial susceptibility testing and breakpoints,and have the ability to use pharmacokinetic and pharmacodynamic (PK/PD) principles to optimize antimicrobial therapy regimen.(Chin J Lab Med,2013,36:289-291)

Surveillance of antimicrobial resistance of Haemophilus influenzae in Peking U-nion Medical College Hospital during 2008 and 2011 / 中国感染与化疗杂志

Objective To investigate the antimicrobial resistance of Haemophilus influenzae in Peking Union Medical College Hospital for rational clinical treatment.Methods A total of 223 strains of H .influenzae were collected from patients from Jan-uary 2008 to December 2011.The antimicrobial susceptibility was tested by Kirby-Bauer method.Production of beta-lactamase was detected using nitrocefin disks.WHONET 5.6 software was used to analyze the data of susceptibility testing.Results Tri-methoprim-sulfamethoxazole and tetracycline were the two antimicrobial agents to which the H .influenzae strains were most resistant.Theβ-lactamase positive ampicillin resistant strains accounted for 15.9 %,andβ-lactamase negative ampicillin resist-ant strains accounted for 8.9%.Conclusions H .influenzae is mainly isolated from respiratory specimens.Majority of the anti-microbial agents still show good antibacterial activity against H .influenzae strains.However,H .influenzae isolates are highly resistant to trimethoprim-sulfamethoxazole and tetracycline.

In vitro susceptibility of commonly used antibiotics on community-acquired uncomplicated urinary tract infection pathogens in Beijing / 中华泌尿外科杂志

Objective To investigate the distribution and susceptibility patterns of common uropathogens causing community-acquired urinary tract infection (UTI) in Beijing.MethodsA total of 300non-duplicate isolates were randomly collected from 3 hospitals in Beijing between Jan,1 2010 and Mar,312011.Minimal inhibitory concentrations (MICs) were determined by the broth microdilution methods,which were performed and interpreted according to the guidelines established by the Clinical and Laboratory Standards Institute (CLSI).A panel of 8 antimicrobial agents were tested:amikacin,cefaclor,cefepime,cefoperazone/sulbactam,ciprofloxacin,levofloxacin,gentamicin and nitrofurantoin. Fosfomycin trometamol MICs were determined by the agar-dilution method in cation-adjusted MH agar supplemented with glucose 6-phosphate at a concentration of 25 mg/L as detailed in the guidelines issued by 2010 CLSI. All the Escherichia coli,Klebsiella pneumoniae and Proteus mirabilis strains were screened and confirmed by double-disk synergy test for extended-spectrum β-lactamase (ESBLs).Results Among the organisms cultured,E.coli wasthepredominantpathogen(65.0％ ), followedby Enterococcus(11.7％ ),Staphylococcus( 6.3％ ), Klebsiella pneumoniae( 5. 3％ ), Proteus mirabilis( 4. 7％ ), and Pseudomonas aeruginosa (3.0％).Lower susceptibility rates to ciprofloxacin and levofloxacin (31.4％ -47.4％ ) were observed among all the stains.Amikacin,cefoperazone/sulbactam,nitrofurantoin and fosfomycin trometamol were the most active drugs (92.1％,92.1％,88.4％ and 87.9％ susceptible strains,respectively) among the Gram-negative strains.Isolates of Staphylococcus were highly sensitive to amikacin ( 100.0％ ),cefoperazone/sulbactam (94.7％),nitrofurantoin ( 100.0％ ).Higher susceptibility rates to nitrofurantoin (91.4％) and fosfomycin trometamol (90.0％) were observed in Enterococcus.ESBLs-producing strains accounted for 52.3％ (102/195) in E.coli,43.8％ (7/16) in K.pneumoniae and 14.3％(2/14) in P.mirabilis,respectively.ConclusionsResistance is most common to ciprofloxacin and levofloxacin of all the stains.Currently,the most appropriate agents for the empirical management of uncomplicated UTI seems to be amikacin,cefoperazone/sulbactam,nitrofurantoin and fosfomycin trometamol.

The microbiological and clinical analysis of bloodstream infections with identifiable sources / 中华内科杂志

ObjectiveTo evaluatethe microbial spectrum and clinical characteristics of microbiological diagnosed bloodstream infections ( BSI ) with identified infective sources. Methods The hospitalized patients microbiologically diagnosed as BSI with identified infective sources were included in this study from January 2008 to December 2009.Data were collected retrospectively and analyzed by software SPSS 17.0.ResultsIn this 2-year study,301 strains of microbes were isolated from 249 patients.There were 205 ( 82.33％ ) patients with monomicrobial BSI,while the other 44 ( 17.67％ ) patients with polymicrobial BSI.The most common identified source of bloodstream infections was lower respiratory tract infection (125,41.5％ ),followed by intraabdominal infection (55,18.3％ ) and intravascular devices related infection (54,17.9％ ).The four most common isolated pathogens were Acinetobacter species (60,19.9％ ),Escherichia coli (50,16.6％ ),Pseudomonas species (35,11.6％ ) and Staphylococcus Aureus (34,11.3％ ).Eighty-eight (35.3％) patients died during hospitalization due to all causes,out of which 62(24.9％ ) patients died owing to BSI.The patients with BSI originated from lower respiratory tract had a higher crude in-hospital case-fatality ratio than those with BSI originated from other resources ( OR =2.186 ; 95％ CI 1.260-3.792; x2 =7.879,P =0.005). In the multivariate regression,age ≥ 65,invasive mechanical ventilation, reservation of central line and polymicrobial BSI during hospitalization were independent risk factors of death due to all causes. Conclusions Lower respiratory tract is the most common originated source of BSI with microbiological identified sources. Gram-negative bacillus taking advantage,the microbial spectrum of BSI with identified sources in our study is different from those reported before both in primary and secondary BSI.The patients with BSI originated from respiratory tract have a higher crude in-hospital case-fatality ratio.

Antimicrobial resistance surveillance study among Streptococcus pneumoniae clinically isolated from 14 teaching hospitals in 2005-2008 in China / 中华检验医学杂志

Objective To investigate antimicrobial resistance among Streptococcus pneumoniae clinically isolated from 14 teaching hospitals located at different areas in China in 2005-2008 and to give logical guidance for clinical empirical therapy.Methods A total of 1 317 non-repetitive S.pneumoniae isolates in 14 teaching hospitals from 2005-2008 were collected and sent to the central lab for reidentification and susceptibility testing, including 271 isolates collected in 2005, 391 isolates collected in 2006, 363 isolates collected in 2007 and 292 isolates collected in 2008. Most of the isolates were from community-acquired respiratory tract infections, which were isolated from outpatient or emergency department patients with respiratory tract infections or those patients with respiratory tract infections within ≤48 hours hospitalization.The districts where the organisms were isolated include North China, Northeast China, South China, Central and Northwest China and East China.The patients included adults, teenagers and children.The minimum inhibitory concentrations (MICs) or inhibitory zone diameter of 17 antimicrobial agents were determined by Etest method, agar dilution method or disk diffusion method.WHONET5.5 software was used to analyze susceptibility rate, intermediate rate, resistance rate, MIC50 and MIC90.Results Linezolid (100%) and fluoroquinolones (95.2%-99.7%) showed excellent activities against S.pneumoniae.Among β-lactams, amoxicillin-clavulanic acid remained high activities (73.8%-92.1%),followed by penicillin, ceftriaxone and cefepime with year-over-year decrease in activities.The activities of three second-generation cephalosporins were low (36.3%-38.4% in 2008).The activities of erythromycin, azithromycin, clindamycin, trimethoprim/sulfamethoxazole and tetracycline against S.pneumoniae were poor and decreased year over year.The incidence of penicillin non-susceptible S.pneumoniae (PNSP) was increasing especially for PISP (from 4.4% in 2005 to 20.2% in 2008).The incidence of PNSP in North China was low (6.0%), while this value were high in central China and East China (30.1% and 38.7%, separately).The incidence of PNSP in adults (15.7%) was obviously lower than that in children(≤5 years:33.0%) and teenagers (6-17 years:38.2%).Conclusions linezolid and fluoroquinolones showed excellent in vitro activity against S.pneumoniae, followed by penicillin and cephalosporins with year-over-year decrease of activity. Clinicians should pay more attention when using those antimicrobial agents with poor activity against S.pneumoniae, which include macrolides, clindamycin, trimethoprim/sulfamethoxazole and tetracycline.

Antimicrobial resistance surveillance among nosocomial pathogens in 13 teaching hospitals in China in 2009 / 中华检验医学杂志

Objective To investigate distribution and antimicrobial resistance among nosocomial pathogens from 13 teaching hospitals in China in 2009. Methods Non-repetitive pathogens from nosocomial BSI, HAP and IAI were collected and sent to the central lab for MIC determination by agar dilution method.WHONET5.6 software was used to analyze the data. Results A total of 2 502 clinical isolates were collected. The top three pathogens of BSI were Escherichia coli [27. 1% (285/1 052 )] , coagulase-negutive staphylococcus [12. 6% ( 133/1 052)] and Klebsiella pneumoniae [10. 8% ( 114/1 052)]. The top three pathogens of HAP were Acinetobacter baumannii [28. 8% (226/785)], Pseudomonas aeruginosa [16. 1% (126/785)] and Klebsiella pneumoniae [14.6% (115/785 )] . The top three pathogens of IAI were Escherichia coli[31.0% ( 206/665 )], Klebsiella pneumonia [11.3% ( 75/665 )] and Enterococcus faecium [10. 8% (72/665)]. Against Escherichia coil and Klebsiella spp. , the antimicrobial agents with higher than 80% susceptibility rate included imipenem and meropenem (98. 1%-100% ), tigecycline (95.3%-100% ), piperacillin-tazobactam ( 88.6% -97. 1% ) and amikacin ( 88. 3% -92. 5% ). Against Enterobacter spp. , Citrobacter spp. and Serratia spp. , the susceptibility rates of tigecycline were 93.5% -100% whereas the value of imipenem and meropenem were 92.9% -100%. Other antimicrobial agents with high activity included amikacin ( 85.2% -96. 7% ), pipcracillin-tazobactam ( 82.4% -96.4% ), cefepime ( 79. 6% -96. 7% ) and cefoperazonc-sulbactam (78. 7%-90. 0% ). Polymyxin B showed the highest susceptibility rateagainst Pseudomonas aeruginosa ( 100% ), followed by amikacin ( 81.9% ) and piperacillin-tazobactam (80.1% ). Polymyxin B also showed the highest susceptibility rate against Acinetobacter baumannii (98. 8% ), followed by tigecycline (90. 1% ) and minocycline (72. 0% ). The incidence of carbapenemresistant Acinetobacter baumannii was 60. 1%. The MRSA rate was 60. 2% and the MRSCoN rate was 84. 2%. All Staphylococcus strains were susceptible to tigecycline, vancomycin, teicoplanin and linezolid except for one isolate of Staphylococcus haemolysis with intermediate to teicoplanin. Two Enterococcus faecalis isolates which were intermediate to linezolid and one Enterococcus faecium isolate which was resistant to vancomycin and teicoplanin was found in this surveillance, while the MICs of tigecycline against these three isolates were 0. 032-0. 064 μg/ml. Conclusions Tigecycline, carbapenems, piperacillin-tazobactam,amikacin and cefepime remain relatively high activity against nosocomial Enterobacteriaceae. Pseudomonas aeruginosa exhibite high susceptibility to polymyxin B, while Acinetobacter baumanni shows high susceptibility to polymyxin B and tigecycline. Tigecycline, vancomycin, teicoplanin and linezolid remain high activity against nosocomial gram-positive cocci.

Evaluation of the susceptibility interpretation on Escherichia coli, Klebsiella pneumonia, Proteus mirabilis in China by agar dilution method according to the changes of cephalosporin breakpoints in CLSI 2010 / 中华检验医学杂志

Objective To evaluate the influences of susceptibility interpretation of Escherichia coli,Klebsiella pneumonia and Proteus mirabilis in China mainland according to the old and new ceftazidime,cefotaxime and ceftriaxone breakpoints in CLSI M100-S20 and CLSI M100-S19. Methods First, We analyzed the antibacterial susceptibility results of the three bacteria by agar dilution method in the SEANIR surveillance item, which were collected from 15 national hospitals between the year of 2005 and 2007 and excluded the AmpC enzyme positive isolates according to the PGR-DNA sequencing method and/or the antibacterial susceptibility phenotype. ESBL phenotype was confirmed by the CLSI phenotypic confirmatory test. Antibacterial susceptibility of the total 2733 Escherichia coli, Klebsiella pneumonia, Proteus mirabilis isolates was retrospectively analyzed by WHONET 5. 4 software according to the breakpoints of the CLSI M100-S19 (S19) and CLSI M100-S20 (S20). Second, 207 isolates of Peking Union Medical College Hospital with the results of both agar dilution method and disk diffusion method were performed by recurrent analysis. Then we observed the inter-method agreement through the scatter diagram according to the breakpoints of S19 and S20. Results First, as to the ESBL positive Escherichia coli, Klebsiella pneumonia and Proteus mirabili.s, the resistant rate of cefotaxime increased from 65.2% , 55.5%, 14. 6% under S19 (64 μg/ml) to 99. 7%, 96. 2% , 93. 8% under S20 (4 μg/ml). The susceptibility rates decreased from 6. 0%, 11.5%, 33.3% under S19 (8 μg/ml) to 0%, 0. 2%, 0% under S20 ( 1 μg/ml). Ceftriaxone had the same trend as cefotaxime. Though ceftazidime was more active than cefotaxime and ceftriaxone, as to the ESBL positive Escherichia coli and Klebsiella pneumonia, the resistant rates slightly increased from 30. 3%,43. 2% under S19 (32 μg/ml) to42.0%, 56. 0% under S20 (16 μg/ml). The susceptibility rates slightly decreased from 58. 1%, 44. 1% under S19 (8 μg/ml) to 44. 7%, 28.0% under S20 (4 μg/ml). Second,as to the ESBL negative Escherichia coli, Klebsiella pneumonia and Proteus mirabilis, all the susceptibility rates of ceftazidime, cefotaxime and ceftriaxone were between 99. 2%-100. 0%, the resistant rate were between 0%-0. 4%. Third, the S20 MIC breakpoints had a good correspondence with the ESBL phenotype.Fourth, according to the recurrent analysis of MIC testing and disk dilution method, r value was 0. 67,0. 79, 0. 77 for ceftazidime, cefotaxime and ceftriaxone, respectively, and all P value were under 0. 01. The intermethod rates of S19 and S20 were both acceptable. Conclusions If the cefotaxime and ceftriaxone S20 new breakpoints were used, the concordance of antibacterial susceptibility results and ESBL phenotype would increase greatly. The clinician could select proper antibiotics according to the antibacterial susceptibility results and clinical symptoms. It is no longer necessary to edit results for cephalosporins, aztreonam, or penicillins from susceptible to resistant. However, until laboratories implement the new interpretive criteria,ESBL testing should be performed as described in Supplemental Table 2A-S1. The relationship between the new breakpoints of ceftazidime and clinical outcomes need to be further evaluated.

Performance of modified Hodge test on the detection of carbapenemase among Enterobacteriaceae / 中华检验医学杂志

Objective To evaluate the performance of modified Hodge test on the detection of carbapenemases among Enterobacteriaceae with decreased susceptibility to carbapenems. Methods Fortynine Enterobacteriaceae isolates with decreased susceptibility to carbapenems ( MIC of imipenem, meropenem or ertapenem was ≥ 2 μg/ml ) were collected from 16 teaching hospitals from 2004 to 2008. MICs of imipenem, meropenem and etapenem were determined by agar dilution method. Carbapenemases were detected by modified Hodge test. Carbepenemase-causing positive results and AmpCs-causing positive results were differentiated by phenyl boronic acid and oxacillin. Beta-lactamases encoding genes including blaNDM-1were detected by PCR and sequencing. Results Thirty-six of 49 isolates were non-susceptible to imipenem (MIC >4 μg/ml), 31 were non-susceptible to meropenem (MIC > 4 μg/ml) and 47 were non-susceptible to ertapenem (MIC > 2 μg/ml). Twenty-three isolates showed positive modified Hodge test result, including 9 weak-positive results and 14 strong-positive results. Through PCR detection and sequencing, 2 out of 9 isolates showing weak-positive results carried blaKPC-2 and other 7 did not carry any carbapenemase genes but AmpCs/ESBLs genes. Among the 14 isolates showing strong-positive results, 4 carried blaKPC-2, 8 carried blaIMP-4 and 2 caried blaIMP-8. All 26 isolates with negative modified Hodge test result didn't carry any carbapenemase genes. No isolate carried blaNDM-1. Carbapenemases genes PCR detection was regarded as a gold standard, and the sensitivity, specificity, positive predictive value and negative predictive value of modified hodge test was 100%, 79%, 70% and 100% on the detection of carbapenemases among Enterobacteriaceae with decreased susceptibility to carbapenems. Conclusions Modified Hodge test revealed great sensitivity but showed a few false positive results. True and false positive results can be effectively differentiated by phynel boronic acid and oxacillin.

In vitro activity of cefminox and comparators against Escherichia coli, Klebsiella pneumoniae and Bacteroides species / 中华检验医学杂志

Objective To compare the in vitro activity of cefminox with other antimicrobial agents against clinical Escherichia coil, Klebsiella pneumoniae isolates and Bacteroides species. Methods MICs of sixteen antimicrobial agents against 945 Escherichia coli and 588 Klebsiella pneumoniae isolates from 15 teaching hospitals and MICs of four antimicrobial agents against 50 Bacteroides species isolates were determined by agar dilution method. WHONET 5.4 software was used to analyze the data. Results Among 1533 Escherichia coli and Klebsiella pneumoniae isolates, 628 isolates produced neither extended-spectrum beta-lactamases (ESBLs) nor AmpC, while 837 isolates produced only ESBLs and 68 isolates produced AmpC enzymes. The susceptibility rate of cefminox against non-ESBLs-producing or ESBLs-producing isolates was above 90%. MIC_(50) of eefminox was 2-4 fold lower than cefometazole and 8-16 fold lower than cefoxitin. MIC50 of cefminox was 2-8 fold lower than cefometazole and 8-16 fold lower than cefoxitin. Against ESBLs-producing isolates, the in vitro activity of cefminox was superior to the third and fourth generation cephalosporins, aztreonam, cefoperazone/sulbactam, levofloxacin, amikacin and inferior to carbapenems. Its activity was similar to piperacillin-tazobactam. The susceptibility rate of cefminox against AmpC-producing isolates was less than 20%. The susceptibility rate of cefminox against Bacteroides species was 90%, which was higher than that of cefometazole (50% -70%) and penicillin (0%) and similar to that of metronidazole. Conclusion Cefminox exhibites good activity against ESBLs-producing and non-ESBLs-producing Escherichia coli and Klebsiella pneumoniae isolates and Bacteroides species, which indicates that cefminox could be one of the options for the treatment of infections caused by these organisms.

In vitro activity of daptomycin and other antimicrobial agents against 499 strains of gram-positive cocci causing bloodstream infection / 中华内科杂志

Objective To evaluate the in vitro activity of daptomycin, vancomycin, teicoplanin, tigecycline, ceftobiprole and linezolid against 499 strains of blood-isolated gram-positive cocci. Methods Determination of the minimal inhibitory concentration (MICs) of daptomycin with microbrothdilution method and the MICs of other 9 antimicrnhial agents with agar dilution method against 499 strains of blood-isolated gram positive cocci was carried out. The data was analyzed with WHONET 5.4 software. Results The susceptibility rates of staphylococci to daptomycin, tigecycline, linezolid, ceftobiprole, vancomyein and teicoplanin were 100%. All staphylococcus strains were inhibited by daptomycin at a MIC of 1 mg/L. The MIC50 and MIC60 of daptomyein were both 0.5 mg/L against methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus coagalase-negative (MRSCnN). Among Enterococcus spp, the highest MIC of daptomycin was 4 mg/L. The MIC50 and MIC90 of daptomycin were both 2 mg/L against E.faecalis, whereas they were 2 mg/L and 4 mg/L against E.faecium. One strains of linezolid-resistant E.faecalis(MIC:8 mg/L)was susceptible to daptomycin (MIC: 1 mg/L). Three strains of E.faecium carrying vanA gene with vancomycin MICs above 32 mg/L and teicoplanin MICs also 32 mg/L were susceptible to daptomycin, tigeeycline and linezolid. The MIC range of daptomycin against Streptococcus pneumoniae and Streptococcus viridans was 0.032-0.25 mg/L and 0.125-1.000 mg/L separately. Conclusions Daptomycin has excellent in vitro activity against common gram-positive pathogens isolated from blood. It may be a good choice for clinicians to treat drug-resistant gram-positive cocci.