Antimicrobial Resistance Patterns, Sequence Types, Virulence and Carbapenemase Genes of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates from a Tertiary Care Teaching Hospital in Zunyi, China.

Purpose: Carbapenem-resistant Klebsiella pneumoniae (CRKP) has seriously threatened public health worldwide. This study aimed to investigate the antimicrobial resistance patterns, sequence types (STs), virulence and carbapenemase genes of CRKP isolates from patients in Zunyi, China. Methods: CRKP isolates were collected from the First People's Hospital of Zunyi between January 2018 and December 2020. Antimicrobial susceptibility was determined using a VITEK®2 analyzer and confirmed using either the broth dilution method, Kirby-Bauer method, or E-test assays. Carbapenemase production was examined using a modified carbapenem inactivation method. STs of the studied isolates were determined by multilocus sequence typing, and the presence of carbapenemase and virulence genes was examined using polymerase chain reaction assays. Results: In total, 94 CRKP isolates were collected. All studied isolates produced carbapenemase, and the most common carbapenemase gene was New Delhi metallo-ß-lactamase (NDM; 72.3%), followed by Klebsiella pneumoniae carbapenemase (KPC; 24.5%), and Verona integron-encoded metallo-ß-lactamase (VIM; 3.2%). Of the studied isolates, 74.3% exhibited multidrug-resistant (MDR) phenotype, and 25.7% were either pandrug-resistant (PDR) or extensively drug-resistant (XDR) phenotypes. The most prevalent sequence type was ST2407 (37.2%), followed by ST76 (21.3%) and ST11 (11.7%). The NDM gene was present in 97.1% of ST2407 isolates and 90.0% of ST76 isolates, whereas the KPC gene was present in 90.9% of ST11 isolates. The majority of the isolates carried wabG, uge, and fimH virulence genes, with prevalence rates of 94.7%, 92.6%, and 94.7%, respectively. Conclusion: This study describes NDM-producing ST2407 and ST76, as well as KPC-producing ST11, as the major clonal types of CRKP isolates in Zunyi, China. All CRKP isolates were resistant to multiple types of antibiotics, and the majority of isolates carried carbapenemase and virulence genes. Clonal spread of NDM-producing CRKP ST2407 and ST76, and KPC-producing CRKP ST11 should be strictly monitored.

Molecular epidemiology and antimicrobial resistance patterns of carbapenem-resistant Acinetobacter baumannii isolates from patients admitted at ICUs of a teaching hospital in Zunyi, China.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundation for the development of infection prevention and control strategies. This study aimed to determine the antimicrobial susceptibility profile, the molecular epidemiology and conduct homology analysis on CRAB strains isolated from ICUs. Methods: The sensitivity to various antimicrobials was determined using the minimum inhibitory concentration (MIC) method, Kirby-Bauer disk diffusion (KBDD), and E-test assays. Resistance genes were identified by polymerase chain reaction (PCR). Molecular typing was performed using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Results: Among the 79 isolates collected, they exhibited high resistance to various antimicrobials but showed low resistance to levofloxacin, trimethoprim-sulfamethoxazole, and tetracyclines. Notably, all isolates of A. baumannii were identified as multidrug-resistant A. baumannii (MDR-AB). The bla OXA-51-like, adeJ, and adeG genes were all detected, while the detection rates of bla OXA-23-like (97.5%), adeB (93.67%), bla ADC (93.67%), qacEΔ1-sul1 (84.81%) were higher; most of the Ambler class A and class B genes were not detected. MLST analysis on the 79 isolates identified five sequence types (STs), which belonged to group 3 clonal complexes 369. ST1145Ox was the most frequently observed ST with a count of 56 out of 79 isolates (70.89%). MLST analysis for non-sensitive tigecycline isolates, which were revealed ST1145Ox and ST1417Ox as well. By using the MLVA assay, the 79 isolates could be grouped into a total of 64 distinct MTs with eleven clusters identified in them. Minimum spanning tree analysis defined seven different MLVA complexes (MCs) labeled MC1 to MC6 along with twenty singletons. The locus MLVA-AB_2396 demonstrated the highest Simpson's diversity index value at 0.829 among all loci tested in this study while also having one of the highest variety of tandem repeat species. Conclusion: The molecular diversity and clonal affinities within the genomes of the CRAB strains were clearly evident, with the identification of ST1144Ox, ST1658Ox, and ST1646Oxqaq representing novel findings.

Molecular typing and drug resistance analysis of carbapenem-resistant Klebsiella pneumoniae from paediatric patients in China.

INTRODUCTION: There are few studies on paediatric carbapenem-resistant Klebsiella pneumoniae (CRKP) in China. The present study investigated the molecular epidemiological and drug resistance characteristics of CRKP from paediatric patients in China to provide a reference for the prevention and control of CRKP infection. METHODOLOGY: In total, 20 nonrepetitive clinical CRKP isolates were collected between February 2019 and February 2020 in a tertiary hospital in China. Strain identification and drug susceptibility testing were carried out using the VITEK® 2 Compact Bacterial Identification and Monitoring System. Sequence typing, phylogenetic relationships, and antibiotic resistance-associated genes were analysed by whole genome sequencing (WGS). RESULTS: sequence typing (MLST) and Core genome multilocus sequence typing (cgMLST) analysis revealed the most frequently represented were ST2407-CT3536 (30%), ST76-CT5893 (25%), and ST309-CT7864 (25%). All 20 CRKP isolates were divided into three clusters. All isolates were highly resistant to a variety of ß-lactams and were highly susceptible to quinolones, aminoglycosides, and sulphonamides. All isolates mainly carried the carbapenem resistance genes blaNDM-1 and blaKPC-2, among which 10 isolates carried both blaNDM-1 and blaKPC-2 simultaneously. CONCLUSIONS: Sequence typing, phylogenetic relationships, and antibiotic resistance genes can be determined using WGS technology. This can guide CRKP infection control and clinical treatment for paediatric patients.

Molecular Characterization Based on Whole-Genome Sequencing of Streptococcus pneumoniae in Children Living in Southwest China During 2017-2019.

Background: Streptococcus pneumoniae is an important pathogen causing high morbidity and high mortality in children and undergoes frequent recombination for capsule switching to neutralize the 13-valent pneumococcal conjugate vaccine (PCV13). This study aimed to investigate the prevalence, and molecular characteristics including serotypes and antibiotic susceptibility of S. pneumoniae isolated from children living in Southwest China from 2017 to 2019 to facilitate the selection of effective vaccine formulations and appropriate antibiotic treatment regimens. Methods: This study was conducted at West China Second University Hospital (Chengdu, Sichuan Province, China), Zunyi Medical University Third Affiliated Hospital/First People's Hospital of Zunyi (Zunyi, Guizhou Province, China) and Chengdu Jinjiang District Maternal and Child Healthcare Hospital (Chengdu, Sichuan Province, China). Demographic and clinical characteristics of children infected with S. pneumoniae were collected and analysed. Next-generation sequencing and sequence analysis were used to determine the serotypes, sequence types, antibiotic resistance and potential protein vaccine target genes of the pneumococcal isolates. The coverage rate provided by PCV13 was estimated by calculating the percentage of the specific serotypes that were specifically the PCV13-included serotypes. Antimicrobial susceptibility was determined by the microdilution broth method. Results: The most prevalent pneumococcal serotypes were 19F (25.8%), 19A (14.1%), 6B (12.5%), 6A (9.4%) and 14 (7.8%). The predominant STs were ST271 (23.3%), ST320 (15.5%) and ST90 (8.6%), dominated by the clonal complex Taiwan19F-14 (39.1%). The coverage rate of PCV13 was 77.3% in all the isolates, with relatively higher values in invasive isolates (86.4%). Over the decade, the rates of resistance to penicillin, amoxicillin and cefotaxime were 5.6%, 5.3% and 5.1%, respectively, with significantly higher values in invasive isolates (22.4%, 14.9% and 11.9%). Almost all the isolates were resistant to erythromycin (99.1%) and clindamycin (95.9%). All isolates carried virulence-related genes, including ply, psaA, piaA, piuA, phtE, nanA, pepO, danJ, pvaA, clpP, pcsB, stkP, potD, and strH. The carriage of virulence and resistance genes varied among serotypes and clades, with serotype 19F/ST271 showing higher resistance to antibiotics and being more likely to carry pilus genes and other virulence genes. Conclusion: These data provide valuable information for the understanding of pneumococcal pathogenesis, antimicrobial resistance and the development of protein-based vaccines against pneumococcal infection.

Molecular Epidemiology and Clinical Features of Enteroviruses-Associated Hand, Foot, and Mouth Disease and Herpangina Outbreak in Zunyi, China, 2019.

Background: Hand, foot and mouth disease (HFMD) and herpangina (HA), two of the most common childhood infectious diseases, are associated with enteroviruses (EVs) infection. The aim of this study was to identify the molecular epidemiology of enterovirus causing HFMD/HA in Zunyi, China, during 2019, and to describe the clinical features of the cases. Methods: We collected the information on demographic and clinical characteristics, laboratory data of laboratory-confirmed EVs associated HFMD/HA cases in Zunyi Medical University Third Affiliated Hospital between March 1 and July 31, 2019. EV types were determined by either one-step real time RT-PCR or partial VP1 gene sequencing and sequence alignment. Phylogenetic analysis of CVA6, CVA2, and CVA5 were established based on the partial VP1 gene sequences by neighbor-joining method. Differences in clinical characteristics and laboratory results of the cases were compared among patients infected with the most prevalent EV types. Results: From 1 March to 31 July 2019, 1,377 EVs associated HFMD/HA inpatients were confirmed. Of them, 4 (0.3%, 4/1,377) were EV-A71-associated cases, 84 (6.1%, 84/1,377) were CVA16-associated cases, and 1,289 (93.6%, 1,289/1,377) were non-EV-A71/CVA16-associated cases. Of the randomly selected 372 non-EV-A71/CVA16 cases, EV types have been successfully determined in 273 cases including 166 HFMD and 107 HA cases. For HFMD cases, the three most common types were CVA6 (80.7%, 134/166), CVA2 (5.4%, 9/166) and CVA5 (3.0%, 5/166); similarly, for HA cases, the three most prevalent serotypes were CVA6 (36.5%, 39/107), CVA2 (21.5%, 23/107) and CVA5 (18.7%, 20/107). Phylogenetic analysis showed that subclade D of CVA5, and subclade E of CVA6 and CVA2 were predominant in Zunyi during the outbreak in 2019. Compared with the cases caused by CVA16, the incidence of high fever and severe infection associated with CVA2, CVA5, and CVA6 was higher. Conclusions: The recent HFMD/HA outbreak in Zunyi is due to a larger incidence of CVA6, CVA2, and CVA5. Novel diagnostic reagents and vaccines against these types would be important to monitor and control EV infections.

Serotype prevalence and antibiotic susceptibility patterns of pneumococcal isolates in Zunyi city, China.

OBJECTIVES: To assess the serotype distribution and antimicrobial susceptibility of pneumococci isolated from inpatients of all ages suspected of having bacterial infections. METHODS: In this retrospective study, pneumococcal isolates were consecutively collected  from the Third Affiliated Hospital of Zunyi Medical University, in Zunyi city, China, between January 2014 and December 2016. Pneumococci were identified using routine microbiological assays. We performed antimicrobial susceptibility analyses using the bacteria identification/susceptibility system VITEK2 and E-tests. Capsular types of all isolates were determined by multiplex polymerase chain reaction. RESULTS: We identified 778 pneumococcal isolates. Serotypes 19F, 6A/6B, 19A, 23F, and 15B/15C were the most prevalent strains, accounting for 71.5% (556/778) of all isolates. Data show that 409 (70.4%) isolates could be covered by the PCV13 vaccine in children less than 2 years old. Irrespective of serotypes, 747 (96%) isolates were sensitive to penicillin, while 720 to 778 (90% to 100%) isolates were not susceptible to erythromycin, tetracycline, and trimethoprim/sulfamethoxazole. For isolates resistant to penicillin, ceftriaxone, cefotaxime, and meropenem, 22 to 39 (70% to 81.25%) strains belonged to PCV13 serotypes. CONCLUSION: We found a substantial increase in the annual number of pneumococcal isolates since 2014. The theoretical impact of PCV13 was high in children less than 2 years old, and penicillin might be effective against pneumococcal infections in this region.