Molecular characterization and environmental mapping of Campylobacter isolates in a subset of intensive poultry flocks in Ireland

Irish breeder and intensive broiler flocks together with the corresponding poultry farm environment were sampled for the presence of Campylobacter with the aim of identifying potential sources and transmission routes of poultry flock contamination. The genetic diversity of a subset of Campylobacter isolates was examined by analysis of the flaA-short variable region (SVR). Additional discrimination for a further subset of these isolates was achieved using multilocus sequence typing (MLST) analysis. Twenty-four flaA-SVR alleles and 15 FlaA peptides were detected among 92 Campylobacter jejuni and Campylobacter coli isolates. MLST data have been determined for 30 of 92 (32.6%) flaA-SVR-typed isolates with 13 sequence types (STs) present, which were assigned to seven clonal complexes. ST45 was the most common ST identified. Vertical transmission was not found to have played a role in transmission of the pathogen to the poultry flocks. Subtyping by flaA-SVR and MLST identified the practice of partial thinning of flocks as a potential source and route of flock contamination on one broiler farm and implicated a probable source of flock contamination on another. Although there have been several studies reported in the scientific literature, the findings from this study confirmed previous studies and suggested some new transmission pathways including via transport crates. Cross-contamination from adjacent cattle is a new development, and molecular evidence of the role of transport crates in introducing Campylobacter spp. into the broiler house is a recent finding. Further, this study reports the discovery of five new flaA-SVR allele types and eight new STs. These were widespread and persistent in the poultry environment. This new knowledge may explain why despite the on-farm Campylobacter data published to date, there are still no completely effective on-farm control measures to prevent Campylobacter contamination of broiler flocks.     

Genotypic characterization of Streptococcus pneumoniae serotype 19F in Malaysia

Streptococcus pneumoniae is an epidemiologically important bacterial pathogen. Recently, we reported the antibiotic susceptibility patterns of a limited collection of pneumococcal isolates in Malaysia with a high prevalence of erythromycin resistant strains. In the present study, 55 of the pneumococcal isolates of serotype 19F were further analysed by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The generated genotypic patterns were then correlated with the antibiograms previously reported. Forty-seven different PFGE profiles (PTs) were obtained, showing that the isolates were genetically diverse. MLST identified 16 sequence types (STs) with ST-236 being predominant (58.2%), followed by ST-81 (10.3%). Among the ST-236 isolates, 22 were erythromycin resistant S. pneumoniae (ERSP) and 15 were trimethoprim/sulfamethoxazole (TMP/SMX) resistant, while among ST-81, four isolates were ERSP and two were TMP/SMX resistant. The high prevalence of erythromycin resistant serotype 19F isolates of ST-236 in this study has also been reported in other North and South East Asian countries.     

Genetic diversity among clonal lineages within Escherichia coli O157:H7 stepwise evolutionary model

Escherichia coli O157:H7 variants were examined for trait mutations and by molecular subtyping to better define clonal complexes postulated on the O157:H7 evolution model. Strains of beta-glucuronidase-positive, sorbitol-negative O157:H7 isolated in United States and Japan were identical to A5 clonal strain and shared sequence type (ST)-65 by multilocus sequence typing (MLST); thus, they belong in A5. However, these strains exhibited pulsed-field gel electrophoresis (PFGE) profile differences that suggested genomic divergence between populations. Sorbitol-fermenting O157 (SFO157) strains from Finland, Scotland, and Germany were identical to A4 clonal strain and belong in A4. Some SFO157 strains, isolated years apart and from different countries, had identical PFGE profiles, suggesting a common origin. Despite similarities, some Finnish and Scottish and all of the German strains have ST-75 ("German clone"), whereas others have ST-76, a new variant ("Scottish clone"). MLST of strains in other clonal complexes also discriminated strains thought to be identical and showed that genetic differences will further distinguish clonal populations into subclones.     

浙江省61株嗜肺军团菌血清1型菌株的SBT序列分型

目的了解浙江省空调冷却塔/冷凝水中嗜肺军团菌血清1型(Lp1)菌株的序列分型特征。方法选取2005～2011年间浙江省10个地区空调冷却塔/冷凝水中分离的61株Lp1型嗜肺军团菌菌株,采用欧盟军团菌感染工作组(EWGLI)军团菌序列分型(SBT)方法,PCR扩增7对管家基因,对扩增产物进行测序、比对、递交,以获取等位基因号以及SBT序列型,运用DNAsp 5.0软件对测序结果进行核苷酸多态性分析,采用SplitsTree及eBURST软件对分型结果进行聚类分析。结果 61株Lp1型嗜肺军团菌可分为11种SBT序列型,其中5株(5/61)均为新发现序列型;ST-1型在10个地区(市)的冷却塔/冷凝水中均有分布,该序列型菌株占81.9%(50/61)。7个管家基因的核苷酸多态性(Pi)范围为0.01095(mip)～0.05355(pilE)。聚类分析显示,浙江省Lp1型菌株分属多个克隆系,但主要分属ST-1序列群、ST-154序列群和ST-149三大序列群,另有1株为不属于任何序列群的单体。结论聚类分析表明浙江省空调冷却塔/冷凝水中分离的Lp1型嗜肺军团菌存在遗传多样性,序列群分布与国内部分省份的结果相似,以ST-1序列型为主。     

贵州与中国大陆其它地区空肠弯曲菌MLST特征的比较分析

目的 了解贵州省鸡源空肠弯曲菌的分子流行特征,阐明各地菌株间的亲缘关系和进化特征。方法 在贵州省随机抽取7个大型养鸡场,共采集210份鸡的新鲜粪便样本,分离培养出38株空肠弯曲菌,采用多位点序列分型对分离株的序列型及克隆复合体进行构成和聚类分析,与PubMLST数据库中来自国内的分离株分子特征进行比较。结果 贵州省38株鸡源空肠弯曲菌分为23种ST型和8个克隆复合体,其中9种是目前中国大陆地区已有的ST型,2个等位基因和8种序列型为新发现的。ST型构成比前四位分别是ST - 45、ST - 161、ST - 354、ST - 4 324,与数据库中已有的6株贵州来源菌株相比,不存在共同的ST型。优势克隆复合体（CC - 45、CC - 354、CC - 52）与数据库中鸡源分离株的前三位克隆复合体没有重叠。菌株遗传进化树显示,本研究中属于优势克隆复合体的18株菌与国内部分人源、猪源、野生鸟源、鹅源分离株有较近的遗传距离。结论 贵州省鸡源空肠弯曲菌具有高度遗传多样性,在一定程度上表现出地域流行特征。序列型与国内华东地区的分离株有较高的交叉性,部分分离株与国内人、野生鸟、鹅等来源分离株遗传距离近,应加强对不同地区、不同宿主来源空肠弯曲菌的动态监测。     

广州市两例B群流脑病例分离株的MLST分型研究

目的对从广州市报告的两例B群流行性脑脊髓膜炎（流脑）病例中分离的4株脑膜炎奈瑟菌（Neisseria meningitidis,Nm）进行多位点序列分型（multi—locus sequence typing,MLST）研究。方法分纯并提取菌株DNA、运用MI。ST分析对7个管家基因进行扩增并测序,确定菌株的序列型,对其相关性进行分析。结果两例病例分离株7个管家基因位点序列均不相同,第一例病例分离株的序列型为ST-7型,属高致病性ST-5complex／subgroupIII克隆系;第二例病例分离株的序列型为新发现的ST一9804型。结论广州两例B群流脑病例虽然发生时间相近,但分属不同的序列型,无同源性。MLST分型技术对研究不同流脑病例间的流行病学关系有重要意义。     

Vibrio parahaemolyticus isolates from southeastern Chinese coast are genetically diverse with circulation of clonal complex 3 strains since 2002

Multilocus sequence typing (MLST) was used to examine the clonal relationship and genetic diversity of 71 Vibrio parahaemolyticus isolates from clinical and seafood-related sources in southeastern Chinese coast between 2002 and 2009. The tested isolates fell into 61 sequence types (STs). Of 17 clinical isolates, 7 belonged to ST3 of the pandemic clonal complex 3, with 3 strains isolated in 2002. Although there was no apparent clonal relationship found between clinical strains and those from seafood-related sources positive with pathogenic markers, there were clonal relationships between clinical strains from this study and those from environmental sources in other parts of China. Phylogenetic analysis showed that strains of 112 STs (61 STs from this study and 51 retrieved from PUBMLST database covering different continents) could be divided into four branches. The vast majority of our isolates and those from other countries were genetically diverse and clustered into two major branches of mixed distribution (of geographic origins and sample sources), whereas five STs representing six isolates split as two minor branches because of divergence of their recA genes, which had 80%-82% nucleotide identity to typical V. parahaemolyticus strains and 73.3%-76.9% identity to the CDS24 of a Vibrio sp. plasmid p23023, indicating that the recA gene might have recombined by lateral gene transfer. This was further supported by a high ratio of recombination to mutation (3.038) for recA. In conclusion, MLST with fully extractable database is a powerful system for analysis of clonal relationship for strains of a particular region in a national or global scale as well as between clinical and environmental or food-related strains.     

Population Structure and Antimicrobial Resistance of Invasive Serotype IV Group B Streptococcus,Toronto, Ontario,Canada

We recently showed that 37/600 (6.2%) invasive infections with group B Streptococcus (GBS) in Toronto, Ontario, Canada, were caused by serotype IV strains. We report a relatively high level of genetic diversity in 37 invasive strains of this emerging GBS serotype. Multilocus sequence typing identified 6 sequence types (STs) that belonged to 3 clonal complexes. Most isolates were ST-459 (19/37, 51%) and ST-452 (11/37, 30%), but we also identified ST-291, ST-3, ST-196, and a novel ST-682. We detected further diversity by performing whole-genome single-nucleotide polymorphism analysis and found evidence of recombination events contributing to variation in some serotype IV GBS strains. We also evaluated antimicrobial drug resistance and found that ST-459 strains were resistant to clindamycin and erythromycin, whereas strains of other STs were, for the most part, susceptible to these antimicrobial drugs.     

2008 - 2014年北京市山夫登堡沙门菌耐药性及分子流行病学特征分析

目的 分析北京市2008 - 2014年山夫登堡沙门菌临床分离株的分子流行病学特征。方法 对从腹泻病例分离到的91株山夫登堡沙门菌进行药敏试验、脉冲场凝胶电泳（PFGE）分子分型及多位点序列分型（MLST）。结果 2011 -2012年山夫登堡沙门菌在北京地区高水平流行,占所有分离株的87.9%,2008 - 2010年,2013 - 2104年各年份高度散发,病例主要集中在20～59岁成人组,5 - 6月为发病高峰;所有菌株对萘啶酸有较高耐药性（76.9%）,对磺胺异噁唑（53.9%）和链霉素（49.5%）中度耐药,对其他抗菌药物均较敏感;PFGE分型将91株腹泻株分成23种型别,形成三大克隆群,引起2011 - 2012年暴发流行的64株菌形成绝对优势克隆株;42株菌的MLST分型结果显示包括暴发流行在内的绝大多数菌株属于常见型ST14,5株散发菌株为新型ST1923。结论 北京市山夫登堡沙门菌具有明显的克隆株优势带型,引起2011 - 2012年的本地流行,对抗生素敏感性较高。     

Antimicrobial susceptibility, serotype and genotype distribution of meningococci in Portugal, 2001-2002

One hundred and eighteen Neisseria meningitidis isolates were recovered from patients with invasive meningococcal disease in Portugal, over one year. Our study was undertaken to evaluate antimicrobial susceptibility, serogroup, serotype and genotype of isolates. One quarter (24.6%) of the isolates showed moderate resistance to penicillin and 47.4% were resistant to sulphadiazine. The two most common serosubtypes were C:2b:P1.5,2 (31.3%) and B:4:P1.15 (3.4%). Half (53.6%) of the isolates with moderate resistance to penicillin were phenotype C:2b:P1.5,2 (n=14), C:2b:P1.2 (n=1) or C:2b:NST (n=1); Pulsed-field gel electrophoresis (PFGE) showed that all these isolates were genetically related. Multilocus sequence typing (MLST) analysis of representative clones from each PFGE pattern showed the predominance of the ST-8 complex/cluster A4 among N. meningitidis with moderate resistance to penicillin. This clonal complex has been principally found in Southern Europe. The apparent emergence and dissemination of the hypervirulent ST-8 complex/cluster A4 among serogroup C strains increases the need for a continued surveillance of antimicrobial susceptibility of meningococci and of genotypic markers in Portugal.     

河北省19F型和19A型侵袭性肺炎链球菌耐药性分析及多位点序列分型分析

目的 了解河北省侵袭性肺炎链球菌(Streptococcus pneumoniae,Spn)19F型和19A型的耐药特征及多位点序列分型(multilocus sequence type,MLST)分布.方法 19F 型和 19A 型采用多重聚合酶链式反应(multiplex polymerase chain reac...     

人源与动物源大肠埃希菌的同源性分析

目的研究某大规模养殖场与某院临床患者分离的大肠埃希菌的同源性。方法泰安地区某大规模养殖场分离出4株耐多粘菌素大肠埃希菌,泰安中心医院临床患者分离出12株耐碳青霉烯类大肠埃希菌;对目的菌株进行耐药基因测序,通过多位点序列分型(MLST)和脉冲场凝胶电泳(PFGE)进行同源性检测,探讨分析人源与鸭源大肠埃希菌的同源性。结果共有16株大肠埃希菌,4株鸭源菌株中2株ST为5912型;12株人源菌株中5株ST为167型,3株ST为405型;1株鸭源与1株人源ST相同,为ST10,但PFGE分型发现这2株菌相似度为64.7%。结论泰安地区人源与鸭源大肠埃希菌菌株同源性不高。     

Wide geographical distribution of internationally rare Campylobacter clones within New Zealand

During the southern hemisphere winter of 2006 New Zealand experienced a significant increase in the number of reported cases of Campylobacter infection. In total, 112 Campylobacter isolates from eight district health boards (DHBs) located across New Zealand were submitted for PFGE, MLST and Penner serotyping analysis. Distinct clusters of Campylobacter isolates were identified, several of which were composed of isolates from up to five different DHBs located on both the North and South islands of New Zealand. One sequence type, ST-474, was identified in 32 of the 112 isolates and may represent an endemic sequence type present in New Zealand. The spatial pattern of genotypes, combined with the generalized increase in notifications throughout the country is consistent with a common source epidemic, most likely from a source contaminated with the dominant sequence types ST-474 and ST-190 and may also represent widely distributed stable clones present in New Zealand.     

Molecular characteristics of Salmonella enterica Paratyphi A in Yunnan Province,southwest China

Previously, the prevalence of Salmonella enterica Paratyphi A in Yunnan was high; and recently Yunnan was the predominant endemic province in China. To identify the molecular epidemiology, antibiotic resistance profile and genotypic diversity of the S. Paratyphi A isolates from 1995 to 2013 in Yunnan, we performed the study. Antibiotic susceptibility tests, pulse-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to identify the characteristics of the bacterial isolates. The results showed from 1995 to 2013, 366 S. Paratyphi A were isolated: 295 isolates (80.6%) from Yuxi and 68 isolates (18.58%) from Honghe. All of the strains were resistant to nalidixic acid, and some were resistant to ampicillin and trimethoprim/sulfamethoxazole in different years. All the isolates were sensitive to cefotaxime and ciprofloxacin. Identical PFGE with two enzyme digestion patterns were found for 339 isolates. Some environmental isolates in different years were homologous with the strains isolated from food and patients. MLST showed 349 strains were ST85, only 17 isolates were ST129. S. Paratyphi A isolates from Yunnan showed a high similarity, and we found the pathogen isolated from patients, the environment and food had the close epidemiological relationship, forming a transmission circulation. These findings have important implications for paratyphoid-control strategies.     

Genomic characterization of Japanese meningococcal strains isolated over a 17-year period between 2003 and 2020 in Japan

While invasive meningococcal disease (IMD) is a major public concern worldwide, IMD is categorized as a rare infectious disease in Japan and, thus, its causative agents and epidemiology have not yet been characterized in detail. In the present study, we used molecular methods to epidemiologically characterize 291 meningococcal strains isolated in Japan over a 17-year period between 2003 and 2020 by whole genome sequencing (WGS). Serogroup Y meningococci (MenY) were the most abundant, followed by B (MenB) and then C and W among meningococci from IMD patients, while non-groupable as well as MenY and MenB were the most abundant among isolates from healthy carriers. Sequence type (ST) defined by multilocus sequence typing (MLST) showed that ST-1655 and ST-23 belonging to clonal complex (cc) 23 were dominant among Japanese IMD isolates, while ST-11026 (cc32) unique to Japan as well as ST-23 were dominant among Japanese non-IMD isolates. Phylogenetic analyses of ST by MLST revealed that Japanese isolates were classified with 12 ccs, including recently reported cc2057. Phylogenic analyses by WGS showed that isolates of ST-11026 and of ST-1655 were genetically close, whereas ST-23 isolates appeared to be diverse. Moreover, comparisons with other cc11 isolates isolated worldwide indicated that some Japanese cc11 isolates were genetically close to those isolated in Europe and China. An in silico analysis suggested that 14.3 and 44.2% of Japanese MenB were cross-reactive with 4CMenB and rLP2086 MenB vaccines, respectively. The results in the present study revealed that some epidemiological features were unique to Japan.     

Novel Chlamydia trachomatis Strains in Heterosexual Sex Partners,Indianapolis, Indiana,USA

Chlamydia trachomatis causes a high number of sexually transmitted infections worldwide, but reproducible and precise strain typing to link partners is lacking. We evaluated multilocus sequence typing (MLST) for this purpose by detecting sequence types (STs) concordant for the ompA genotype, a single-locus typing standard. We tested samples collected during April 2000–October 2003 from members of established heterosexual partnerships (dyads) in the Indianapolis, Indiana, USA, area who self-reported being coital partners within the previous 30 days. C. trachomatis DNA from 28 dyads was tested by MLST; sequences were aligned and analyzed for ST and phylogenetic relationships. MLST detected 9 C. trachomatis STs, 4 unique to Indianapolis; STs were identical within each dyad. Thirteen unique strains were identified; 9 (32%) dyads harbored novel recombinant strains that phylogenetically clustered with strains comprising the recombinants. The high rate of novel C. trachomatis recombinants identified supports the use of MLST for transmission and strain diversity studies among at-risk populations.     

Development of a multilocus sequence typing (MLST) scheme for Mannheimia haemolytica and assessment of the population structure of isolates obtained from cattle and sheep

Mannheimia haemolytica is an important veterinary pathogen affecting cattle and sheep. Previous typing methods, including restriction enzyme analysis, pulsed-field gel electrophoresis and multilocus enzyme electrophoresis (MLEE) have indicated a clonal population structure. Multilocus sequence typing (MLST) has now almost replaced MLEE and is a definitive and portable typing method, allowing global data exchange. The purpose of this study was to develop a MLST scheme for M. haemolytica. A collection of isolates from 10 countries, including the type strain and reference strains for all recognized serotypes were included in the study. Partial sequences of the housekeeping genes adk, aroE, deoD, gapDH, gnd, mdh and zwf were used to define the MLST scheme. The 95 isolates demonstrated 34 different sequence types (ST) of which 19 were connected in three clonal complexes (CC). ST1 constituted more than one-third of the isolates and was most frequently demonstrated among isolates from bovine sources. The analysis indicated a common evolutionary origin of 33 isolates from the French alps, collected from domestic and wild animals and demonstrating several related STs. An analysis of 17 isolates from the USA demonstrated the same ST in 14 of the isolates. In conclusion, an unambiguous typing scheme is presented for M. haemolytica and results obtained confirm previous observations of a clonal population of the organism.     

Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages

Clostridium difficile is an anaerobic bacillus that resides in the gut and has rapidly emerged as a leading cause of antibiotic associated diarrheal disease in humans. The genetic basis of the pathogenicity of C. difficile remains poorly understood. In this study we aimed at characterizing the genetic diversity of C. difficile strains by three different methods (PCR ribotyping, multilocus sequence typing and genetic markers) to improve the typing of C. difficile. Our study was performed on a reference collection (Leeds–Leiden/ECDC) of C. difficile PCR ribotype (RT) strains (n = 70) expanded with six PCR RT strains highly related to the emerging PCR RTs 027 and 078. Besides PCR ribotyping we used multilocus sequence typing (MLST) using seven housekeeping genes (MLST 7HG) that has recently been developed for characterizing C. difficile isolates as well as analysis of unique genetic markers. Evolutionary relatedness of the sequences determined by MLST 7HG was analyzed in phylogenetic analysis. In total 56 MLST 7HG sequence types (STs) were identified, nine of which were new. Phylogeny reconstruction of the reference set of strains supplemented with the online available C. difficile MLST reference database, revealed six monophyletic lineages of closely related STs. ST-122 (PCR RT131) formed a well-separated branch in the tree and was thus designated as a novel lineage. Furthermore, we confirmed that several PCR RTs are highly related to the emerging PCR RTs 027 and 078 since these types display the same STs (ST-1 and ST-11, respectively). Based on the observed results, we conclude that MLST 7HG is a valuable method to study C. difficile phylogeny.     

纹带棒状杆菌多位点序列分型及应用

目的 建立纹带棒状杆菌的多位点序列分型（MLST）方法,探讨临床分离纹带棒状杆菌的种群结构和遗传进化关系。方法 筛选出7个管家基因（gyrA、gyrB、hsp65、sodA、secA1、rpoB、16S rRNA）,设计引物并进行PCR扩增和测序,测序所得序列通过SeqMan软件进行拼接。采用DnaSP 5.10.01软件、Splits tree 4.14.2软件对管家基因的多样性及基因重组特征进行评价;采用MEGA 7.0.14软件基于序列型别（ST）采用M-L法构建系统发育树,采用BioNumerics软件基于ST特征值构建最小生成树,并用eBURST软件分析ST间遗传进化关系。结果 所选的7个位点在所有试验菌株中均获得了预期的扩增产物;Splits tree表明所有纹带棒状杆菌的聚类一致,提示基因重组是推动纹带棒状杆菌进化的潜在动力;MLST将344株纹带棒状杆菌分成72个STs,85.7%的菌株形成克隆复合体（CC）结构,CC19形成了优势克隆复合体,但包含菌株数最多的ST为该克隆复合体中的ST16。ST具有一定的地域聚集性且与分离年份具有一定的相关性。结论 我国纹带棒状杆菌呈现高度的遗传多样性,CC19为优势克隆复合体。本研究建立的MLST分型方案可用于纹带棒状杆菌的分型,但尚需优化改进。     

肺炎克雷伯菌脉冲场凝胶电泳及多位点序列分型技术的联合应用

目的 联合使用脉冲场凝胶电泳(PFGE)及多位点序列分型(MLST)对肺炎克雷伯菌进行分型研究.方法 参照美国疾病预防控制中心及亚太地区PulseNet提供的PFGE相关标准化操作程序,优化相关电泳条件,对某儿童医院于2005-2006年分离到的59株菌分型分析,对其中高度相似性菌株进行MLST分型分析.结果 59株菌经PFGE分型分析,可分成47个PFGE型,19个PFGE群,具有高度相似性的菌株经MLST分型,其型别分别为ST-340、ST-342、ST-343、ST-344、ST-345,其中ST-342、ST-343、ST-344、ST-345为MLST数据库中中国新发现的ST型.结论 具有PFGE高度相似性的肺炎克雷伯菌可以通过MLST进一步确认或区分.