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Objective:To investigate the impact of SARS-CoV-2 pandemic on the prevalence of viral pathogens in hospitalized children with acute respiratory tract infections (ARTIs) in Shanghai.Methods:A total of 6 020 throat swab specimens were collected from hospitalized children with ARTIs in Shanghai Children′s Hospital from August 1, 2019 to February 28, 2022. Eleven common respiratory pathogens were detected using multiplex PCR and capillary electrophoresis. Pre-epidemic data referred to the data from August to December, 2019, and the data from August to December, 2020 and August to December, 2021 were used as the post-epidemic data for comparison. Based on the data from March 2020 to February 2022 (the epidemic period), the epidemiology of respiratory pathogens in children with ARTIs in different seasons were compared (spring: March to May, summer: June to August, autumn: September to November, winter: December to February of the next year).Results:Of the 6 020 specimens obtained from the patients, 3 753 (62.34%) were positive for at least one pathogen. Human rhinovirus (HRV) was the most commonly detected pathogen (22.76%, 1 442/6 020), followed by human respiratory syncytial virus (HRSV) (16.05%, 966/6 020). From August to December, the detection rate of single respiratory pathogen was 87.94% (569/647) in 2019, 66.21% (480/725) in 2020 and 60.33% (1 075/1 782) in 2021, and the co-infection rate was 25.66% (166/647) in 2019, 9.93% (72/725) in 2020 and 8.87% (158/1 782) in 2021, showing a decreasing trend (χ 2=165.19 and 127.79, P<0.01). Compared with the pre-epidemic period, human metapneumovirus (HMPV), HRV and human parainfluenza virus (HPIV) were the most prevalent pathogens in 2020 [4.97%(36/725), 34.21%(248/725) and 14.48%(105/725); χ 2=26.16, 42.04 and 60.52; P<0.01] and HRSV was the predominant pathogen in 2021 [21.27%(387/1 782), χ 2=44.26, P<0.01]. During the epidemic period, the detection rate of pathogens was 64.49%(1 340/2 078) in 2020, which was significantly higher than that in 2021 [57.48%(1 771/3 081), χ 2=25.43, P<0.01]. Only two respiratory pathogens, Mycoplasma pneumonia and human coronavirus, were detected in the spring of 2020; HRV, human adenovirus and HPIV were detected since the summer of 2020; influenza virus B was detected since the spring of 2021; influenza virus A was detected in only one case in 2020 and other respiratory pathogens were detected since the autumn of 2020. HRV+ HRSV were the main pathogens of co-infections. Conclusions:A series of prevention and control measures taken after the SARS-CoV-2 epidemic caused major changes in the prevalence and the epidemiology of respiratory pathogens in hospitalized children in Shanghai. With the normalization of epidemic prevention and control, the cancellation of strict epidemic prevention policy might lead to the outbreak of some pathogens (HMPV, HRV, HPIV and HRSV) and much attention should be paid to the outbreaks of other respiratory pathogen infections in children.
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Objective:To investigate the genetic characteristics of norovirus (NoV) in children with acute gastroenteritis in Shanghai.Methods:A total of 709 stool specimens were collected from outpatients with acute gastroenteritis in Children′s Hospital of Shanghai from October 2018 to September 2019. Real-time RT-PCR was used for qualitative detection of NoV, and RT-PCR was used to identify the genotypes of NoV with the primers of VP1 gene, RdRp region and RdRp-VP1 region. SPSS20.0 statistical software was used for data processing and bioinformatics software was used for homology, phylogenetic and recombination analysis of NoV gene sequences.Results:NoV was detected in 265 out of the 709 stool specimens with a positive rate of 37.4%. Sequence analysis of RdRp region and VP1 gene showed that seven different genotypes including GⅡ.P16-GⅡ.2, GⅡ.P12-GⅡ.3, GⅡ.Pe-GⅡ.4_Sydney 2012, GⅡ.P7-GⅡ.6, GⅡ.P8-GⅡ.8, GⅡ.P21-GⅡ.13 and GⅡ.P17-GⅡ.17 were detected from 111 NoV-positive specimens. The predominated genotype was GⅡ.P16-GⅡ.2 (30.6%, 34/111), followed by GⅡ.Pe-GⅡ.4_Sydney 2012 (27.0%, 30/111) and GⅡ.P12-GⅡ.3 (24.3%, 27/111). Two new NoV recombinant strains belonging to GⅡ.P21-GⅡ.13 genotype were identified and the recombination site was in the junction region of ORF1 and ORF2. NoV infection occurred every month, but the predominant genotype was different. No significant difference in the positive rates of NoV was found between male and female patients ( P=0.329). However, there were significant differences between different age groups ( P=0.011) and the children in the age groups of >11-12 years old and >2-3 years old had higher rates of NoV infection. Conclusions:The predominated recombinant NoV strains belonged to GⅡ.P16-GⅡ.2, GⅡ.Pe-GⅡ.4_Sydney 2012 and GⅡ.P12-GⅡ.3 genotypes, and two new recombinant NoV strains (GⅡ.P21-GⅡ.13) were found in Shanghai during October 2018 to September 2019. Gene sequencing across ORF1 and ORF2 was conducive to better understanding the NoV genotypes and recombination.
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Objective To investigate the effect of lean management on emergency biochemistry test turnaround time(TAT) in clinical laboratories.Methods Based on the approaches of standardized operations,5S on-site management,the efficiency evaluation of batch processing and one piece flow,and visual management,the median time of each workflow,the qualified rate of emergency biochemistry test TAT,the unqualified rate in a relatively concentrated period of TAT timeout and the unqualified rate of collected samples were compared before and after optimization.Results The median times (interquartile ranges) of each workflow including sample receipt and storage,result audit and sample storage-result report before and after lean management were 30 (35) min,7 (13) min,17 (8) min and 16(19) min,5(9) min,16(7) min,respectively,and there were significant differences in the former two(all P ＜0.01) but not the third (P ＞ 0.05).The median times (interquartile ranges) of TAT before and after lean management were 63 (51) min and 46 (33) min,respectively(P ＜ 0.05).The qualified rate of TAT increased from 86.00％ to 95.37％ after lean management(P ＜ 0.01).The unqualified rates in a relatively concentrated period of TAT timeout and collected samples decreased from 3.42％ to 1.00％ (P ＜0.01) and from 0.24％ to 0.17％ (P ＜ 0.01),respectively.Conclusion Lean management may improve process efficiency,reduce errors,and shorten emergency biochemistry test TAT in clinical laboratories.
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Objective To understand the mutations of macrolide resistance gene locus (23S rRNA) of Mycoplasma pneumoniae (MP) and its correlation with clinical features .Methods A total of 354 respiratory tract samples were collected from children pa-tients with pneumonia .MP and its mutations in 23S rRNA gene locus were detected by real-time PCR .The children cases of MP positive were divided into the mutation group and non-mutation group .Then the clinical data were compared between the two groups .Results Among 354 respiratory tract samples ,166 cases(46 .9% ) were MP positive ,moreover the mutation of 23S rRNA gene locus existed in 135 MP positive samples with the positive detection rate of 81 .3% ,while no 23S rRNA gene locus mutations were detected in 31 samples .Analyzing the clinical data of the mutation group and non-mutation group found that there was no sta-tistical difference in the aspects of age and gender between the two groups .The occurrence rates of severe pneumonia and extrapul-monary complications in the mutation group were higher than those in the non-mutation group (P<0 .05) ,moreover the average hospitalization time and fever duration in the mutation group were longer than those in the non-mutation group (P<0 .05) .Conclu-sion 23S rRNA gene locus mutation has higher detection rate ,prompting that MP shows high resistant rate to macrolides ,which could provide a certain basis for treatment of M P infections .