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Objective:To analyze the features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected with other common respiratory pathogens among coronavirus disease 2019 (COVID-19) patients in Shanghai City, and to provide a reference for scientific prevention and control of COVID-19 and other respiratory infectious diseases.Methods:Descriptive epidemiological approaches were used to analyze the data of COVID-19 reported cases in Shanghai City from January 2020 to February 2021 in the information system of Chinese Disease Prevention and Control. Clinical data of the participants were collected, and their SARS-CoV-2 nucleic acid-positive respiratory specimens were collected at the time of illness onset or admission. Multiplex reverse transcription-polymerase chain reaction (RT-PCR) was performed to detect the 22 respiratory pathogens. Independent-samples t test was used for statistical analysis. Results:Of the 272 patients with COVID-19, 15(5.5%) had co-infection of SARS-CoV-2 with other respiratory pathogens, all of which were double infection. There were three cases infected with enterovirus/rhinovirus, two of each with adenovirus, human metapneumovirus and coronavirus NL63/HKU1, and one of each with coronavirus 229E, influenza A virus H1N1, parainfluenza virus 1 and respiratory syncytial virus B. Two cases infected with Mycoplasma pneumoniae. Among the 272 COVID-19 patients, 212(77.9%) had fever, 117(43.0%) had cough, 46(16.9%) had fatigue, and 35(12.9%) had sore throat. The white blood cell count of co-infection cases was higher than that of non-co-infection cases ((6.8±1.7)×10 9/L vs (5.3±1.6)×10 9/L), and the difference was statistically significant ( t=3.09, P=0.008). Conclusions:There is a certain proportion of co-infection of SARS-CoV-2 with other respiratory pathogens among the COVID-19 cases in Shanghai City, mainly viral pathogens, especially enterovirus/rhinovirus. A rational combination of drugs was recommended to improve the cure rate. Surveillance of acute respiratory infection should be further strengthened as well.
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ObjectiveTo determine the distribution of various antibiotic resistance genes （ARGs） in raw water from drinking water source， and to explore the correlation between the ARGs and common carbapenem-resistant and multidrug-resistant bacteria isolated from drinking water source， so as to provide scientific evidence for improving the safety of urban drinking water. MethodsA total of 30 raw water samples were collected from a major drinking water source in Shanghai in 2020. Bacterial strains were selectively cultured on Columbia blood agar medium containing 1 μg·μL-1 meropenem， and then identified by MALDI-TOF-MS mass spectrometry system. Minimum inhibitory concentration （MIC） of the strains was detected by broth microdilution method. The water samples were filtered through a 0.45 μm filter membrane and diversity of ARGs was determined by using high-throughput metagenomic sequencing. ResultsA total of 64 strains of carbapenem-resistant bacteria were isolated from the water samples， including Stenotrophomonas maltophilia， Enterococcus faecium， Pseudomonas aeruginosa， Acinetobacter baumannii and Klebsiella pneumoniae， which were resistant to a variety of common antibiotics. Using metagenomic sequencing，1 244 ARGs were identified. The relative average abundance of the top 100 ARGs accounted for 96.1%， and that of the multidrug-resistant ARGs accounted for 63.41%. Furthermore， the multidrug-resistant ARGs were mainly adeJ， mexT， adeC， oprM， mexF， mdfA， mexB， mdtK， adeK， etc. Using Spearman's correlation， five multidrug-resistant bacteria isolated from the drinking water source were significantly associated with the ARGs. ConclusionRelative abundance of multidrug-resistant ARGs is high in raw water from main drinking water source. The five isolated carbapenem-resistant and multidrug-resistant bacteria are significantly correlated with the ARGs. It warrants strengthening the rational and standardized application of antibiotics to protect water resources and ensure the safety of drinking water.
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Objective@#To understand the epidemiological characteristics and antibiotic resistance profiles of Campylobacter spp. in Shanghai from 2013 to 2016.@*Methods@#Stool samples collected from diarrhea outpatients were cultured for Campylobacter spp., using the membrane filter method in 23 hospitals under the sentinel programs, from 2013 to 2016. All the strains were identified by biochemical tests and PCR. Broth microdilution method was used to investigate the antibiotic resistance of 179 Campylobacter spp. strains that including azithromycin, ciprofloxacin, erythromycin, gentamicin, tetracycline, nalidixic acid, telycin, klinthromycin and flurbenicol.@*Results@#A total of 179 Campylobacter spp. strains were isolated from 10 444 stool samples (1.7%). Campylobacter jejuni and Campylobacter coli appeared as the predominant ones (94.4% and 5.6%). The incidence rate was higher in children than that in adults, with peaks of infections mainly from April to June and October to December. Campylobacter jejuni strains seemed highly resistant to ciprofloxacin (96.4%), tetracycline (83.4%) and nalidixic acid (81.7%). The resistant rates appeared higher on Campylobacter coli strains that isolated from patients. Some strains were resistant to multi-drugs.@*Conclusions@#Campylobacter spp. seemed one of the important pathogens that isolated from outpatients with diarrhea, in Shanghai. Both age and season related characteristics of Campylobacter spp. were seen. Campylobacter spp. isolated from patients was highly resistant to ciprofloxacin, tetracycline and nalidixic acid.
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Objective@#To understand the seasonality and etiological characteristics of infectious diarrhea in adults from Shanghai.@*Methods@#Adult patients with diarrhea who had visited the enteric disease clinics in 22 hospitals that carrying on the Diarrhea Comprehensive Surveillance sentinel programs in Shanghai during 2014-2017, were surveyed. Stool specimens were collected according to the different intervals of sampling and detected for 12 bacteria and 5 viruses. Concentration ratio and circular distribution method were used for data analysis.@*Results@#From 2014 to 2017, a total of 9 573 stool specimens were collected from the targeted diarrhea patients ≥18 years old (n=96 067), through the Shanghai Diarrhea Comprehensive Surveillance program. The positive rate of detection was 46.44%. Seasonal peaks of infectious diarrhea were both seen in summer (bacteria peak, diarrheagenic Escherichia coli and Vibrio parahaemolyticus, etc.) and in winter (virus peak, Norovirus, etc.). Both bacterial and viral infections presented seasonal concentration (Raleigh’s test P<0.001) but more obvious with bacterial infection. Viral infection accounted for 60.19% of the cause of infectious diarrhea. The top five predominant pathogens appeared as Norovirus, Rotavirus, diarrheagenic Escherichia coli, Vibrio parahaemolyticus, and Salmonella spp..@*Conclusions@#Among the adult outpatients with infectious diarrhea in Shanghai, obvious seasonality was seen, with peaks in both summer and winter. Viral infection with Norovirus in particular, appeared as the predominant source of infection. Active, continuous and comprehensive diarrhea-related surveillance programs would be able to monitor the changing dynamic of pathogen spectrum, and lead to the adoption of targeted preventive measures.
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Objective@#To investigate the molecular characterization of adult diarrhea cases caused by enterotoxic Escherichia coli (ETEC) and explore the practical model of epidemiology for laboratory technique and data needs based on the surveillance network.@*Methods@#Epidemiological design and sampling targeted adult cases ETEC caused diarrhea in epidemic season. The enterotoxin type, serogroup, resistance, colonization factor and molecular type of ETEC were identified. Multiple dynamic phenotypic characteristics of ETEC were indicated by multidimensional and multivariable data.@*Results@#From 2016 to 2018, 84 eligible ETEC strains were detected. The dominant serums/toxins were O∶6 (STh), O∶25 (LT), O∶159 (STh), O∶153 (STh). O∶6 (STh+CS21), which replaced O∶25 and O∶159 as the popular clones in 2018. Six cases of O∶153 (STh+CFA/I+CS8+PT34) in outbreak in 2017 were imported ones. The resistance rates of ETEC strains detected in adults to sulfasoxazole, naproxinic acid, ampicillin and azithromycin were more than 30%, multidrug resistance (MDR) reached 58.3%. Serum/toxin types suggested that attenuated strains were more likely to become MDR. Molecular typing confirmed that the genetic similarity of the dominant clone of O∶6 serogroup (PT20-24) was higher than O∶25 and O∶159. There was a high correlation between the minimal inhibitory concentration (MIC) of azithromycin and the resistant gene mphA (87.5%, 28/32). O∶6 (STh+CS21+mphA) resistant clone was first detected in 2016.@*Conclusion@#A new epidemic clone in adult ETEC diarrhea cases in Shanghai was O∶6 (STh+CS21+mphA). For the first time the association between azithromycin resistance gene mphA and a serum group of ETEC was observed. Multidimensional and multivariate analysis techniques based on epidemiology can help reveal the potential transmission pattern of ETEC for the accurate surveillance and early warning of outbreaks.
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Objective To investigate the antimicrobial characteristics of shigella flexneri and to analyze the correlation between acquired resistance genes and mobile genetic elements.Methods 139 strains of shigella flexneri collected from each district of Centers for Disease Control and Prevention in Shanghai from 2010 to 2014 were recovered.The K-B method was used to determine the susceptibility of the strains to 13 antibiotics.And then 17 kinds of acquired resistance genes to β-lactams, sulfonamides, aminoglycosides and 7 kinds of genetic markers of mobile genetic elements were analyzed by PCR.Index cluster analysis was performed to explore the correlation between them.Results Among 139 strains of Shigella flexneri,3 kinds of genetic markers of mobile genetic elements,ISEcp1,intI1 and trbC,3 kinds of acquired β-lactam-resistance genes,CTX-M,OXA and TEM,2 kinds of acquired aminoglycoside-resistance genes,ant(3")-I and aac(6′)-Ib, 1 kind of overlapping gene of quaternary ammonium disinfectant and sulfonamides, qacEΔ1-sull and 1 kind of sulfamethoxazole/trimethoprim-resistant gene, dfrA1 were detected.The resistence genes,OXA,ant(3")-I and drfA1 were highly related with each other,which were mediated by Class 1 integron.TEM,qacEΔl-sull and aac(6′)-Ib were highly related with each other,which were mediated by trbC.Conclusion Acquired multidrug resistance gene transfer mediated by a variety of mobile genetic elements may have largely contributed to the spreading of resistant strains of Shigella.
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Objective To investigate the antimicrobial resistance proifle of Shigella flexneri in Shanghai from 2010 to 2014 and examine the mechanism of fluoroquinolone resistance.Methods Kirby-Bauer method was used to determine the susceptibility of the S. flexneri strains to 14 antibiotics. The minimum inhibitory concentration (MIC) of ciprofloxacin was tested by E-test. Mutations within quinolone resistance determining regions (QRDR) of gyrA and parC and plasmid-mediated quinolone resistance (PMQR) genes,qnrA,qnrB,qnrS andaac(6')-Ib-crwere identified by polymerase chain reaction (PCR). All the products were subjected to sequencing analysis.Results More than 90 % of the 139S. flexneri isolates were resistant to ampicillin, streptomycin, tetracycline, and nalidixic acid, 40.3 % to ciprofloxacin and 30.2 % to cefepime, respectively. Genetic mutation of gyrA and parC was found in 98.6 % and 97.8 % of the strains, respectively. Three point mutations (Ser83, Asp87 and His211) were detected in gene gyrA and one point mutation (Ser80) was found in in gene parC. Plasmid-mediated resistant gene qnrS was found in 9 strains and aac(6')-Ib-cr in 6 strains.Conclusions The antibiotic resistance of S. flexneri is serious in Shanghai. The mutation rate within QRDR is high. Point mutation in Asp87 of gyrA is the main mechanism of quinolone resistance. The plasmid-mediated quinolone-resistant genes also play an important supplementary role.
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Objective To establish a rapid staining method for facilitating initial identification of Legionella pneumophila in amoebal trophozoite. Methods Acanthamoeba polyphaga and Legionella pneumophila were co-cultured under laboratory condition. At consecutive time points during the culture, smears of the cultured products were made on glass slides for staining purposes. Different types of stainings including Gram′s staining, Gimenez staining, Giemsa staining and immunofluorescence were used to determine the best method for the identification of amoebal pathogens. Results Gimenez staining technique is simpler and yields better results as compared with the other three stainings. Gimenez stain gives the best color and contrast for amoeba and amoebal Legionella Amoeba trophozoites and/or cysts showed a distinct purplish blue with amoebal Legionella in red. Amoebal Legionella can be distinguished clearly at an earlier time of co-culture, providing a proper sensitivity. It takes only 10 minutes to finish the operation. The other techniques require the use of expensive reagents, are relatively time-consuming, and involve complex staining procedures. Conclusion Gimenez staining is of value for the initial identification of amoebal pathogens, and it is suitable for laboratory diagnosis.