Antimicrobial susceptibility and fluctuations in clonal complexes of serogroup 6 Streptococcus pneumoniae isolates collected from children in Beijing, China, between 1997 and 2016

ABSTRACT This study examined the antimicrobial susceptibility patterns and clonal complex (CC) characteristics of serogroup 6 Streptococcus pneumoniae isolates collected from children in Beijing, China, between 1997 and 2016. Serotypes were determined using the Quellung reaction, and the antimicrobial susceptibility profiles of the isolates were determined using the disc-diffusion method or by E-test. Sequence types (STs) were assigned based on multilocus sequence typing. A total of 250 isolates were examined, with 55.2%, 30.0%, 12.8%, and 2.0% of isolates identified as serotypes 6A, 6B, 6C, and 6D, respectively. All of the isolates were susceptible to levofloxacin and vancomycin, and the non-suceptibitility rate to penicillin was 41.6%. Eighty-two distinct STs, assigned to 13 CCs and 28 singletons, were identified. CC982 was the most prevalent CC amongst serotype 6A isolates (34%), followed by CC9789 and CC3173. Amongst serotype 6B isolates, CC90 and CC4542 were the most common, accounting for 25.3% and 14.7% of isolates respectively. Over the study period, the prevalence of CC982, CC4542, and CC4536 isolates showing susceptibility to penicillin and cefuroxime decreased, and the proportion of CC3173, CC9789, CC855, and CC902 isolates showing non-susceptibility to these two antibiotics increased.

Methicillin-resistant Staphylococcus aureus isolated from an intensive care unit in Minas Gerais, Brazil, over a six-year period

ABSTRACT To characterize methicillin-resistant Staphylococcus aureus isolates from an intensive care unit of a tertiary-care teaching hospital, between 2005 and 2010. A total of 45 isolates were recovered from patients admitted to the intensive care unit in the study period. Resistance rates higher than 80% were found for clindamycin (100%), erythromycin (100%), levofloxacin (100%), azithromycin (97.7%), rifampin (88.8%), and gentamycin (86.6%). The SCCmec typing revealed that the isolates harbored the types III (66.7%), II (17.8%), IV (4.4%), and I (2.2%). Four (8.9%) isolates carried non-typeable cassettes. Most (66.7%) of the isolates were related to the Brazilian endemic clone from CC8/SCCmec III, which was prevalent (89.3%) between 2005 and 2007, while the USA100/CC5/SCCmec II lineage emerged in 2007 and was more frequent in the last few years. The study showed high rates of antimicrobial resistance among methicillin-resistant S. aureus isolates and the replacement of Brazilian clone, a well-established hospital lineage, by the USA100 in the late 2000s, at the intensive care unit under study.

Prevalence of Complement-Mediated Cell Lysis-like Gene (sicG) in Streptococcus dysgalactiae subsp. equisimilis Isolates From Japan (2014–2016)

BACKGROUND: Streptococcus dysgalactiae subsp. equisimilis (SDSE; a β-hemolytic streptococcus of human or animal origin) infections are emerging worldwide. We evaluated the clonal distribution of complement-mediated cell lysis-like gene (sicG) among SDSE isolates from three central prefectures of Japan. METHODS: Group G/C β-hemolytic streptococci were collected from three institutions from April 2014 to March 2016. Fifty-five strains (52 from humans and three from animals) were identified as SDSE on the basis of 16S rRNA sequencing data.; they were obtained from 25 sterile (blood, joint fluid, and cerebrospinal fluid) and 30 non-sterile (skin-, respiratory tract-, and genitourinary tract-origin) samples. emm genotyping, multilocus sequence typing, sicG amplification/sequencing, and random amplified polymorphic DNA (RAPD) analysis of sicG-positive strains were performed. RESULTS: sicG was detected in 30.9% of the isolates (16 human and one canine) and the genes from the 16 human samples (blood, 10; open pus, 3; sputum, 2; throat swab, 1) and one canine sample (open pus) showed the same sequence pattern. All sicG-harboring isolates belonged to clonal complex (CC) 17, and the most prevalent emm type was stG6792 (82.4%). There was a significant association between sicG presence and the development of skin/soft tissue infections. CC17 isolates with sicG could be divided into three subtypes by RAPD analysis. CONCLUSIONS: CC17 SDSE harboring sicG might have spread into three closely-related prefectures in central Japan during 2014–2016. Clonal analysis of isolates from other areas might be needed to monitor potentially virulent strains in humans and animals.

Clonal and Virulence Distribution of Uropathogenic Escherichia coli Isolated from Children in Korea

Urinary tract infections (UTI) are one of the most frequent infectious diseases. Uropathogenic Escherichia coli (UPEC) are among major pathogens causing UTI. A variety of virulence genes are mainly responsible for the severity of these emerging infection. This study investigate the influences of virulence properties of UPEC isolates with reference to multi-locus sequence typing (MLST). The aim of this study was targeted that investigation of the bacterial pathogenicity associated with UTI in children. A total of 58 UPEC isolates were collected from urine samples from patients with clinical diagnosis of uncomplicated UTI. The MLST of UPEC strains were assessed by methods based on polymerase chain reaction. Motility was evaluated using soft-agar plates. Biofilm formation was analyzed in microtiter dish biofilm formation assay. Cell death assay was analyzed by Annexin V/Phosphatidylserine staining and DNA fragmentation assay. According the result, the predominant sequence type (ST) was ST95 (24.1%) and ST73 (17.2%). There were some difference in virulence gene and antibiotics resistance between ST95 and ST73. The number of 11 (18.9%) isolates were strongly adherent. Based on the detected biofilm formation, these strongly adherent are almost ST73. The ST95 was higher than ST73 in population, but ST95 was lower than ST73 in motility and cell death induction. This study indicated that the UPEC molecular strains are related to some virulence traits. Furthermore, the virulence factors carried by ST73 strains contribute to their abilities to colonize the host and cause disease.

Epidemiological characterisation of Streptococcus pneumoniae from India using multilocus sequence typing.

Objective: The aim of this study was to utilize the multilocus sequence typing (MLST) technique to characterise Streptococcus pneumoniae among clinical isolates in India. MLST was used to determine clonality, to establish genetic relatedness, to check for correlation between serotypes and sequence types (STs) and its relevance associated with antibiotic resistance. Methods: Forty consecutive invasive S. pneumoniae isolates in children <5 years were characterised. Preliminary identification of serotype and antibiotic susceptible profile was followed with MLST technique to identify the STs of the isolates. STs were then analysed for clonality using an eBURST algorithm and genetic relatedness using Sequence Type Analysis and Recombinational Tests version 2 software. Results: The most common ST was ST63. Among the forty isolates, we identified nine novel STs, six of which had known alleles but in new combinations, three of which had new alleles in their sequence profile. The new STs assigned were 8501–8509. One clonal complex was found among the 40 strains characterised. The most common serotypes in this study were serotype 19F, 14 and 5. Non-susceptibility to penicillin and erythromycin was observed in 2.5% and 30% of the isolates, respectively. Conclusion: This study shows a significant number of novel STs among the 40 isolates characterised (9/40, 22.5%), however, internationally recognised strains were also circulating in India, indicating, there could be greater geographical variation in pneumococcal STs in India. Molecular epidemiology data is essential to understand the population dynamics of S. pneumoniae in India before the introduction of pneumococcal vaccines in NIP in India.

Population analysis of clinical Vibrio parahaemolyticus strains from Asia based on multilocus sequence typing and AA-multilocus sequence typing / 军事医学

Objective To find out more about the population structure and clonal complex of clinical Vibrio parahaemolyticus strains in Asia.Methods Clinical Vibrio parahaemolyticus strains data were screened in Asia with complete ST and pST types from PubMLST public database,their subgroup and complex were analyzed,and the minimum spanning tree based on ST and pST types respectively was completed.Results From the database,341 items of ST and pST types of Asian clinical Vibrio parahaemolyticus strains were screened,including 157 ST,most of which were of ST3 type.Totally 214 items of data came from China (including Hong Kong and Taiwan),and covered 133 ST,most of which were of ST3 type.eBURST software was used and 17 groups and 94 singletons were found.Software STRUCTURE analysis showed that the appropriate subset number of clinical V.parahaemolyticus strains in Asia was 7,and that the average distance between samples in each subgroup was 0.9113.Conclusion Clinical V.parahaemolyticus strains in Asia show high diversity and can be subdivided into seven subgroups.ST3 type is dominating when multilocus sequence typing(MLST)is used and pST2 type is the majority by AA-MLST typing.

MÉTODOS DE TIPIFICACIÓN Y EPIDEMIOLOGÍA MOLECULAR DE Staphylococcus aureus CON RESISTENCIA A LA METICILINA / TIPIFICATION METHODS AND MOLECULAR EPIDEMIOLOGY OF Staphylocuccus aureus WITH METHICILLIN RESISTANCE

El interés actual del estudio de Staphylococcus aureus deriva de su elevada frecuencia de cepas resistentes a los antibióticos que causa frecuentes brotes de infección, especialmente, el S. aureus con resistencia a meticilina (SARM). El objetivo de esta revisión fue estudiar la estructura genética poblacional y el origen de los aislamientos de SARM. La tipificación del cassette cromosómico mec estafilocócico es el método más importante para identificar y definir la naturaleza clonal del S. aureus con resistencia a meticilina. Los estudios de epidemiología molecular evidencian un patrón de diseminación de unas pocas cepas que son las responsables del importante problema mundial. Existe el predominio de clones pandémicos de SARM asociado a infecciones hospitalarias (SARM-AH), que ha han sido reemplazados en la actualidad por clones de origen comunitario (SARM-AC). En Colombia, predomina el clon pediátrico y el chileno entre los aislamientos hospitalarios. Sin embargo, en la actualidad una variante del clon comunitario USA300 prevalece en las infecciones adquiridas en la comunidad y en el hospital, desplazando los clones hospitalarios como ocurre en el resto de mundo. El entendimiento de la epidemiología y clonalidad de las infecciones por S. aureus tiene importantes implicaciones en el control de la emergencia de cepas con multirresistencia y el esparcimiento de clones resistentes y sensibles a meticilina.

Recent interest in the study of Staphylococcus aureus derives from the high frequency of antibiotic-resistant strains that cause frequent outbreaks of infection, especially Methicillin-resistant S. aureus (MRSA). The objective of this review was to study the population genetic structure and the origin of MRSA isolation. Classification of staphylococcal cassette chromosome mec (SCCmec) is the most important method to identify and define the S. aureus methicillin-resistant clonal nature. Molecular epidemiologic studies have demonstrated dissemination patterns of few strains which are responsible for the important worldwide problem. There is a predominance of pandemic clones of MRSA associated to hospital-acquired infections (HA-MRSA) which has been replaced today by community-acquired strains (CA-MRSA). In Colombia, the pediatric clone and the Chilean clone predominate between hospital isolations. However, currently, there is a variant community clone USA300 prevailing in infections acquired in the community and in the hospital, displacing HA-MRSA as it happens in the rest of world. Understanding the epidemiology and clonality of S. aureus infections has important implications for future efforts to control of the emergence of multidrug-resistant strains and the spread of clones resistant and sensible to methicillin.

Typing of Vibrio parahaemolyticus strains from aquatic products in East-China coastal areas based on multilocus sequence typing and AA-multilocus sequence typing / 军事医学

Objective To learn more about virulence genes and clonal complex group structure of Vibrio parahaemolyticus (VPH)strains separated from aquatic products in East China coastal areas between 2007 and 2012.Methods Seventy-nine strains separated from aquatic products in eastern coastal areas(Guandong,Fujian,Shanghai,Shandong,Jiangsu and Beijing)of China between 2007 and 2012 were identified as VPH by real-time-PCR with gene tlh.Gene tdh,trh and orf8 were also detected.Subgroup analysis and complex analysis were conducted of the VPH strains to build the minimum spanning tree respectively based on ST and pST types.Results In 79 VPH strains,gene tlh was positive while 8.86%(7 /79)of the isolates of gene tdh were positive.The carrying rate of gene orf8 was 8.86%.These 79 strains were of 69 ST types,involving 3 clonal complex and 62 singleton.By amino acid(AA)-multilocus sequence typing(MLST),79 strains covered the 23 pST types,2 clonal complexes and 1 singleton.The 363 single nucleotide polymorphisms(SNPs)were divided into 68 patterns.Conclusion VPH strains from aquatic products in eastern coastal areas of China are characterized by high polymorphisms and a low carrying rate of virulence genes.ST3 type is dominating when MLST typing is used while pST1 type is the majority by AA-MLST typing.

Vancomycin-resistant Enterococcus faecium of multi locus sequence type 18 in Malaysia

Vancomycin-resistant Enterococcus faecium (VREF) in human infections mostly belong to the high-risk, epidemic, clonal complex-17 (CC17) group. Treatment limitation and high conjugation frequency makes it dominant in hospitals worldwide. We investigated positive cultures by Pulse-field gel electrophoresis (PFGE), multi locus sequence typing (MLST). DNA of two strains (A2 and C) appeared to be clonally related by PFGE. Three strains were of ST 18 type (A1, B and C) and strain A2 is of a new ST 596. This ST 18 type strain found in our study is crucial and is believed to be the first in Malaysia.

Antimicrobial Resistance and Multilocus Sequence Typing of Vancomycin-Resistant Enterococcus faecium Isolated from the Chungcheong Area / 대한임상미생물학회지

BACKGROUND: Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal complex 17 (CC17). In the present study, characterization of the glycopeptide resistance mechanism, genetic relatedness, and pathogenicity in isolates of vancomycin-resistant E. faecium in the Chungcheong area were investigated. METHODS: A total of 37 consecutive, non-duplicate, vancomycin-resistant E. faecium were isolated at three university hospitals in the Chungcheong area. The mechanism of glycopeptide resistance and pathogenicity factors were studied using PCR, and the genetic relatedness was determined via multilocus sequence type and esp repeat profile analysis. Additionally, the quinolone resistance-determining regions of parC and gyrA were sequenced to identify mutations involved in ciprofloxacin resistance. RESULTS: Two genotypes of VRE were confirmed: VanA-phenotype vanA genotype VRE (25 isolates) and VanB-phenotype vanA genotype VRE (12 isolates). MLST analysis revealed five sequence types. A significant result was that ST414 and CNS4 (4-1-1-1-1-1-1) were considered as belonging to CC17. The esp and hyl genes were found in 100% and 86.4% of the isolates, respectively. A total of 37 isolates showed genetic mutations in parC and gyrA. CONCLUSION: All isolated strains in the present study belonged to one of the CC17 genotypes including ST414 and CNS4 (4-1-1-1-1-1-1), which were not previously detected in Korea. The combination of MLST and the esp gene repeat profiles can be useful for genetic characterization of VREF isolates with regard to the evolutionary process and epidemiology of the clones.