Evaluation of VITEK matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of anaerobes

Rapid and adequate identification of anaerobic bacterial species still presents a challenge for most diagnostic laboratories, hindering the selection of appropriate therapy. In this study, the identification capacity of 16S rRNA sequence analysis, VITEK 2 (BioMérieux, Lyon, France) compact analysis and VITEK MS-mediated identification for anaerobic bacterial species was compared. Eighty-five anaerobic bacterial isolates from 11 provinces in China belonging to 14 genera were identified by these three methods. Differences in identification between these three methods were compared. Consistent identification results were obtained for 54 (54/85, 63.5%) isolates by all three methods, the most discordant results being concentrated in Clostridium XI (n = 8) and Bacteroides fragilis (n = 9) clusters. Using the VITEK MS system, 74 (74/90, 82.2%) isolates were identified as single species consistent with 16S rRNA sequence analysis, which was significantly better than the results obtained with VITEK 2 Compact (P < 0.01). Misidentifications by the Vitek 2 Compact and Vitek MS systems were mainly observed in the Clostridium XI (n = 8)and B. fragilis clusters (n = 9). VITEK MS identified anaerobic bacteria even after they had been exposed to oxygen for a week. Identification by the Vitek MS system was more consistent with 16S rRNA sequence analysis than identification by Vitek 2 Compact. Continuous expansion of the VITEK MS database with rare described anaerobic species is warranted to improve both the efficiency and accuracy of VITEK MS identification in routine diagnostic microbiology.

Genomic Analysis of a New Serovar of Leptospira weilii Serogroup Manhao

Leptospirosis, caused by pathogenic Leptospira spp., is recognized as an important emerging zoonotic disease throughout the world. In this study, multiple approaches were used to characterize the recently discovered serovar Heyan strain L231. This strain can infect guinea pigs and belonged to the pathogenic species L. weilii. Genome sequencing analysis revealed the draft genome of 4.2 M bp with a G+C content of 40.67% for strain L231, and a total of 4,794 ORFs were identified. The strain L231 genome was found to have a larger LPS biosynthesis locus than that of strains L. interrogans serovar Lai and L. borgpetersenii serovar Hardjobovis. Phylogenomic reconstructions showed that the evolutionary position of L. weilii serovar Heyan was different from that of other serovars from serogroup Manhao. These findings may lead us to a better understanding of Leptospira pathogenesis and evolution.

A hybrid method for quantifying China's nitrogen footprint during urbanisation from 1990 to 2009

In this study, we devise a national nitrogen footprint method to evaluate the life cycle nitrogen flows through the national economy of China from 1990 to 2009. To this end, we build a hybrid method based on two well-established techniques, namely material flow analysis (MFA) and input-output analysis (IOA). This integration allows for the evaluation of the effects of international trade and interdependencies among economic sectors. Our results suggest that China's nitrogen footprint (NF) has increased from 30.3Teragrams (Tg) in 1990 to 54.0Tg in 2009, whereas the NF per capita has increased from 25.9 to 39.5kgN/yr. Relationship between the world NF per capita and human development index (HDI) appears to show an inverted U curve, whilst China shows an increase both in NF per capita and HDI. We find that an increase in China's NF is largely associated with high levels of urbanisation. Although the energy NF (E_NF) has increased more drastically than the food NF (F_NF), the latter still dominates China's total NNF, with proportions of 91% in 1990 and 82% in 2009. Taking international trade into account, our results demonstrate that China was a net exporter of F_NF, whilst a net importer of E_NF over this time period. There are many measures considered to reduce China's nitrogen footprint, including improvements in N use efficiency of food systems, transformation of meat-based diets and optimisation of China's economic structure.

Measuring Urban Carbon Footprint from Carbon Flows in the Global Supply Chain

A global multiregional input-output (MRIO) model was built for eight Chinese cities to track their carbon flows. For in-depth understanding of urban carbon footprint from the perspectives of production, consumption, and trade balance, four kinds of footprints and four redefined measurement indicators were calculated. From the global supply chain, urban carbon inflows from Mainland China were larger than outflows, while the carbon outflows to European, principal North American countries and East Asia were much larger than inflows. With the rapid urbanization of China, Construction was the largest consumer and Utilities was the largest producer. Cities with higher consumption (such as Dalian, Tianjin, Shanghai, and Beijing) should change their consumption patterns, while cities with lower production efficiency (such as Dalian, Shanghai, Ningbo, and Chongqing) should improve their technology. The cities of net carbon consumption tended to transfer carbon emissions out of them by trading in carbon-intensive products, while the cities of net carbon production tended to produce carbon-intensive products for nonlocal consumers. Our results indicated that urban carbon abatement requires not only rational consumption and industrial symbiosis at the city level, but also tighter collaboration along all stages of the global supply chain.

Bulk Fermi Surface of Charge-Neutral Excitations in SmB_{6} or Not: A Heat-Transport Study

Recently, there have been increasingly hot debates on whether a bulk Fermi surface of charge-neutral excitations exists in the topological Kondo insulator SmB_{6}. To unambiguously resolve this issue, we perform the low-temperature thermal conductivity measurements of a high-quality SmB_{6} single crystal down to 0.1 K and up to 14.5 T. Our experiments show that the residual linear term of thermal conductivity at the zero field is zero, within the experimental accuracy. Furthermore, the thermal conductivity is insensitive to the magnetic field up to 14.5 T. These results demonstrate the absence of fermionic charge-neutral excitations in bulk SmB_{6}, such as scalar Majorana fermions or spinons and, thus, exclude the existence of a bulk Fermi surface suggested by a recent quantum oscillation study of SmB_{6}. This puts a strong constraint on the explanation of the quantum oscillations observed in SmB_{6}.

Emergence and Diversity of Salmonella enterica Serovar Indiana Isolates with Concurrent Resistance to Ciprofloxacin and Cefotaxime from Patients and Food-Producing Animals in China

Salmonellosis is a major global foodborne infection, and strains that are resistant to a great variety of antibiotics have become a major public health concern. The aim of this study was to identify genes conferring resistance to fluoroquinolones and extended-spectrum β-lactams in nontyphoidal Salmonella (NTS) from patients and food-producing animals in China. In total, 133 and 21 NTS isolates from animals and humans, respectively, exhibiting concurrent resistance to ciprofloxacin and cefotaxime were cultured independently from 2009 to ∼2013. All of the isolates were identified, serotyped, and subjected to antimicrobial susceptibility testing. Importantly, the isolates with concurrent resistance to ciprofloxacin and cefotaxime all were confirmed as S. enterica serovar Indiana. The presence of fluoroquinolone resistance genes and extended-spectrum β-lactamases (ESBLs) was established by PCR and DNA sequencing. The occurrence and diversity of different genes conferring fluoroquinolone resistance [qepA, oqxAB, and aac(6')-Ib-cr] with mutations in topoisomerase-encoding genes (gyrA and parC) and several ESBLs (including CTX-M-65, CTX-M-27, CTX-M-15, CTX-M-14, and CTX-M-14/CTX-M-15) were noteworthy. Genes located on mobile genetic elements were identified by conjugation and transformation. Pulsed-field gel electrophoresis, used to determine the genetic relationships between these isolates, generated 91 pulsotypes from 133 chicken isolates and 17 pulsotypes from the 21 clinical isolates that showed considerable diversity. Analysis of the pulsotypes obtained with the isolates showed some clones appeared to have existed for several years and had been disseminating between humans and food-producing animals. This study highlights the emergence of ciprofloxacin- and cefotaxime-resistant S. enterica serovar Indiana, posing a threat to public health.

Genetic stability of vaccine strains by multilocus sequence typing and pulsed-field gel electrophoresis analysis: Implications for quality control of the leptospiral vaccine

Quality control of vaccine strains is directly associated with the safety and efficacy of inactivated whole bacterial vaccines. The assessment of genetic stability is one of the essential elements to guarantee the quality of vaccine strains. The multiple-valence inactivated leptospiral vaccine, comprising the main circulating serogroups, has played an important role in the control of Leptospira infection in China. In the present study, to assess the genetic stability of vaccine strains and develop novel quality control tests that enhance and extend the existing procedures, 7 Chinese leptospiral vaccine strains were characterized during in vivo and in vitro passages by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis. The seven vaccine strains were found to have distinct sequence types (STs) and PFGE profiles. Further analysis showed that the ST and PFGE pattern of each vaccine strain, after in vivo or serial in vitro passages (up to 20 passages), were identical to those of the initial strain, demonstrating that these strains were genetically stable and homogeneous. Taken together, PFGE and MLST provide a reproducible and reliable means for confirming the identity and genetic stability of vaccine seeds, suggesting that these approaches can be used to evaluate the quality of leptospiral vaccine strains.

Prevalence of Salmonella Isolates from Chicken and Pig Slaughterhouses and Emergence of Ciprofloxacin and Cefotaxime Co-Resistant S. enterica Serovar Indiana in Henan, China

The prevalence of Salmonella from chicken and pig slaughterhouses in Henan, China and antimicrobial susceptibility of these isolates to antibiotics was determined. From 283 chicken samples and 240 pig samples collected, 128 and 70 Salmonella isolates were recovered with an isolation rate of 45.2 and 29.2% respectively. The predominant serovars in chicken samples were S. enterica serovar Enteritidis, S. enterica serovar Hadar and S. enterica serovar Indiana, while those in pig samples were S. enterica serovar Typhimurium, S. enterica serovar Derby and S. enterica serovar Enteritidis. Resistance to ciprofloxacin was 8.6 and 10.0% for isolates from chickens and pigs respectively, whereas resistance to cefotaxime was 5.5 and 8.6%, respectively. Multidrug resistance (resistance to three or more classes of antimicrobial agent) was markedly higher in pig isolates (57.1%) than in chicken isolates (39.8%). Of particular concern was the detection of ciprofloxacin and cefotaxime co-resistant S. enterica serovar Indiana isolates, which pose risk to public health. All 16 S. enterica serovar Indiana isolates detected were resistant to ciprofloxacin, among which 11 were co-resistant to cefotaxime. The S. enterica serovar Indiana isolates accumulated point mutations in quinolone resistance determination regions of gyrA (S83F/D87G or S83F/D87N) and parC (T57S/S80R). Two plasmid mediated quinolone resistant determinants were found with aac (6')-Ib-cr and oqxAB in 16 and 12 S. enterica serovar Indiana isolates respectively. Cefotaxime-resistance of S. enterica serovar Indiana was associated with the acquisition of a bla_CTX-M-65 gene. The potential risk of ciprofloxacin and cefotaxime co-resistant S. enterica serovar Indiana infection is a significant concern due to limited alternative treatment options. Reduction of Salmonella in chicken and pig slaughterhouses, in particular, ciprofloxacin and cefotaxime co-resistant S. enterica serovar Indiana will be an important measure to reduce the public health burden of Salmonella infections.

Changing urban phosphorus metabolism: Evidence from Longyan City, China

Rapid worldwide urbanization calls for a better understanding of phosphorus (P) metabolism and the interaction of the physical, ecological and social drivers of P cycling in urban systems. We quantified the P metabolism in Longyan, a city with a major agricultural economy, and analyzed its long-term trends over the rapid urbanization period of 1985-2010. Both input P (from 4811 t P to 14,296 t P) and output P (from 4565 t P to 13,509 t P) increased significantly. The agricultural subsystem contributed most to the P metabolism, accounting for 85% of total P input. The share of P input lost to the environment, i.e. discharge to water, accumulation in the soil and landfill, increased from 66% to 72%, while food production efficiency decreased from 48% to 29%. Per capita P input showed linear relationships with the Human Development Index (HDI), S-curve relationship with the urbanization rate, and logistic curve relationship with per capita disposable income. A more meat-based diet shift both in Longyan and surrounding cities greatly affected Longyan's food production structure. Our results demonstrate that P metabolic quantity, configuration, and efficiency in production systems can change drastically in response to changes in consumer and producer behavior as well as in socioeconomic structure. A larger regional scale should be considered in urban P management, when trying to mitigate the increase in P use. The results also imply that sustainable urban P management will require a system-wide, cross-sector and cross-boundary approach.

Current advances in the novel functions of hypoxia-inducible factor and prolyl hydroxylase in invertebrates

Oxygen is essential for aerobic life, and hypoxia has very severe consequences. Organisms need to overcome low oxygen levels to maintain biological functions during normal development and in disease states. The mechanism underlying the hypoxic response has been widely investigated in model animals such as Drosophila melanogaster and Caenorhabditis elegans. Hypoxia-inducible factor (HIF), a key gene product in the response to oxygen deprivation, is primarily regulated by prolyl hydroxylase domain enzymes (PHDs). However, recent findings have uncovered novel HIF-independent functions of PHDs. This review provides an overview of how invertebrates are able to sustain hypoxic damages, and highlights some recent discoveries in the regulation of cellular signalling by PHDs. Given that some core genes and major pathways are evolutionarily conserved, these research findings could provide insight into oxygen-sensitive signalling in mammals, and have biomedical implications for human diseases.

[Epidemic condition and molecular subtyping of ciprofloxacin and cefotaxime co-resistant Salmonella Indiana isolated from retail chicken carcasses in six provinces, China]

OBJECTIVE

To elucidate the epidemic condition and molecular subtyping of ciprofloxacin and cefotaxime co-resistant Salmonella Indiana (S. Indiana) isolated from retail chicken carcasses in six provinces of China.

METHODS

A total of 2 647 Salmonella strains isolated from retail chicken carcasses collected from six provinces of China were subjected to antimicrobial susceptibility testing. All Salmonella isolates co-resistant to ciprofloxacin and cefotaxime were further characterized by serotyping, extended-spectrum beta-lactamases (ESBLs) producing strains screening and pulsed field gel electrophoresis (PFGE) typing.

RESULTS

Among 2 629 Salmonella isolates tested, 227 (8.52%) isolates were co-resistant to ciprofloxacin and ceftazidime/cefotaxime (Beijing: 11.67% (99/874), Jilin: 8.20% (60/726), Guangdong: 1.39% (7/502), Jiangsu: 15.61% (42/260), Shaanxi: 8.56% (16/186), Inner Mongolia: 0 (0/81)), and 224 of them were identified as S. Indiana. 213 (95.10%) isolates of S. Indiana were ESBLs producing strains. All ciprofloxacin and cefotaxime co-resistant S. Indiana isolates developed a multi-drug resistant profile and 17.86% (40/224) of them were resistant to all antibiotics tested except carbapenems, and 50.89% (114/224) of them resistant to 9 antibiotics, additionally, 25.45% (57/224) of them showed multi-drug resistance to 8 antibiotics. All ciprofloxacin and cefotaxime co-resistant S. Indiana isolates were divided into 32 PFGE clusters and 150 PFGE patterns. Strains of S. Indiana from same or different sampling site and time seemed to either share the same PFGE patterns or be differential to each other in different regions.

CONCLUSION

The results indicated that chicken carcasses collected from parts of China were heavily contaminated by ciprofloxacin and cefotaxime co-resistant S. Indiana and could serve as an important reservoir of ciprofloxacin and cefotaxime co-resistant Salmonella. Molecular subtyping results indicated that cross contamination or common pollution source might be in these strains.

Ultrasensitive UPLC-MS/MS method for analysis of etheno-DNA adducts in human white blood cells

Etheno-DNA adducts are generated by interaction of cellular DNA with exogenous environmental carcinogens and end products of lipid peroxidation. It has been determined that 1,N(6)-etheno-2'-deoxyadenosine (εdA) and 3,N(4)-etheno-2'-deoxycytidine (εdC) adducts formed in human white blood cells can be used to serve as biomarkers of genetic damage mediated by oxidative stress. In this study, we developed an ultrasensitive ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method used to detect and quantify εdA and dC adducts in human white blood cells. The percent recoveries of εdA and dC adducts were found to be 88.9% ± 2.8 and 95.7% ± 3.7, respectively. The detection limits were ∼ 1.45 fmol for εdA and ∼ 1.27 fmol for εdC in 20 μg of human white blood cell DNA samples, both εdA and εdC adducts could be detected using only ∼ 5 μg of DNA per sample. For validation of the method, 34 human blood cell DNA samples were assayed and the results revealed a significant difference (P < 0.01) between levels (fmol/μg DNA) of 0.82 ± 0.83 (standard deviation [SD]) (range: 0.15-3.11) for εdA, 3.28 ± 3.15 (SD) (range: 0.05-9.6) for εdC in benzene-exposed workers; and 0.04 ± 0.08 (SD) (range: 0.0-0.27) for εdA and 0.77 ± 1.02 (SD) (range: 0.10-4.11) for εdC in non-benzene-exposed workers. Our method shows a high sensitivity and specificity when applied to small amounts of human white blood cell DNA samples; background levels of εdA and εdC could be reproducibly detected. The ultrasensitive and simple detection method is thus suitable for applications in human biomonitoring and molecular epidemiology studies.

Clinical Safety and Preliminary Efficacy of Plasmid pUDK-HGF Expressing Human Hepatocyte Growth Factor (HGF) in Patients with Critical Limb Ischemia

OBJECTIVE

Critical limb ischemia (CLI) is the most severe form of peripheral arterial disease and a major unmet public health care need. This phase I clinical study was performed to assess the safety and preliminary efficacy of naked plasmid DNA (pUDK-HGF) expressing human hepatocyte growth factor (HGF) in patients with critical limb ischemia (CLI).

DESIGN

Twenty-one patients with CLI were enrolled and randomly divided into four dose groups (4-16 mg) to receive local injection of pUDK-HGF into ischemic calf and/or thigh muscles twice on days 1 and 15. Safety, including adverse events and physiological parameters, and preliminary efficacy, including pain severity score (VAS), ulcer size, transcutaneous oxygen pressure (TcPO2), and ankle brachial index (ABI), were evaluated throughout a 3 month follow up period.

RESULTS

All doses of pUDK-HGF were well tolerated by the patients. None of the adverse effects was considered to be related to pUDK-HGF injection. Two significant clinical results were observed after pUDK-HGF administration. The mean VAS value of all patients decreased from 4.52 at baseline to 0.30 (p < .01), and pain had disappeared in 14 out of 17 evaluable patients by day 91. Two of four ulcers had completely healed, with the other two patients having more than 25% ulcer size reduction in the long axis diameter. Of five patients with gangrene, one gangrenous wound had healed completely and two patients showed marked size reduction by day 91. The mean hemodynamic parameters (ABI, TcPO2) were also improved.

CONCLUSION

Intramuscular injection of pUDK-HGF is safe, and may provide symptomatic relief for CLI patients. A larger, randomized, double blinded phase II trial will provide more information on safety and efficacy.

The cultivation of bone marrow mesenchymal stem cells derived from patients with high altitude polycythemia

The aim of this study was to isolate and culture bone marrow mesenchymal stem cells (MSCs) from patients with high altitude polycythemia (HAPC) in order to provide a foundation for further exploration of their biological characteristics. MSCs were isolated and cultured from 10 HAPC patients and 10 healthy controls by using a density gradient centrifugation and an adherent screening method. The morphous of MSCs were observed under an inverted microscope, and its surface antigens were determined using flow cytometry. The growth of the MSCs was also detected to evaluate its proliferation. Bone marrow mononuclear cells were isolated from the bone marrow using a density gradient centrifugation, and they were cultured in vitro. The bone marrow MSCs were successfully isolated and cultured, which presented as fusiform and adherent cells. The MSCs in both groups expressed CD90,CD44,CD29,CD105, CD106, CD146, CD166,Stro&mdash;1 and CD13, but they did not express CD45, CD4,CD8,CD19,CD20,CD80,CD14,CD3,CD34 or HLA&mdash;DR (P>0.05). The bone marrow MSCs from HAPC patients had a higher proliferation than the bone marrow MSCs from the healthy controls (P&lt;0.01). The bone marrow MSCs from HAPC patients can be effectively cultured in vitro.