As an important rice disease, rice bacterial leaf blight (RBLB, caused by the bacterium Xanthomonas oryzae pv.oryzae), has become widespread in east China in recent years. Significant losses in rice yield occurred as ...As an important rice disease, rice bacterial leaf blight (RBLB, caused by the bacterium Xanthomonas oryzae pv.oryzae), has become widespread in east China in recent years. Significant losses in rice yield occurred as a result ofthe disease’s epidemic, making it imperative to monitor RBLB at a large scale. With the development of remotesensing technology, the broad-band sensors equipped with red-edge channels over multiple spatial resolutionsoffer numerous available data for large-scale monitoring of rice diseases. However, RBLB is characterized by rapiddispersal under suitable conditions, making it difficult to track the disease at a regional scale with a single sensorin practice. Therefore, it is necessary to identify or construct features that are effective across different sensors formonitoring RBLB. To achieve this goal, the spectral response of RBLB was first analyzed based on the canopyhyperspectral data. Using the relative spectral response (RSR) functions of four representative satellite or UAVsensors (i.e., Sentinel-2, GF-6, Planet, and Rededge-M) and the hyperspectral data, the corresponding broad-bandspectral data was simulated. According to a thorough band combination and sensitivity analysis, two novel spectralindices for monitoring RBLB that can be effective across multiple sensors (i.e., RBBRI and RBBDI) weredeveloped. An optimal feature set that includes the two novel indices and a classical vegetation index was formed.The capability of such a feature set in monitoring RBLB was assessed via FLDA and SVM algorithms. The resultdemonstrated that both constructed novel indices exhibited high sensitivity to the disease across multiple sensors.Meanwhile, the feature set yielded an overall accuracy above 90% for all sensors, which indicates its cross-sensorgenerality in monitoring RBLB. The outcome of this research permits disease monitoring with different remotesensing data over a large scale.展开更多
BACKGROUND With the widespread use of antimicrobial drugs,bacterial resistance has become a significant problem,posing a serious threat to public health.The prevalence of clinical infection strains in hospitals and th...BACKGROUND With the widespread use of antimicrobial drugs,bacterial resistance has become a significant problem,posing a serious threat to public health.The prevalence of clinical infection strains in hospitals and their drug sensitivities are key to the appropriate use of antibiotics in clinical practice.AIM To identify prevalent bacteria and their antibiotic resistance profiles in a hospital setting,thereby guiding effective antibiotic usage by clinicians.METHODS Specimens from across the institution were collected by the microbiology laboratory.The VITEK 2 compact fully automatic analyzer was used for bacterial identification and antibiotic sensitivity testing,and the WHONET5.6 software was utilized for statistical analysis.RESULTS A total of 12062 bacterial strains of key monitoring significance were detected.Staphylococcus aureus demonstrated widespread resistance to penicillin,but none of the strains were resistant to vancomycin or linezolid.Moreover,219 strains of methicillin-resistant coagulase-negative staphylococci and 110 strains of methicillin-resistant Staphylococcus aureus were detected.Enterococcus faecalis showed moderate resistance to the third-generation quinolones ciprofloxacin and levofloxacin,but its resistance to nitrofurantoin and tetracycline was low.Enterococcus faecium displayed significantly lower resistance to third-and fourthgeneration quinolones than Enterococcus faecalis.The resistance of two key monitoring strains,Escherichia coli and Klebsiella pneumoniae,to piperacillin/tazobactam was 5%-8%.However,none of the Escherichia coli and Klebsiella pneumoniae strains were resistant to meropenem.The resistance of Acinetobacter baumannii to piperacillin/sulbactam was nearly 90%.Nonetheless,the resistance to tigecycline was low,and Pseudomonas aeruginosa demonstrated minimal resistance in the antibiotic sensitivity test,maintaining a resistance of<10%to the cephalosporin antibiotics cefotetan and cefoperazone over the last 6 years.The resistance to amikacin remained at 0.2%over the past 3 years.CONCLUSION Our hospital’s overall antibiotic resistance rate was relatively stable from 2017 to 2022.The detection rates of key monitoring strains are reported quarterly and their resistance dynamics are monitored and communicated to the entire hospital,which can guide clinical antibiotic selection.展开更多
Objective:To observe and analyze the effect of bacterial resistance monitoring in clinical microbiology testing.Methods:600 microbial specimens collected in our hospital in the past year(April 2021 to April 2022)were ...Objective:To observe and analyze the effect of bacterial resistance monitoring in clinical microbiology testing.Methods:600 microbial specimens collected in our hospital in the past year(April 2021 to April 2022)were used as the test subjects of this study.The specimens were divided into Group A(control group)and Group B(research group),with 300 cases in each group.Group A consisted of blood culture specimens,while Group B consisted of sputum specimens.After the tests were completed,the rates of unfavorable and favorable results,bacterial species distribution,and bacterial drug resistance of the specimens in both groups were compared.Results:Among group A specimens,29 cases were positive(9.67%)and 271 cases were negative(90.33%);among group B specimens,99 cases were positive(33.00%)and 201 cases were negative(66.00%);the difference between the two groups of data was statistically significant(P<0.05).As for the distribution of the types of bacteria,there were 472 cases of Gram-negative bacteria and 128 cases of Gram-positive bacteria.Conclusion:Bacterial resistance monitoring is helpful in clinical microbiology testing.Through proper monitoring,bacterial resistance can be well understood.In this way,patients get to receive appropriate treatment measures and suitable antibacterial prescriptions,thereby improving the patient outcome.展开更多
AIM: To evaluate the epidemiology and outcomes of culture-positive spontaneous bacterial peritonitis (SBP) and spontaneous bacteremia (SB) in decompensated cirrhosis.METHODS: We prospectively collected clinical, labor...AIM: To evaluate the epidemiology and outcomes of culture-positive spontaneous bacterial peritonitis (SBP) and spontaneous bacteremia (SB) in decompensated cirrhosis.METHODS: We prospectively collected clinical, laboratory characteristics, type of administered antibiotic, susceptibility and resistance of bacteria to antibiotics in one hundred thirty cases (68.5% males) with positive ascitic fluid and/or blood cultures during the period from January 1, 2012 to May 30, 2014. All patients with SBP had polymorphonuclear cell count in ascitic fluid > 250/mm<sup>3</sup>. In patients with SB a thorough study did not reveal any other cause of bacteremia. The patients were followed-up for a 30-d period following diagnosis of the infection. The final outcome of the patients was recorded in the end of follow-up and comparison among 3 groups of patients according to the pattern of drug resistance was performed.RESULTS: Gram-positive-cocci (GPC) were found in half of the cases. The most prevalent organisms in a descending order were Escherichia coli (33), Enterococcus spp (30), Streptococcus spp (25), Klebsiella pneumonia (16), S. aureus (8), Pseudomanas aeruginosa (5), other Gram-negative-bacteria (GNB) (11) and anaerobes (2). Overall, 20.8% of isolates were multidrug-resistant (MDR) and 10% extensively drug-resistant (XDR). Health-care-associated (HCA) and/or nosocomial infections were present in 100% of MDR/XDR and in 65.5% of non-DR cases. Meropenem was the empirically prescribed antibiotic in HCA/nosocomial infections showing a drug-resistance rate of 30.7% while third generation cephalosporins of 43.8%. Meropenem was ineffective on both XDR bacteria and Enterococcus faecium (E. faecium). All but one XDR were susceptible to colistin while all GPC (including E. faecium) and the 86% of GNB to tigecycline. Overall 30-d mortality was 37.7% (69.2% for XDR and 34.2% for the rest of the patients) (log rank, P = 0.015). In multivariate analysis, factors adversely affecting outcome included XDR infection (HR = 2.263, 95%CI: 1.005-5.095, P = 0.049), creatinine (HR = 1.125, 95%CI: 1.024-1.236, P = 0.015) and INR (HR =1.553, 95%CI: 1.106-2.180, P = 0.011).CONCLUSION: XDR bacteria are an independent life-threatening factor in SBP/SB. Strategies aiming at restricting antibiotic overuse and rapid identification of the responsible bacteria could help improve survival.展开更多
Plant diseases severely reduce crop yields and threaten global food security.Broad-spectrum resistance(BSR)is a desirable trait because it confers resistance against more than one pathogen species or the majority of r...Plant diseases severely reduce crop yields and threaten global food security.Broad-spectrum resistance(BSR)is a desirable trait because it confers resistance against more than one pathogen species or the majority of races/strains of the same pathogen.To control plant diseases,breeders have selected BSR to reduce disease occurrence and prolong the life-span of newly released cultivars in the last several decades(Mundt,Phytopathology 108(7):792–802,2018).Although effective,breeding of BSR cultivars in crop plants is still time-consuming and technically challenging.Recently,new gene-editing technologies such as CRISPR/Cas9 have dramatically accelerated the process of plant breeding and provided an approach for rapidly creating new varieties with BSR and other beneficial traits(Borrelli et al.,Front Plant Sci 9:1245,2018).In addition,close surveillance of pathogen populations in the field can provide useful information for the deployment of appropriate resistance genes in the target regions.In this mini-review,we focus on the significance and application of the exciting results from two recent companion papers published in Nature Biotechnology that provide new strategies to develop crop plants with BSR against pathogens through targeted promoter editing of susceptibility genes in plants as well as pathogen population monitoring.展开更多
Our aim was to determine the epidemiological characteristics, the resistance patterns and the spread of Gram negative bacteria related to colonization of patients in adult Intensive Care Units. Methods: A prospective ...Our aim was to determine the epidemiological characteristics, the resistance patterns and the spread of Gram negative bacteria related to colonization of patients in adult Intensive Care Units. Methods: A prospective cohort of patients colonized and/or infected with Gram negative bacteria was conducted at two adult ICUs from hospitals in Brazil (April 2012 to February 2013). Nasal, groin and perineum swabs were performed. Samples were incubated on MacConkey and cetrimide agar (48 h at 37℃) and identification tests (Vitek-BioMérieux), antibiogram (Bauer-Kirby method), Carba NP test, Polymerase Chain Reaction (PCR) and sequencing were performed. The patterns of resistant microorganisms were compared by rep-PCR (Diversilab). Results: There were 53 cases of colonization. In these cases, we identified imipenem-resistant Acinetobacter baumannii (51%), Pseudomonas aeruginosa (32%), Klebsiella pneumoniae ESBL (38%) or imipenem resistant (5.6%). The use of antimicrobials and medical devices were related to colonization (p The resistance patterns expressed by Klebsiella pneumoniae were ESBL (CTX-M, SHV e TEM) and KPC2. A verified profile of Acinetobacter baumannii was related to OXA-23 and OXA-253 (OXA-143 variant). The profiles ESBL and KPC2 expressed by Klebsiella pneumoniae were distributed between the both ICUs. The distribution of OXA-23 and OXA-253 was verified only in one ICU. The similarity of strains ranged from 80% to 95%, highlighting the horizontal transference of these microorganisms.展开更多
Impedance measurements using graphite electrodes were used to detect the increase in culture medium conductivity due to bacteria growth in real time along with simultaneous voltammetric monitoring of pyocyanin concent...Impedance measurements using graphite electrodes were used to detect the increase in culture medium conductivity due to bacteria growth in real time along with simultaneous voltammetric monitoring of pyocyanin concentration.Electrochemical methods were compared to conventional continuous monitoring of bacterial cultures using turbidity measurement at an optical density of 600 nm(OD600).A practical osmotic system was further designed for concentrating bacterial cultures during growth to enable earlier detection using the electrochemical methods.Bacterial cultures,starting from an initial culture density of 1×10^(8) cells/mL,were grown inside a sealed cellulose ester dialysis membrane,while polyethylene glycol in LB medium was used as the draw solution outside the membrane to gradually concentrate the growing cultures.0.7-mm-diameter graphite for mechanical pencils was utilized as working and counter electrodes with a platinum wire reference electrode for electrochemical measurements with and without the osmotic system.In the absence of forward osmosis,impedance meas-urements detected culture growth~1 h faster than conventional OD600.Integrating osmosis showed a twofold decrease in the time to detect pyocyanin production as an indicator for bacterial growth.For impedance monitoring,removal of water by osmosis was conflated with the impedance decrease due to cell growth;however,the results show a promising ability to detect bacteria growth via an observed shift in osmotic impedance profile when bacteria are present in a sample.By monitoring the deviation in the impedance profile,a threefold improvement in detection time was achieved when compared to conventional OD600 measurements.展开更多
基金the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA28010500)National Natural Science Foundation of China(Grant Nos.42371385,42071420)Zhejiang Provincial Natural Science Foundation of China(Grant No.LTGN23D010002).
文摘As an important rice disease, rice bacterial leaf blight (RBLB, caused by the bacterium Xanthomonas oryzae pv.oryzae), has become widespread in east China in recent years. Significant losses in rice yield occurred as a result ofthe disease’s epidemic, making it imperative to monitor RBLB at a large scale. With the development of remotesensing technology, the broad-band sensors equipped with red-edge channels over multiple spatial resolutionsoffer numerous available data for large-scale monitoring of rice diseases. However, RBLB is characterized by rapiddispersal under suitable conditions, making it difficult to track the disease at a regional scale with a single sensorin practice. Therefore, it is necessary to identify or construct features that are effective across different sensors formonitoring RBLB. To achieve this goal, the spectral response of RBLB was first analyzed based on the canopyhyperspectral data. Using the relative spectral response (RSR) functions of four representative satellite or UAVsensors (i.e., Sentinel-2, GF-6, Planet, and Rededge-M) and the hyperspectral data, the corresponding broad-bandspectral data was simulated. According to a thorough band combination and sensitivity analysis, two novel spectralindices for monitoring RBLB that can be effective across multiple sensors (i.e., RBBRI and RBBDI) weredeveloped. An optimal feature set that includes the two novel indices and a classical vegetation index was formed.The capability of such a feature set in monitoring RBLB was assessed via FLDA and SVM algorithms. The resultdemonstrated that both constructed novel indices exhibited high sensitivity to the disease across multiple sensors.Meanwhile, the feature set yielded an overall accuracy above 90% for all sensors, which indicates its cross-sensorgenerality in monitoring RBLB. The outcome of this research permits disease monitoring with different remotesensing data over a large scale.
文摘BACKGROUND With the widespread use of antimicrobial drugs,bacterial resistance has become a significant problem,posing a serious threat to public health.The prevalence of clinical infection strains in hospitals and their drug sensitivities are key to the appropriate use of antibiotics in clinical practice.AIM To identify prevalent bacteria and their antibiotic resistance profiles in a hospital setting,thereby guiding effective antibiotic usage by clinicians.METHODS Specimens from across the institution were collected by the microbiology laboratory.The VITEK 2 compact fully automatic analyzer was used for bacterial identification and antibiotic sensitivity testing,and the WHONET5.6 software was utilized for statistical analysis.RESULTS A total of 12062 bacterial strains of key monitoring significance were detected.Staphylococcus aureus demonstrated widespread resistance to penicillin,but none of the strains were resistant to vancomycin or linezolid.Moreover,219 strains of methicillin-resistant coagulase-negative staphylococci and 110 strains of methicillin-resistant Staphylococcus aureus were detected.Enterococcus faecalis showed moderate resistance to the third-generation quinolones ciprofloxacin and levofloxacin,but its resistance to nitrofurantoin and tetracycline was low.Enterococcus faecium displayed significantly lower resistance to third-and fourthgeneration quinolones than Enterococcus faecalis.The resistance of two key monitoring strains,Escherichia coli and Klebsiella pneumoniae,to piperacillin/tazobactam was 5%-8%.However,none of the Escherichia coli and Klebsiella pneumoniae strains were resistant to meropenem.The resistance of Acinetobacter baumannii to piperacillin/sulbactam was nearly 90%.Nonetheless,the resistance to tigecycline was low,and Pseudomonas aeruginosa demonstrated minimal resistance in the antibiotic sensitivity test,maintaining a resistance of<10%to the cephalosporin antibiotics cefotetan and cefoperazone over the last 6 years.The resistance to amikacin remained at 0.2%over the past 3 years.CONCLUSION Our hospital’s overall antibiotic resistance rate was relatively stable from 2017 to 2022.The detection rates of key monitoring strains are reported quarterly and their resistance dynamics are monitored and communicated to the entire hospital,which can guide clinical antibiotic selection.
文摘Objective:To observe and analyze the effect of bacterial resistance monitoring in clinical microbiology testing.Methods:600 microbial specimens collected in our hospital in the past year(April 2021 to April 2022)were used as the test subjects of this study.The specimens were divided into Group A(control group)and Group B(research group),with 300 cases in each group.Group A consisted of blood culture specimens,while Group B consisted of sputum specimens.After the tests were completed,the rates of unfavorable and favorable results,bacterial species distribution,and bacterial drug resistance of the specimens in both groups were compared.Results:Among group A specimens,29 cases were positive(9.67%)and 271 cases were negative(90.33%);among group B specimens,99 cases were positive(33.00%)and 201 cases were negative(66.00%);the difference between the two groups of data was statistically significant(P<0.05).As for the distribution of the types of bacteria,there were 472 cases of Gram-negative bacteria and 128 cases of Gram-positive bacteria.Conclusion:Bacterial resistance monitoring is helpful in clinical microbiology testing.Through proper monitoring,bacterial resistance can be well understood.In this way,patients get to receive appropriate treatment measures and suitable antibacterial prescriptions,thereby improving the patient outcome.
文摘AIM: To evaluate the epidemiology and outcomes of culture-positive spontaneous bacterial peritonitis (SBP) and spontaneous bacteremia (SB) in decompensated cirrhosis.METHODS: We prospectively collected clinical, laboratory characteristics, type of administered antibiotic, susceptibility and resistance of bacteria to antibiotics in one hundred thirty cases (68.5% males) with positive ascitic fluid and/or blood cultures during the period from January 1, 2012 to May 30, 2014. All patients with SBP had polymorphonuclear cell count in ascitic fluid > 250/mm<sup>3</sup>. In patients with SB a thorough study did not reveal any other cause of bacteremia. The patients were followed-up for a 30-d period following diagnosis of the infection. The final outcome of the patients was recorded in the end of follow-up and comparison among 3 groups of patients according to the pattern of drug resistance was performed.RESULTS: Gram-positive-cocci (GPC) were found in half of the cases. The most prevalent organisms in a descending order were Escherichia coli (33), Enterococcus spp (30), Streptococcus spp (25), Klebsiella pneumonia (16), S. aureus (8), Pseudomanas aeruginosa (5), other Gram-negative-bacteria (GNB) (11) and anaerobes (2). Overall, 20.8% of isolates were multidrug-resistant (MDR) and 10% extensively drug-resistant (XDR). Health-care-associated (HCA) and/or nosocomial infections were present in 100% of MDR/XDR and in 65.5% of non-DR cases. Meropenem was the empirically prescribed antibiotic in HCA/nosocomial infections showing a drug-resistance rate of 30.7% while third generation cephalosporins of 43.8%. Meropenem was ineffective on both XDR bacteria and Enterococcus faecium (E. faecium). All but one XDR were susceptible to colistin while all GPC (including E. faecium) and the 86% of GNB to tigecycline. Overall 30-d mortality was 37.7% (69.2% for XDR and 34.2% for the rest of the patients) (log rank, P = 0.015). In multivariate analysis, factors adversely affecting outcome included XDR infection (HR = 2.263, 95%CI: 1.005-5.095, P = 0.049), creatinine (HR = 1.125, 95%CI: 1.024-1.236, P = 0.015) and INR (HR =1.553, 95%CI: 1.106-2.180, P = 0.011).CONCLUSION: XDR bacteria are an independent life-threatening factor in SBP/SB. Strategies aiming at restricting antibiotic overuse and rapid identification of the responsible bacteria could help improve survival.
基金We gratefully acknowledge grant supports from the National Natural Science Foundation of China(#31901829)the China Postdoctoral Science Foundation(2019M660894)to J.W.
文摘Plant diseases severely reduce crop yields and threaten global food security.Broad-spectrum resistance(BSR)is a desirable trait because it confers resistance against more than one pathogen species or the majority of races/strains of the same pathogen.To control plant diseases,breeders have selected BSR to reduce disease occurrence and prolong the life-span of newly released cultivars in the last several decades(Mundt,Phytopathology 108(7):792–802,2018).Although effective,breeding of BSR cultivars in crop plants is still time-consuming and technically challenging.Recently,new gene-editing technologies such as CRISPR/Cas9 have dramatically accelerated the process of plant breeding and provided an approach for rapidly creating new varieties with BSR and other beneficial traits(Borrelli et al.,Front Plant Sci 9:1245,2018).In addition,close surveillance of pathogen populations in the field can provide useful information for the deployment of appropriate resistance genes in the target regions.In this mini-review,we focus on the significance and application of the exciting results from two recent companion papers published in Nature Biotechnology that provide new strategies to develop crop plants with BSR against pathogens through targeted promoter editing of susceptibility genes in plants as well as pathogen population monitoring.
文摘Our aim was to determine the epidemiological characteristics, the resistance patterns and the spread of Gram negative bacteria related to colonization of patients in adult Intensive Care Units. Methods: A prospective cohort of patients colonized and/or infected with Gram negative bacteria was conducted at two adult ICUs from hospitals in Brazil (April 2012 to February 2013). Nasal, groin and perineum swabs were performed. Samples were incubated on MacConkey and cetrimide agar (48 h at 37℃) and identification tests (Vitek-BioMérieux), antibiogram (Bauer-Kirby method), Carba NP test, Polymerase Chain Reaction (PCR) and sequencing were performed. The patterns of resistant microorganisms were compared by rep-PCR (Diversilab). Results: There were 53 cases of colonization. In these cases, we identified imipenem-resistant Acinetobacter baumannii (51%), Pseudomonas aeruginosa (32%), Klebsiella pneumoniae ESBL (38%) or imipenem resistant (5.6%). The use of antimicrobials and medical devices were related to colonization (p The resistance patterns expressed by Klebsiella pneumoniae were ESBL (CTX-M, SHV e TEM) and KPC2. A verified profile of Acinetobacter baumannii was related to OXA-23 and OXA-253 (OXA-143 variant). The profiles ESBL and KPC2 expressed by Klebsiella pneumoniae were distributed between the both ICUs. The distribution of OXA-23 and OXA-253 was verified only in one ICU. The similarity of strains ranged from 80% to 95%, highlighting the horizontal transference of these microorganisms.
基金This work was supported in part by award#1740961 from the National Science Foundation.
文摘Impedance measurements using graphite electrodes were used to detect the increase in culture medium conductivity due to bacteria growth in real time along with simultaneous voltammetric monitoring of pyocyanin concentration.Electrochemical methods were compared to conventional continuous monitoring of bacterial cultures using turbidity measurement at an optical density of 600 nm(OD600).A practical osmotic system was further designed for concentrating bacterial cultures during growth to enable earlier detection using the electrochemical methods.Bacterial cultures,starting from an initial culture density of 1×10^(8) cells/mL,were grown inside a sealed cellulose ester dialysis membrane,while polyethylene glycol in LB medium was used as the draw solution outside the membrane to gradually concentrate the growing cultures.0.7-mm-diameter graphite for mechanical pencils was utilized as working and counter electrodes with a platinum wire reference electrode for electrochemical measurements with and without the osmotic system.In the absence of forward osmosis,impedance meas-urements detected culture growth~1 h faster than conventional OD600.Integrating osmosis showed a twofold decrease in the time to detect pyocyanin production as an indicator for bacterial growth.For impedance monitoring,removal of water by osmosis was conflated with the impedance decrease due to cell growth;however,the results show a promising ability to detect bacteria growth via an observed shift in osmotic impedance profile when bacteria are present in a sample.By monitoring the deviation in the impedance profile,a threefold improvement in detection time was achieved when compared to conventional OD600 measurements.