The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent ...phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae ( Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S . hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.
The Escherichia coli sequence type (ST) 131 C2/H30Rx clade with the blaCTX-M-15 gene had been most responsible for the global dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. ...ST131 C1/H30R with blaCTX-M-27 emerged among ESBL-producing E. coli in Japan during the late 2000s. To investigate the possible expansion of a single clade, we performed whole-genome sequencing for 43 Japan and 10 global ST131 isolates with blaCTX-M-27 (n = 16), blaCTX-M-14 (n = 16), blaCTX-M-15 (n = 13), and others (n = 8). We also included 8 ST131 genomes available in public databases. Core genome-based analysis of 61 isolates showed that ST131 with blaCTX-M-27 from 5 countries formed a distinct cluster within the C1/H30R clade, named C1-M27 clade. Accessory genome analysis identified a unique prophage-like region, supporting C1-M27 as a distinct clade. Our findings indicate that the increase of ESBL-producing E. coli in Japan is due mainly to emergence of the C1-M27 clade.
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bloodstream infection (BSI) isolates from a particular geographic area have been reported to comprise a relatively small number of the major sequence types (STs) by multilocus sequence typing (MLST) ...analysis. Yet little is known about the characteristics of major ST strains of
. To address this question in Korea, we investigated antifungal resistance and non-synonymous mutations of the mismatch repair gene (
mutations) in
BSI isolates, as well as associated clinical characteristics, and compared the results according to MLST genotype. We assessed a total of 209
BSI isolates from seven hospitals in Korea for 2 years (2009 and 2014). Clinical features of candidemia and their outcomes were analyzed for 185 available cases. According to MLST, ST7 (47.8%) was the most common type, followed by ST3 (22.5%); the remainder represented 28 types of minor STs (29.7%). Fluconazole-resistance (FR) rates for ST7, ST3, and other strains were 9.0% (9/100), 8.5% (4/47), and 4.8% (3/62), respectively, and all were susceptible to amphotericin B and micafungin. All ST7 isolates harbored the V239L mutation in
, known to confer hypermutability, while 91.5% of ST3 isolates did not harbor the
mutation. Overall, isolates of the same ST had identical
mutations, with the exception of nine isolates. The
mutations were identified in 68.8% (11/16) of the FR isolates and 67.4% (130/193) of the fluconazole susceptible-dose dependent isolates. There was no significant difference in all clinical characteristics between ST3 and ST7. However, the 30-day mortality of
candidemia due to the two major ST (ST3 or ST7) strains was significantly higher than that of candidemia due to other minor ST strains (45.1 vs. 25.0%,
< 0.05). Multivariate logistic regression analysis also showed that two major STs (ST3 and ST7) were independent predictors of 30-day mortality. This study showed for the first time that two STs (ST7 and ST3) were predominant among BSI isolates in Korea, and that
BSI isolates belonging to two major MLST genotypes are characterized by higher mortality. In addition, most
mutations align with MLST genotype, irrespective of FR.
Acinetobacter spp. are opportunistic pathogens being A. baumannii the most frequently identified in nosocomial settings. A. ursingii was mainly described as causing bacteremia and outbreaks in ...neonatal intensive care units. Ten A. ursingii isolates were recovered from rectal swab screening for carbapenemase-producing bacteria between June 2013 and December 2015 from a children hospital in Argentina. All ten isolates were metallo-β-lactamase-producing, nine were positive for blaIMP-1 and one for blaNDM-1. IMP-positive isolates were also positive for blaOXA-58 gene. All isolates were susceptible to ciprofloxacin, colistin and minocycline, and nine were susceptible to ampicillin-sulbactam and gentamicin. Two A. ursingii displayed high level of resistance to aztreonam associated with blaCTX-M-15 in one isolate, and blaVEB-1 in the other. Eight SmaI-PFGE patterns were recognized. We evaluated the usefulness of Acinetobacter MLST-Pasteur scheme, to analyse A. ursingii isolates, however the rpoB gene was not amplified. A new set of primers were designed for specific amplification and sequencing, allowing the analysis of rpoB gene for this species. New alleles and the sequence types 748, 749, 750, 751, 993, 1186, 1187, and 1189 were included at the Acinetobacter MLST-Pasteur database. Those isolates showing related PFGE patterns were assigned to the same ST. To the best of our knowledge, this is the first report of MBL-producing A. ursingii in Argentina. The inclusion of A. ursingii species to the Acinetobacter MLST-Pasteur scheme allows deeper molecular characterization and a better understanding about the epidemiology of this germen.
•MBL-producing clinical isolates of A. ursingii•blaIMP-1 and blaNDM-1A. ursingii-producing clinical isolates•ESBL-producing A. ursingii•Acinetobacter multilocus sequence-typing•Acinetobacter MLST for A. ursingii
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Klebsiella pneumoniae is an important cause of community-onset pneumonia in Asian countries and South Africa. We investigated the clinical characteristics of K. pneumoniae causing community-onset ...pneumonia, and the associated microbiological features between K. pneumoniae isolates from pneumonia and those from the nasopharynx in Taiwan. This study was conducted at the Taipei Veterans General Hospital during July, 2012 to February, 2014. The clinical characteristics in patients with community-onset K. pneumoniae pneumonia were analyzed. K. pneumoniae isolates from the nasopharynx of adults attending otorhinolaryngology outpatient clinics were collected to compare their microbiological features with those from pneumonia. Capsular genotypes, antimicrobial susceptibility, and multilocus sequence type (MLST) were determined among these strains. Ninety-one patients with community-onset K. pneumoniae pneumonia were enrolled. We found a high mortality (29.7%) among these patients. Capsular types K1, K2, K5, K20, K54, and K57 accounted for ∼70% of the K. pneumoniae isolates causing pneumonia, and ∼70% of all the K. pneumoniae strains isolated from the nasopharynx of patients in outpatient clinics. The MLST profiles further demonstrated the genetic relatedness between most pneumonia isolates and those from the nasopharynx. In conclusion, our results show that community-onset pneumonia caused by K. pneumoniae was associated with high mortality and could have a reservoir in the nasopharynx. To tackle this high-mortality disease, the distribution of capsular types in the nasopharynx might have implications for future vaccine development.
, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as
typing, are vital for the control and, when typing can ...be made more timely, prevention of
spread around healthcare settings. The current study aims to review the literature to report the most common clinical
types around the world, which is important for epidemiological surveys and nosocomial infection control policies.
A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent
types among
isolates. The search terms were "
."
The most prevalent
types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to
type t032 were MRSA. In addition,
type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.
This review documents the presence of the most prevalent
types in countries, continents and worldwide and shows big local differences in clonal distribution.
•Four pathogenic Leptospira from animal origin were characterized by MLST approach.•Eighteen different MLST sequence types (STs) were found (22 new alleles and 11 new STs).•The Leptospira santarosai ...population demonstrated intraspecific variability as high as the interspecific of Leptospira spp.
In the current context of the emergence of certain infectious diseases and discussion of the One Health concept for many of these, the study of leptospirosis – both in domestic and wild hosts – cannot be neglected. The study of animal leptospirosis has evolved in recent years. It has been demonstrated that the human-animal-environment interface is more important than previously thought. In the present study, 35 strains of five pathogenic Leptospira species were isolated from different animal species in Brazil and characterized by rrs, secY, and Multilocus Sequence Typing (MLST) sequencing. Phylogenetic inferences were performed and the molecular diversity of the populations (intra- and inter-population levels) was evaluated. Among the five studied species, 18 different sequence types (STs) were found (22 new alleles and 11 new STs). eBURST analysis revealed two clonal complexes (CCs) and seven singletons. A high genetic diversity was demonstrated (H = 0.954 ± 0.017), mainly for the L. santarosai population (H = 0.942 ± 0.034, n = 20). The same strain was identified in different host species, as well as strains with zoonotic potential circulating in the country. Although the difficulty of culturing Leptospira strains is well known, the high variability of the strains found in Brazil highlights the importance of animals in maintaining the biological cycle of the bacterium in nature. Moreover, the selection of autochthonous strains for the development of vaccines becomes a challenge.
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One hundred and forty two Listeria monocytogenes strains isolated from different food matrices in Switzerland between 2011 and 2014 were characterized with respect to their genotypic and phenotypic ...properties. Analyzed strains originated from various meat, milk, plant-associated food products and production environments as well as from other types of foods including fish, seafood, and ready to eat (RTE) products. The collection included serotype 1/2a (64%), 4b (15%), 1/2c (12%), 1/2b (7%) and 3c (3%). The strains were genetically diverse representing 61 MLST sequence types (ST) including 24 new STs. The most frequent clonal complexes (CC) were CC9 (15%) and CC121 (12%). PCR screening detected presence of the stress survival islet (SSI-1) in 50% of the strains. Phenotypic resistance to benzalkonium chloride (BC) was detected in 18% of the strains. The BC resistance genetic determinants qacH and bcrABC were detected in 80% and 12% of the strains, respectively. Most (n = 129) of the strains isolated from Swiss food matrices exhibited poor biofilm formation capacity and there were no correlations detected between strain serotypes, genotypes and biofilm production.
•142 Listeria monocytogenes strains isolated from various food matrices were characterized.•The collection included serotype 1/2a, 4b, 1/2c, 1/2b and 3c strains.•Strains were genetically diverse representing 61 MLST sequence types.•The most frequent clonal complexes (CC) were CC9 (15%) and CC121 (12%).•Phenotypic resistance to benzalkonium chloride was detected in 18% of the strains.
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•The resolution order of genotyping methods listed below: PFGE = ST_Pasteur < ST_Oxford < CgMLST.•Core-genome MLST will be ideal tool for genotyping and epidemiology of Bacteria.•MLST was not ...suitable tools for genotyping A. baumannii due to the multicopy of gdhB allele.
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a prevalent pathogen contributing to hospital infections. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and core-genome MLST (cgMLST) are frequently used methods to illuminate the nosocomial transmission of CRAB. In this study, we compared the discriminatory power of the three typing methods.
Antimicrobial susceptibility tests were performed by the broth microdilution and Vitek2 methods. PFGE, MLST and cgMLST were conducted to determine the clonality and phylogenetic relationship of the strains. Whole-genome sequence data were acquired by an Illumina HiSeq 2000, and cgMLST was analysed by the Ridom SeqSphere+ v.7.2.3 software.
A total of 149 carbapenem-resistant A. baumannii isolates had 15 different PFGE profiles (A-O type), and 73 of the isolates had related subtypes (A1 and A2), accounting for the majority of type A isolates. The maximum-likelihood phylogenetic analysis based on the cgMLST genes grouped the same PFGE clonal pattern A into nine different clusters. ST_Pasteur grouped all the strains into ST2, whereas ST_Oxford grouped the PFGE clonal pattern A isolates into six STs. In addition, the gdhB allele in the ST_Oxford scheme had two copies in five strains, which complicated the ST_Oxford typing.
cgMLST was more discriminant than PFGE and MLST. CgMLST is the most suitable and comprehensive method for genotyping A. baumannii in surveillance and epidemiological research.
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Recently, pathogenic
Leptospira
culture isolation is an extremely rare phenomenon in Russia.
The aim of our work
was to synthesize the lessons learned at the Irkutsk Anti-Plague Institute from
...Leptospira
culture isolation and identification since 2011.
Materials and methods
. Material from eight individuals with suspected leptospirosis and from 942 small mammals (SM) was examined using PCR and microscopic agglutination test (MAT), from humans and 260 SM, applying bacteriological method. Bacteriological temperature test, MAT, PCR, MLST and MALDI-TOF mass spectrometry with the original
Leptospira
protein profiles base were used to identify cultures. Six complete genomes were generated at the Central Research Institute of Epidemiology of the Rospotrebnadzor.
Results and discussion
. Leptospira have not been isolated from humans against the background of taking antibiotics, despite the positive PCR and MAT results. Four cultures of
Leptospira borgpetersenii
of the
Javanica
serogroup and three
L. kirschneri (Grippotyphosa
) have been isolated from SM. The results of identification using MLST scheme No. 1 and MALDI-TOF MS are identical. MLST in silico has shown the uniformity of two
Grippotyphosa
serogroup strains from Primorie and Khabarovsk with a sequence-type (ST) profile 110:100:94. ST146 is determined in four
Javanica
serogroup strains according to scheme No. 1, and unique single nucleotide polymorphisms are detected according to schemes No. 2–3. Thus, in Siberia and the Far East, between 2012 and 2016, seven pathogenic
Leptospira
cultures were isolated from carriers in natural foci; carrier infection rate being12.0–48.9 %.
Javanica
serogroup strains differ in the MLST profile characteristics and adapt to nutrient media for a longer time than
Grippotyphosa
serogroup strains.
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