Dataset Information

Molecular Epidemiology and Antimicrobial Resistance of Haemophilus influenzae in Adult Patients in Shanghai, China.

ABSTRACT: Background: The serotype and antimicrobial resistance of Haemophilus influenzae in adult patients have changed due to the application of antimicrobials and H. influenzae type b (Hib) vaccine worldwide. However, the epidemiologic characteristics of H. influenzae in Shanghai are still unavailable. Objective: To determine the serotype distribution, antimicrobial resistance and multilocus sequence type (MLST) of H. influenzae in adult patients in Shanghai. Methods: A total of 51 clinical isolates from adult patients were consecutively collected. Serotypes were determined according to specific capsule gene, bexA, amplified by PCR. Antimicrobial susceptibility test was carried out by the broth microdilution method. ?-lactamase production was detected by cefinase disk and the ftsI gene were amplified and sequenced to determine the penicillin binding protein 3 (PBP3) mutation. Molecular epidemiology was performed by MLST analyses. Results: All isolates studied were nontypeable H. influenzae (NTHi) and three of them (5.88%) caused invasive infection. The resistant rates of ampicillin and trimethoprim/sulfamethoxazole were both 45.10%. One third of these isolates produced TEM-1 type ?-lactamase and 11.76% were ?-lactamase negative ampicillin resistant strains (BLNAR). The PBP3 mutation was detected in 74.51% of the isolates, of which 12 belonged to group III. A total of 36 sequence types (STs) were identified among all isolates. Four isolates of ST103 (7.84%) all produced ?-lactamase without mutation of PBP3. Conclusion: H. influenzae infections among adults in Shanghai are predominately caused by NTHi with genetic diversity among adult patients. The prevalence of both ?-lactamase production and PBP3 mutation may contribute to high ampicillin resistance rate in Shanghai.

SUBMITTER: Li XX

PROVIDER: S-EPMC7135888 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Molecular Epidemiology and Antimicrobial Resistance of Haemophilus influenzae in Adult Patients in Shanghai, China.

Li Xin-Xin XX Xiao Shu-Zhen SZ Gu Fei-Fei FF He Wei-Ping WP Ni Yu-Xing YX Han Li-Zhong LZ

Frontiers in public health 20200327

Background: The serotype and antimicrobial resistance of Haemophilus influenzae in adult patients have changed due to the application of antimicrobials and H. influenzae type b (Hib) vaccine worldwide. However, the epidemiologic characteristics of H. influenzae in Shanghai are still unavailable. Objective: To determine the serotype distribution, antimicrobial resistance and multilocus sequence type (MLST) of H. influenzae in adult patients in Shanghai. < ...[more]

PMID: 32292774

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Project description:BackgroundThe widespread use of antimicrobials and Haemophilus influenzae type b (Hib) vaccine worldwide has altered the epidemiological patterns of invasive H. influenzae. Nonetheless, little is currently known on the epidemiological characteristics of H. influenzae in Guiyang, Guizhou, China.ObjectiveTo determine the serotype distribution, antimicrobial resistance and Multilocus Sequence Typing (MLST) of H. influenzae in hospitalized patients in Guiyang City.MethodsA total of 196 clinical isolates from hospitalized patients were collected. Serotypes were determined according to the specific capsule gene, bexA, amplified by PCR. According to the guidelines of Clinical and Laboratory Standards Institute (CLSI) 2020 drug susceptibility tested, and the results determined. The chromogenic cephalosporin nitrocefin method was used to detect β-lactamase production, β-lactamase negative, ampicillin-resistant (BLNAR) strains were detected by PCR amplification and sequencing of the penicillin-binding protein 3 (PBP3) locus of ftsI. Multilocus Sequence Typing was performed for molecular typing.ResultsAll isolates studied were non-typeable H. influenzae (NTHi). Most patients originated from the pediatrics department (78.6%, 154/196), and suffered from lung with respiratory tract infection (pneumonia and bronchitis, 68.4%, 134/196). The resistance rates of ampicillin, cefaclor and azithromycin were 71.4% (140/196), 36.7% (72/196) and 34.2% (67/196), respectively. 40.3% (79/196) of strains were β-lactamase positive ampicillin-resistant (BLPAR). All BLPAR carried the TEM-1 gene. 9.2% (18/196) were β-lactamase negative ampicillin-resistant strains (BLNAR). The PBP3 mutation was detected in the ampicillin-resistant strains (n = 113), of which 18 belonged to group IIa. A total of 49 sequence types (ST) and 23 clonal complexes (CC) were detected, among which CC107 (ST107, n = 27; ST1002, n = 5; ST1218, n = 5) was the most frequent clonal complexes. BLPAR isolates mostly belonged to ST107 (20/79), while BLNAR was predominantly distributed in ST12 (5/18).ConclusionH. influenzae infections are predominately caused by genetically diverse NTHi among hospitalized patients in Guiyang. The prevalence of β-lactamase production and PBP3 mutation may contribute to the high local ampicillin resistance rate.

Project description:Urinary tract infection (UTI) is one of the most common bacterial infections and UTI is the most common extraintestinal infectious disease entity in women worldwide. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTI. While antimicrobial resistance has emerged as one of the principal problems of UTI, little is known about the epidemiology of UPEC isolated from female patients in Shanghai. This study aimed to describe the antimicrobial resistance and molecular epidemiology of UPEC isolated from female patients in Shanghai, China. UPEC isolates were collected from female patients from July 2019 to June 2020 in Shanghai and a total of 151 isolates were obtained randomly. Antimicrobial susceptibility testing was performed using the disk diffusion method. Multilocus sequencing type, phylogenetic groups, antimicrobial resistance genes, and virulence genes were detected by polymerase chain reaction. In our study, no carbapenem-resistant isolates were found, but fluoroquinolone-resistant and multi-drug resistant UPEC accounted for 62.25% and 42.38%, respectively. The phylogenetic group B2 (58.94%) predominated, followed by phylogenetic group D (26.49%). The most prevalent sequence type was ST1193 (25.83%), which was first reported in Shanghai. The rate of extended-spectrum β-lactamase (ESBL)-positive isolates was 39.74% and the dominant ESBL genotype was bla CTX-M-14 (21/60), followed by bla CTX-M-55 (12/60). Mutations in gyrA were detected in the majority of fluoroquinolone-resistant isolates (90/94), followed by parC (85/94) and parE (71/94). The aac (3) -IIa was also found in 85% of aminoglycoside resistance isolates. Among 151 UPEC isolates, the common virulence genes were csgA (97.35%), fimH (92.72%), sitA (82.12%), and malX (65.56%). In conclusion, the high antimicrobial resistance of UPEC isolated from female patients, harboring a series of virulence genes, are troublesome for medical practitioners in Shanghai. At present, the prevalent ST1193 and emerging bla CTX-M-55 make UTI therapy more challenging.

Project description:Invasive Haemophilus influenzae (Hi) disease has decreased in countries that included Hi type b (Hib) vaccination in their childhood immunization programs in the 1990s. Non-typeable (NT) and non-b strains are now the leading causes of invasive Hi disease in Europe, with most cases reported in young children and the elderly. Concerningly, no vaccines toward such strains are available and beta-lactam resistance is increasing. We describe the epidemiology of invasive Hi disease reported to the Norwegian Surveillance System for Communicable Diseases (MSIS) (2017-2021, n = 407). Whole-genome sequencing (WGS) was performed on 245 isolates. We investigated the molecular epidemiology (core genome phylogeny) and the presence of antibiotic resistance markers (including chromosomal mutations associated with beta-lactam or quinolone resistance). For isolates characterized with both WGS and phenotypic antibiotic susceptibility testing (AST) (n = 113) we assessed correlation between resistance markers and susceptibility categorization by calculation of sensitivity, specificity, and predictive values. Incidence rates of invasive Hi disease in Norway ranged from 0.7 to 2.3 per 100,000 inhabitants/year (mean 1.5 per 100,000) and declined during the COVID-19 pandemic. The bacterial population consisted of two major phylogenetic groups with subclustering by serotype and multi-locus sequence type (ST). NTHi accounted for 71.8% (176). The distribution of STs was in line with previous European reports. We identified 13 clusters, including four encapsulated and three previously described international NTHi clones with bla TEM-1 (ST103) or altered PBP3 (rPBP3) (ST14/IIA and ST367/IIA). Resistance markers were detected in 25.3% (62/245) of the isolates, with bla TEM-1 (31, 50.0%) and rPBP3 (28, 45.2%) being the most frequent. All isolates categorized as resistant to aminopenicillins, tetracycline or chloramphenicol possessed relevant resistance markers, and the absence of relevant substitutions in PBP3 and GyrA/ParC predicted susceptibility to cefotaxime, ceftriaxone, meropenem and quinolones. Among the 132 WGS-only isolates, one isolate had PBP3 substitutions associated with resistance to third-generation cephalosporins, and one isolate had GyrA/ParC alterations associated with quinolone resistance. The detection of international virulent and resistant NTHi clones underlines the need for a global molecular surveillance system. WGS is a useful supplement to AST and should be performed on all invasive isolates.

Project description:BackgroundEnterobacter cloacae is a major nosocomial pathogen causing bloodstream infections. We retrospectively conducted a study to assess antimicrobial susceptibility and phylogenetic relationships of E. cloacae bloodstream isolates in two tertiary university-affiliated hospitals in Shanghai, in order to facilitate managements of E. cloacae bloodstream infections and highlight some unknowns for future prevention.MethodsFifty-three non-duplicate E. cloacae bloodstream isolates were consecutively collected from 2013 to 2016. Antimicrobial susceptibility was determined by disk diffusion. PCR was performed to detect extended-spectrum β-lactamase (ESBL), carbapenemase and colistin resistance (MCR-1) gene. Plasmid-mediated AmpC β-lactamase (pAmpC) genes were detected using a multiplex PCR assay targeting MIR/ACT gene (closely related to chromosomal EBC family gene) and other plasmid-mediated genes, including DHA, MOX, CMY, ACC, and FOX. eBURST was applied to analyze multi-locus sequence typing (MLST).ResultsThe rates of resistance to all tested antibiotics were <40%. Among 53 E. cloacae isolates, 8(15.1%) were ESBL producers, 3(5.7%) were carbapenemase producers and 18(34.0%) were pAmpC producers. ESBL producers bear significantly higher resistance to cefotaxime (100.0%), ceftazidime (100.0%), aztreonam (100.0%), piperacillin (87.5%), tetracycline (75.0%), and trimethoprim-sulfamethoxazole (62.5%) than non-producers (p<0.05). PAmpC- and non-producers both presented low resistance rates (<40%) to all antibiotics (p>0.05). SHV (6/8, 75.0%) and MIR/ACT (15/18, 83.3%) predominated in ESBL and pAmpC producers respectively. Moreover, 2 isolates co-carried TEM-1, SHV-12, IMP-26 and DHA-1. MLST analysis distinguished the 53 isolates into 51 STs and only ST414 and ST520 were assigned two isolates of each (2/53).ConclusionThe antimicrobial resistance rates were low among 53 E. cloacae bloodstream isolates in the two hospitals. Multiclonality disclosed no evidence on spread of these isolates in Shanghai. The simultaneous presence of ESBL, carbapenemase and pAmpC detected in 2 isolates was firstly reported in Shanghai, which necessitated active ongoing surveillances and consistent prevention and control of E. cloacae.

Project description:Streptococcus pneumoniae is a common pathogenic cause of pediatric infections. This study investigated the serotype distribution, antimicrobial susceptibility, and molecular epidemiology of pneumococci before the introduction of conjugate vaccines in Shanghai, China.A total of 284 clinical pneumococcal isolates (270, 5, 4,3, and 2 of which were isolated from sputum, bronchoalveolar lavage fluid, blood, cerebral spinal fluid, and ear secretions, respectively) from children less than 14 years of age who had not been vaccinated with a conjugate vaccine, were collected between January and December in 2013. All isolates were serotyped by multiplex polymerase chain reaction or quellung reactions and antimicrobial susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S.pneumoniae was analyzed by multilocus sequence typing (MLST).Among the 284 pneumococcal isolates, 19F (33.5%), 19A (14.1%), 23F (12.0%), and 6A (8.8%) were the most common serotypes and the coverage rates of the 7-, 10-, and 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, and PCV13) were 58.6%, 59.4% and 85.1%, respectively. Antimicrobial susceptibility showed that the prevalence rates of S.pneumoniae resistance to penicillin were 11.3% (32/284). Approximately 88.0% (250/284) of the isolates exhibited multi-drug resistance. MLST analysis revealed a high level of diversity, with 65 sequence types (STs) among 267 isolates. Specifically, the four predominant STs were ST271 (24.3%, 65/267), ST320 (11.2%, 30/267), ST81 (9.7%, 26/267), and ST3173 (5.2%, 14/267), which were mainly associated with serotypes 19F, 19A, 23F, and 6A, respectively.The prevalent serotypes among clinical isolates from children were 19F, 19A, 23F, and 6A and these isolates showed high resistance rates to β-lactams and macrolides. The Taiwan19F-14 clone played a predominant role in the dissemination of pneumococcal isolates in Shanghai, China. Therefore, continued and regional surveillance on pneumococcal isolates may be necessary.

Project description:The 7th cholera pandemic began in 1961 in Sulawesi, Indonesia, and then spread around the world in at least three waves. However, the lack of genome sequences for Vibrio cholerae strains under long-term surveillance in East Asia, especially in China, has restricted our understanding of the dynamics of the intracountry and intercountry evolution and transmission of the 7th-pandemic clones. In this study, we obtained the genome sequences of 60 V. cholerae strains isolated in Shanghai, the largest port in the world and the largest city in China, from 1961 to 2011. Our whole-genome-based phylogeny of 7th-pandemic strains revealed that all but one fell into five "stages," most of which are single clades and share independent ancestors. Each stage dominated in succession for a period, with little overlap between them. In addition, two near-identical Shanghai strains belonging to a pre-7th-pandemic precursor and 4 nontoxigenic O1/O139 strains attributed to independent recombination events at the O-antigen loci were present. The major lineages of the 7th pandemic in Shanghai appeared to be closely related to V. cholerae strains isolated from South or Southeast Asia. Stage succession was consistently related to changes in society and human activity, implying that human-caused niche change may play a vital role in the cholera dynamics in Shanghai.IMPORTANCEV. cholerae is the causative agent of cholera, a life-threatening disease characterized by severe, watery diarrhea. The 7th pandemic started in Indonesia in 1961 and spread globally, currently infecting 1.3 million to 4 million people annually. Here, we applied whole-genome sequencing to analyze a long-term collection of V. cholerae clinical strains to reveal the phylogenetic background and evolutionary dynamics of the 7th pandemic in Shanghai, which had undergone breathtakingly rapid development in the last half-century. All but one of the Shanghai 7th-pandemic strains fell into five "stages" that were dominant in Shanghai and appeared to be closely related to 7th-pandemic strains of South or Southeast Asia. Our findings extended the understanding of the dynamics of the evolution and transmission of the 7th-pandemic clones in East Asia and the relationship between social changes and cholera epidemiology.

Dataset Information

Molecular Epidemiology and Antimicrobial Resistance of Haemophilus influenzae in Adult Patients in Shanghai, China.

Publications

Molecular Epidemiology and Antimicrobial Resistance of <i>Haemophilus influenzae</i> in Adult Patients in Shanghai, China.

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