scholarly journals The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins

2015 ◽  
Vol 81 (14) ◽  
pp. 4774-4781
Author(s):  
Min Zhang ◽  
Xiaomin Hang ◽  
Jing Tan ◽  
Hong Yang
Keyword(s):  
Multilocus Sequence Typing ◽  
Twin Pair ◽  
Bifidobacterium Longum ◽  
Host Genotype ◽  
Content Type ◽  
Living Together ◽  
Adult Twins ◽  
The Impact ◽  
Mz Twins ◽  
Sequence Types

ABSTRACTTo investigate the influences of host genotype and environment onBifidobacterium longumsubsp.longuminhabiting human intestines at the strain level, six pairs of twins, divided into two groups (children and adults), were recruited. Each group consisted of two monozygotic (MZ) twin pairs and one dizygotic (DZ) twin pair. Child twins had been living together from birth, while adult twins had been living separately for 5 to 10 years. A total of 345B. longumsubsp.longumisolates obtained from 60 fecal samples from these twins were analyzed by multilocus sequence typing (MLST), and 35 sequence types (STs) were finally acquired. Comparison of strains within and between the twin pairs showed that no strains with identical STs were observed between unrelated individuals or within adult DZ twin pairs. Eight STs were found to be monophyletic, existing within MZ twins and child DZ twins. The similarity of strain types within child cotwins was significantly higher than that within adult cotwins, which indicated that environment was one of the important determinants inB. longumsubsp.longumstrain types inhabiting human intestines. However, although these differences between MZ and DZ twins were observed, it is still difficult to reach an exact conclusion about the impact of host genotype. This is mainly because of the limited number of subjects tested in the present study and the lack of strain types tracing in the same twin pairs from birth until adulthood.

scholarly journals Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Sara Kovanen ◽  
Mirko Rossi ◽  
Mari Pohja-Mykrä ◽  
Timo Nieminen ◽  
Mirja Raunio-Saarnisto ◽  
...  
Keyword(s):  
Host Specificity ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Wild Birds ◽  
Whole Genome ◽  
Mallard Duck ◽  
Content Type ◽  
Game Birds ◽  
Hygienic Measures ◽  
Sequence Types

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

scholarly journals Temporal Variation and Host Association in the Campylobacter Population in a Longitudinal Ruminant Farm Study

2011 ◽  
Vol 77 (18) ◽  
pp. 6579-6586 ◽  
Author(s):  
Emma L. Sproston ◽  
Iain D. Ogden ◽  
Marion MacRae ◽  
John F. Dallas ◽  
Samuel K. Sheppard ◽  
...  
Keyword(s):  
Temporal Variation ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Host Association ◽  
Fecal Samples ◽  
Content Type ◽  
Sheep Farm ◽  
Sequence Types ◽  
Over Time ◽  
Cattle And Sheep

ABSTRACTCampylobacter jejuniandC. coliwere quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the averageCampylobacterconcentrations shed by cattle (600 CFU g−1) and sheep (820 CFU g−1), although sheep did show a significant temporal reduction in the number ofCampylobacterorganisms shed in their feces. A total of 21 different sequence types (STs) (97.7%C. jejuni, 2.3%C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6%C. jejuni, 59.4%C. coli). TheCampylobacterpopulation in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage ofCampylobacterspecies, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of aCampylobacterpopulation on a ruminant farm by identifying the existence of both temporal and between-host variations.

scholarly journals Outbreak of NDM-1-Producing Klebsiella pneumoniae in a Neonatal Unit in Colombia

2013 ◽  
Vol 57 (4) ◽  
pp. 1957-1960 ◽  
Author(s):  
Javier Antonio Escobar Pérez ◽  
Narda María Olarte Escobar ◽  
Betsy Castro-Cardozo ◽  
Ismael Alberto Valderrama Márquez ◽  
Martha Isabel Garzón Aguilar ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
South America ◽  
Molecular Analysis ◽  
Multilocus Sequence Typing ◽  
Sequence Type ◽  
Neonatal Unit ◽  
Content Type ◽  
First Report ◽  
Sequence Types

ABSTRACTSix multiresistant, NDM-1-producingKlebsiella pneumoniaestrains were recovered from an outbreak that affected six neonatal patients in a Colombian hospital. Molecular analysis showed that all of the isolates harbored theblaNDM-1,qnrA, andintI1genes and were clonally related. Multilocus sequence typing showed that the isolates belonged to a new sequence type (ST1043) that was different from the sequence types that had previously been reported. This is the first report of NDM-1-producing isolates in South America.

scholarly journals Prospective Multicenter Study of Carbapenemase-Producing Enterobacteriaceae from 83 Hospitals in Spain Reveals HighIn VitroSusceptibility to Colistin and Meropenem

2015 ◽  
Vol 59 (6) ◽  
pp. 3406-3412 ◽  
Author(s):  
Jesús Oteo ◽  
Adriana Ortega ◽  
Rosa Bartolomé ◽  
Germán Bou ◽  
Carmen Conejo ◽  
...  
Keyword(s):  
Health Concern ◽  
Inclusion Criteria ◽  
Prospective Multicenter Study ◽  
Content Type ◽  
E Coli ◽  
New Finding ◽  
Phenotypic Methods ◽  
The Impact ◽  
Sequence Types

ABSTRACTThe aim of this study was to determine the impact of carbapenemase-producingEnterobacteriaceae(CPE) in Spain in 2013 by describing the prevalence, dissemination, and geographic distribution of CPE clones, and their population structure and antibiotic susceptibility. From February 2013 to May 2013, 83 hospitals (about 40,000 hospital beds) prospectively collected nonduplicateEnterobacteriaceaeusing the screening cutoff recommended by EUCAST. Carbapenemase characterization was performed by phenotypic methods and confirmed by PCR and sequencing. Multilocus sequencing types (MLST) were determined forKlebsiella pneumoniaeandEscherichia coli. A total of 702Enterobacteriaceaeisolates met the inclusion criteria; 379 (54%) were CPE. OXA-48 (71.5%) and VIM-1 (25.3%) were the most frequent carbapenemases, andK. pneumoniae(74.4%),Enterobacter cloacae(10.3%), andE. coli(8.4%) were the species most affected. Susceptibility to colistin, amikacin, and meropenem was 95.5%, 81.3%, and 74.7%, respectively. The most prevalent sequence types (STs) were ST11 and ST405 forK. pneumoniaeand ST131 forE. coli. Forty-five (54.1%) of the hospitals had at least one CPE case. ForK. pneumoniae, ST11/OXA-48, ST15/OXA-48, ST405/OXA-48, and ST11/VIM-1 were detected in two or more Spanish provinces. ST11 isolates carried four carbapenemases (VIM-1, OXA-48, KPC-2, and OXA-245), but ST405 isolates carried OXA-48 only. A wide interregional spread of CPE in Spain was observed, mainly due to a few successful clones of OXA-48-producingK. pneumoniae(e.g., ST11 and ST405). The dissemination of OXA-48-producingE. coliis a new finding of public health concern. According to the susceptibilities determinedin vitro, most of the CPE (94.5%) had three or more options for antibiotic treatment.

scholarly journals Multilocus Sequence Typing Reveals Genetic Diversity of Carbapenem- or Ceftazidime-Nonsusceptible Pseudomonas aeruginosa in China

2013 ◽  
Vol 57 (11) ◽  
pp. 5697-5700 ◽  
Author(s):  
Jingshu Ji ◽  
Jie Wang ◽  
Zhihui Zhou ◽  
Haiping Wang ◽  
Yan Jiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Aeruginosa ◽  
Multilocus Sequence Typing ◽  
Genetic Background ◽  
Drug Resistant ◽  
Content Type ◽  
Novel Alleles ◽  
Sequence Types

ABSTRACTIt is unclear whether the genetic background of drug-resistantPseudomonas aeruginosawas disseminated from a certain clone. Thus, we performed MLST (multilocus sequence typing) of 896P. aeruginosaisolates that were nonsusceptible to imipenem, meropenem, or ceftazidime. This revealed 254 sequence types (STs), including 104 new STs and 34 STs with novel alleles. Thirty-three clonal complexes and 404 singletons were found. In conclusion, drug-resistantP. aeruginosaclones can be developed from diverse genetic backgrounds.

scholarly journals Multilocus Sequence Typing Confirms Wild Birds as the Source of a Campylobacter Outbreak Associated with the Consumption of Raw Peas

2014 ◽  
Vol 80 (15) ◽  
pp. 4540-4546 ◽  
Author(s):  
Patrick S. L. Kwan ◽  
Catherine Xavier ◽  
Monica Santovenia ◽  
Janet Pruckler ◽  
Steven Stroika ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Wild Bird ◽  
Wild Birds ◽  
Molecular Evidence ◽  
Content Type ◽  
Southcentral Alaska ◽  
Control And Prevention ◽  
Human Infections ◽  
Sequence Types ◽  
Bird Feces

ABSTRACTFrom August to September 2008, the Centers for Disease Control and Prevention (CDC) assisted the Alaska Division of Public Health with an outbreak investigation of campylobacteriosis occurring among the residents of Southcentral Alaska. During the investigation, pulsed-field gel electrophoresis (PFGE) ofCampylobacter jejuniisolates from human, raw pea, and wild bird fecal samples confirmed the epidemiologic link between illness and the consumption of raw peas contaminated by sandhill cranes for 15 of 43 epidemiologically linked human isolates. However, an association between the remaining epidemiologically linked human infections and the pea and wild bird isolates was not established. To better understand the molecular epidemiology of the outbreak,C. jejuniisolates (n= 130; 59 from humans, 40 from peas, and 31 from wild birds) were further characterized by multilocus sequence typing (MLST). Here we present the molecular evidence to demonstrate the association of many more humanC. jejuniinfections associated with the outbreak with raw peas and wild bird feces. Among all sequence types (STs) identified, 26 of 39 (67%) were novel and exclusive to the outbreak. Five clusters of overlapping STs (n= 32 isolates; 17 from humans, 2 from peas, and 13 from wild birds) were identified. In particular, cluster E (n= 7 isolates; ST-5049) consisted of isolates from humans, peas, and wild birds. Novel STs clustered closely with isolates typically associated with wild birds and the environment but distinct from lineages commonly seen in human infections. Novel STs and alleles recovered from human outbreak isolates allowed additional infections caused by these rare genotypes to be attributed to the contaminated raw peas.

scholarly journals Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014

2016 ◽  
Vol 82 (14) ◽  
pp. 4363-4370 ◽  
Author(s):  
Antoine Nohra ◽  
Alex Grinberg ◽  
Anne C. Midwinter ◽  
Jonathan C. Marshall ◽  
Julie M. Collins-Emerson ◽  
...  
Keyword(s):  
New Zealand ◽  
Environmental Water ◽  
Water Sources ◽  
Human Infection ◽  
Poultry Meat ◽  
Campylobacter Coli ◽  
Content Type ◽  
The Impact ◽  
Sequence Types ◽  
Clinical Cases

ABSTRACTCampylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in New Zealand.Campylobacter jejuniis the predominant species worldwide, accounting for approximately 90% of human cases, followed byCampylobacter coli. Most studies in New Zealand have focused onC. jejuni; hence, the impact ofC. colistrains on human health is not well understood. The aim of this study was to genotypeC. coliisolates collected in the Manawatu region of New Zealand from clinical cases, fresh poultry meat, ruminant feces, and environmental water sources, between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human disease.Campylobacterisolates were identified by PCR and typed by multilocus sequence typing.C. coliaccounted for 2.9% (n =47/1,601) ofCampylobacterisolates from human clinical cases, 9.6% (n =108/1,123) from poultry, 13.4% (n =49/364) from ruminants, and 6.4% (n =11/171) from water. Molecular subtyping revealed 27 different sequence types (STs), of which 18 belonged to clonal complex ST-828. ST-1581 was the most prevalentC. colisequence type isolated from both human cases (n =12/47) and poultry (n =44/110). When classified using cladistics, all sequence types belonged to clade 1 except ST-7774, which belonged to clade 2. ST-854, ST-1590, and ST-4009 were isolated only from human cases and fresh poultry, while ST-3232 was isolated only from human cases and ruminant sources. Modeling indicated ruminants and poultry as the main sources ofC. colihuman infection.IMPORTANCEWe performed a molecular epidemiological study ofCampylobacter coliinfection in New Zealand, one of few such studies globally. This study analyzed the population genetic structure of the bacterium and included a probabilistic source attribution model covering different animal and water sources. The results are discussed in a global context.

scholarly journals Comparison of Two Multilocus Sequence Typing Schemes for Mycoplasma bovis and Revision of the PubMLST Reference Method

2020 ◽  
Vol 58 (6) ◽  
Author(s):  
Karen B. Register ◽  
Inna Lysnyansky ◽  
Murray D. Jelinski ◽  
William D. Boatwright ◽  
Matthew Waldner ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Reference Method ◽  
Mycoplasma Bovis ◽  
Reproductive Disorders ◽  
Genome Sequences ◽  
Alternative Scheme ◽  
Content Type ◽  
Optimal Replacement ◽  
Continued Use ◽  
Sequence Types

ABSTRACT Mycoplasma bovis causes pneumonia, pharyngitis, otitis, arthritis, mastitis, and reproductive disorders in cattle and bison. Two multilocus sequence typing (MLST) schemes have been developed for M. bovis, with one serving as the PubMLST reference method, but no comparison of the schemes has been undertaken. Although the PubMLST scheme has proven to be highly discriminatory and informative, the recent discovery of isolates missing one of the typing loci, adh-1, raises concern about its suitability for continued use. The goal of our study was to compare the performance of the two MLST schemes and identify a new reference scheme capable of fully typing all isolates. We evaluated 448 isolates from diverse geographic and anatomic sites that collectively represent cattle, bison, deer, and a goat. The discrimination indexes (DIs) for the PubMLST and the alternative scheme are 0.909 (91 sequence types [STs]) and 0.842 (77 STs), respectively. Although the PubMLST scheme outperformed the alternative scheme, the adh-1 locus must be retired from the PubMLST scheme if it is to be retained as a reference method. The DI obtained using the six remaining PubMLST loci (0.897, 79 STs) fails to reach the benchmark recommended for a reference method (0.900), mandating the addition of a seventh locus. Comparative analysis of genome sequences from the isolates used here identified the dnaA locus from the alternative scheme as the optimal replacement for adh-1. This revised scheme, which will be implemented as the new PubMLST reference method, has a DI of 0.914 and distinguishes 88 STs from the 448 isolates evaluated.

scholarly journals High Genetic Diversity among Strains of the Unindustrialized Lactic Acid Bacterium Carnobacterium maltaromaticum in Dairy Products as Revealed by Multilocus Sequence Typing

2014 ◽  
Vol 80 (13) ◽  
pp. 3920-3929 ◽  
Author(s):  
Abdur Rahman ◽  
Catherine Cailliez-Grimal ◽  
Cyril Bontemps ◽  
Sophie Payot ◽  
Stéphane Chaillou ◽  
...  
Keyword(s):  
Population Structure ◽  
Lactic Acid ◽  
Multilocus Sequence Typing ◽  
Dairy Products ◽  
High Genetic Diversity ◽  
Content Type ◽  
Opportunistic Bacteria ◽  
Sequence Types ◽  
Discriminatory Index ◽  
High Diversity

ABSTRACTDairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter.Carnobacterium maltaromaticumis a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makesC. maltaromaticuman interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genesdapE,ddlA,glpQ,ilvE,pyc,pyrE, andleuSwas applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.

scholarly journals Comparing the Utilities of Different Multilocus Sequence Typing Schemes for Identifying Outbreak Strains of Mycobacterium abscessus subsp. massiliense

2019 ◽  
Vol 58 (1) ◽  
Author(s):  
Aristine Cheng ◽  
Hsin-Yun Sun ◽  
Yi-Tzu Tsai ◽  
Shu-Yuan Chang ◽  
Un-In Wu ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Mycobacterium Abscessus ◽  
Unique Sequence ◽  
Content Type ◽  
Subspecies Level ◽  
Simultaneous Identification ◽  
Sequence Types

ABSTRACT Outbreaks of infections by Mycobacterium abscessus, particularly subspecies massiliense, are increasingly reported worldwide. Several multilocus sequence typing (MLST) protocols for grouping international outbreak strains have been developed but not yet directly compared. Using the three-gene (hsp65, rpoB, and secA1), seven-gene (argH, cya, glpK, gnd, murC, pta, and purH) and thirteen-gene (all of the preceding genes plus gdhA, pgm, and pknA) MLST schemes, we identified 22, 38, and 40 unique sequence types (STs), respectively, among a total of 139 nonduplicated M. abscessus isolates. Among subspecies massiliense, three-gene MLST not only clustered all outbreak strains together (in 100% agreement with the seven-gene and thirteen-gene schemes), but it also distinguished between two new STs that would have been grouped together by the seven-gene MLST but were distinct by the thirteen-gene MLST owing to differences in hsp65, rpoB, and pknA. Here, we show that an abbreviated MLST may be useful for simultaneous identification of M. abscessus the subspecies level and screening M. abscessus subsp. massiliense isolates with outbreak potential.

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