Multi-Locus Sequence Typing Analysis of Mycoplasma synoviae Isolates Reveals Unique Sequence Types in China

2021 ◽  
pp. 109101
Author(s):  
Xiaorong Zhang ◽  
Yang Chen ◽  
Di Xie ◽  
Mengjiao Guo ◽  
Shuang Ma ◽  
...  
Keyword(s):  
Unique Sequence ◽  
Multi Locus Sequence Typing ◽  
Mycoplasma Synoviae ◽  
Sequence Types

scholarly journals Wide spread of OXA-48-producing Enterobacteriaceae in Algerian hospitals: A four years’ study

2018 ◽  
Vol 12 (11) ◽  
pp. 1039-1044
Author(s):  
Nadjet Aggoune ◽  
Hassiba Tali Maamar ◽  
Farida Assaous ◽  
Badia Guettou ◽  
Rym Laliam ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Genetic Relationships ◽  
Wide Distribution ◽  
Multi Locus Sequence Typing ◽  
Wide Spread ◽  
Multiple Sequence ◽  
Sequence Types ◽  
Susceptibility Patterns ◽  
Urgent Action

Introduction: The aim of this study was to investigate the presence of carbapenemase-producing Enterobacteriaceae (CPE) in Algerian hospitals and to characterize the molecular types of carbapenemases found. Methodology: During a four years study lasting between 2012 and 2015, 81 strains of Enterobacteriaceae with reduced susceptibility to carbapenems were collected from different hospitals. Carbapenemase genes were detected by PCR. Multi locus sequence typing was used to study genetic relationships between carbapenemase- producing Klebsiella pneumoniae isolates. Results: Among 56 confirmed CPE, blaOXA-48 was detected in 98.21% of isolates. Two isolates co-expressed NDM, and a single one was only an NDM producer. The strains displayed various susceptibility patterns to antibiotics with variable levels of resistance to carbapenems. Multilocus sequence typing (MLST) revealed the presence of multiple sequence types in circulation. Conclusions: This report highlights the wide distribution of several clones of OXA-48-producing Enterobacteriaceae in Algeria. Urgent action should be taken to avoid epidemic situations.

scholarly journals Evaluation of a combined Multi-Locus Sequence Typing and Whole-Genome Sequencing Two-step Algorithm for Routine typing of Clostridioides difficile

2020 ◽  
Author(s):  
Mini Kamboj ◽  
Tracy McMillen ◽  
Mustafa Syed ◽  
Hoi Yan Chow ◽  
Krupa Jani ◽  
...  
Keyword(s):  
New York ◽  
Cost Saving ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multi Locus Sequence Typing ◽  
Whole Genome ◽  
Clostridioides Difficile ◽  
Step Algorithm ◽  
Sequence Types ◽  
Bionumerics Software

Multi locus sequence typing (MLST) is a low resolution but rapid genotyping method for Clostridioides difficile. Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing but cost and lack of standardization still limits broad utilization. this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (Hospital A and Hospital B) were selected. WGS single nucleotide polymorphism (wgSNP) were performed using established methods. Sequence types (ST) were determined using PubMLST while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (Hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turn-around time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n=185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs was noted. Two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.

scholarly journals Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

2018 ◽  
Author(s):  
Andrew J. Page ◽  
Jacqueline A. Keane
Keyword(s):  
Error Rates ◽  
Multi Locus Sequence Typing ◽  
Short Read Sequencing ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Standard Tool ◽  
Long Read ◽  
Sequence Types ◽  
Very High

AbstractGenome sequencing is rapidly being adopted in reference labs and hospitals for bacterial outbreak investigation and diagnostics where time is critical. Seven gene multi-locus sequence typing is a standard tool for broadly classifying samples into sequence types, allowing, in many cases, to rule a sample in or out of an outbreak, or allowing for general characteristics about a bacterial strain to be inferred. Long read sequencing technologies, such as from PacBio or Oxford Nanopore, can produce read data within minutes of an experiment starting, unlike short read sequencing technologies which require many hours/days. However, the error rates of raw uncorrected long read data are very high. We present Krocus which can predict a sequence type directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes. It is the only tool which can do this from uncorrected long reads. We tested Krocus on over 600 samples sequenced with using long read sequencing technologies from PacBio and Oxford Nanopore. It provides sequence types on average within 90 seconds, with a sensitivity of 94% and specificity of 97%, directly from uncorrected raw sequence reads. The software is written in Python and is available under the open source license GNU GPL version 3.

scholarly journals Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5233 ◽  
Author(s):  
Andrew J. Page ◽  
Jacqueline A. Keane
Keyword(s):  
Error Rates ◽  
Multi Locus Sequence Typing ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Standard Tool ◽  
Sample Data ◽  
Long Read ◽  
Sequence Types ◽  
Very High

Genome sequencing is rapidly being adopted in reference labs and hospitals for bacterial outbreak investigation and diagnostics where time is critical. Seven gene multi-locus sequence typing is a standard tool for broadly classifying samples into sequence types (STs), allowing, in many cases, to rule a sample out of an outbreak, or allowing for general characteristics about a bacterial strain to be inferred. Long-read sequencing technologies, such as from Oxford Nanopore, can produce read data within minutes of an experiment starting, unlike short-read sequencing technologies which require many hours/days. However, the error rates of raw uncorrected long read data are very high. We present Krocus which can predict a ST directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes. It is the only tool which can do this from uncorrected long reads. We tested Krocus on over 700 isolates sequenced using long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore. It provides STs for isolates on average within 90 s, with a sensitivity of 94% and specificity of 97% on real sample data, directly from uncorrected raw sequence reads. The software is written in Python and is available under the open source license GNU GPL version 3.

scholarly journals Comparative phylogenetic analysis of Neisseria gonorrhoeae clinical isolates in Russia, European Union, and Japan

2020 ◽  
pp. 5-13 ◽  
Author(s):  
B.L. Shaskolskiy ◽  
I.D. Kandinov ◽  
A.V. Chestkov ◽  
V.S. Solomka ◽  
A.A. Kubanov ◽  
...  
Keyword(s):  
European Union ◽  
Phylogenetic Analysis ◽  
Neisseria Gonorrhoeae ◽  
Population Size ◽  
Multidrug Resistant ◽  
Unique Sequence ◽  
European Countries ◽  
Clinical Isolates ◽  
Significance Level ◽  
Sequence Types

Surveillance of multidrug-resistant infections is a priority task for contemporary epidemiology. The aim of this study was to genotype modern clinical isolates of N. gonorrhoeae using the NG-MAST technique (Neisseria gonorrhoeae multi-antigen sequence typing) and to compare the phylogeny of the gonococcal pathogens coming from Russia, European Union and Japan. We studied a total of 822 isolates collected in Russia from 2013 through 2018. We also used NG-MAST data from the following databases: PathogenWatch (European Union, 1,071 isolates) and PubMLST (Japan, 206 isolates). Russian isolates represented 301 different NG-MAST types. The most common were types 807, 228, 1993, 5714, and 9476 (8.3%, 3.3%, 3.2%, 3.2%, and 2.7%, respectively). There were only 3 isolates (0.4%) from Russia that represented the epidemiologically significant sequence type 1407 prevailing in many countries and characterized by multiple determinants of antimicrobial resistance. A phylogenetic tree for the NG-MAST types found in Russia and European countries was constructed. The cluster analysis of the proportion of isolates belonging to unique sequence types and the country population size allowed us to identify 2 clusters (significance level — 0.01): the first cluster included Russia and Japan, the second, European countries. A distribution pattern was identified for unique sequence types: the greater is the population size, the higher is their proportion. The phylogenetic analysis demonstrated a genetic distance between the most common Russian, European and Japanese sequence types, suggesting that the Russian population of N. gonorrhoeae has been evolving relatively locally.

scholarly journals Genotyping genetically heterogeneousCyclospora cayetanensisinfections to complement epidemiological case linkage

Parasitology ◽  
2019 ◽  
Vol 146 (10) ◽  
pp. 1275-1283 ◽  
Author(s):  
Joel L. N. Barratt ◽  
Subin Park ◽  
Fernanda S. Nascimento ◽  
Jessica Hofstetter ◽  
Mateusz Plucinski ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Unique Sequence ◽  
Classification Algorithms ◽  
Cyclospora Cayetanensis ◽  
New Methods ◽  
Trace Back ◽  
Sequence Types

AbstractSexually reproducing pathogens such asCyclospora cayetanensisoften produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness ofC. cayetanensisinfections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containingC. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P< 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of cyclosporiasis.

Molecular characterization of Staphylococcus aureus in Lebanon

2010 ◽  
Vol 138 (5) ◽  
pp. 707-712 ◽  
Author(s):  
S. T. TOKAJIAN ◽  
P. ABOU KHALIL ◽  
D. JABBOUR ◽  
M. RIZK ◽  
M. J. FARAH ◽  
...  
Keyword(s):  
Public Health ◽  
Staphylococcus Aureus ◽  
Molecular Characterization ◽  
Protein A ◽  
Multi Locus Sequence Typing ◽  
Health Concern ◽  
Human Pathogen ◽  
Public Health Concern ◽  
Sequence Types

SUMMARYStaphylococcus aureus is an important human pathogen and is a growing public health concern. In this study, 130 S. aureus, 93 methicillin-resistant S. aureus (MRSA) and 37 methicillin-sensitive S. aureus (MSSA), clinical isolates recovered from Lebanon were typed by protein A gene (spa) sequencing and multi-locus sequence typing (MLST). Forty-eight different spa types were identified and clustered into 30 different groups. MLST revealed 10 sequence types (STs) among the isolates. There were eight major MRSA clones defined as isolates with the same ST and the same SCCmec type. The majority of the PVL-positive isolates (53%) were ST80-MRSA-IVc. Systematic surveillance of both hospital and community isolates in Lebanon together with measures designed to limit the spread are required.

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.

scholarly journals Opa-typing can identify epidemiologically distinct subgroups within Neisseria gonorrhoeae multi-antigen sequence type (NG-MAST) clusters

2007 ◽  
Vol 136 (3) ◽  
pp. 417-420 ◽  
Author(s):  
A. K. MORRIS ◽  
H. M. PALMER ◽  
H. YOUNG
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Geographical Location ◽  
Unique Sequence ◽  
Sequence Type ◽  
Sexual Preference ◽  
Surveillance Data ◽  
Sequence Types

SUMMARYA collection of 106 Neisseria gonorrhoeae ciprofloxacin-resistant isolates were typed using Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST). Opa-typing was performed on 74 isolates which had non-unique sequence types to determine if further discrimination could be achieved and if so whether this had any epidemiological basis. The 74 isolates were separated into 12 sequence types and 20 opa-types (OT). Seven opa-type clusters were congruent with the sequence types and five sequence types could be subdivided by opa-typing. These results demonstrate that opa-typing can add a further level of discrimination compared with NG-MAST. The surveillance data for isolates in the largest sequence type cluster (ST 147) indicated that two major subdivisions OT 1 and OT 2 differed epidemiologically by patients' sexual preference and geographical location. ST 147 is a common strain that has been isolated in several countries since 1999; our results suggest that it has diverged into at least two epidemiologically discrete forms.

scholarly journals Multi-locus sequence types of Mycoplasma bovis isolated from Ontario, Canada in the past three decades have a temporal distribution

2017 ◽  
Vol 30 (1) ◽  
pp. 130-135 ◽  
Author(s):  
Patricia Bell-Rogers ◽  
Lois Parker ◽  
Hugh Y. Cai
Keyword(s):  
Sequence Analysis ◽  
Molecular Typing ◽  
Sequence Variation ◽  
Sequence Data ◽  
Temporal Distribution ◽  
Housekeeping Genes ◽  
Multi Locus Sequence Typing ◽  
Mycoplasma Bovis ◽  
The Past ◽  
Sequence Types

A total of 217 Mycoplasma bovis isolates cultured from clinical cases in Ontario, Canada, over the past 30 y were selected to be characterized by a multi-locus sequence typing (MLST) method. Eleven housekeeping genes were evaluated for suitability for MLST; 2 loci that had been used in prior MLST schemes, dnaN and metS, along with hsp70 were chosen for further sequence analysis. The remaining loci— adk, efp, gmk, gyrB, polC, rpoB, tpiA, and uvrC genes—were not used because they had little to no sequence variation. The sequence data from the chosen loci ( dnaN, hsp70, metS) generated 28 sequence types (STs), with the 3 loci having 15, 5, and 7 alleles, respectively. These molecular typing results revealed that the STs had a temporal distribution; over the course of 3 decades, some STs disappeared and new STs appeared. Recent isolates had a greater variety of STs, which may indicate that new strains are emerging more rapidly now than in the past.

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