Novel genotypes of Leptospira interrogans serogroup Sejroe isolated from human patients in Okinawa Prefecture, Japan

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of Leptospira species. It is a public health issue in the tropics, including Okinawa, the southernmost prefecture of Japan. This study reports the first isolation of L. interrogans serogroup Sejroe from two human patients in Japan, and describes its molecular characterization using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). MLST on the two isolates, 168036 and 178129, showed that pfkB in 178129 is a novel allele, and that both isolates constitute novel sequence types (STs); ST286 for 168036 and ST287 for 178129. A minimum spanning tree based on seven alleles of L. interrogans indicates that both isolates are genetically close, but are distinct from known L. interrogans serogroup Sejroe strains. MLVA using 11 loci demonstrated that seven of the 11 loci were identical between the two isolates, whereas the identity between the isolates and the seven reference strains of L. interrogans serogroup Sejroe was zero to three loci. These results indicate that the isolates investigated in this study have novel genotypes, and are genetically closest to each other among the known L. interrogans serogroup Sejroe strains.

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Population structure and transmission of Mycobacterium bovis in Ethiopia

Microbial Genomics ◽

10.1099/mgen.0.000539 ◽

2021 ◽

Vol 7 (5) ◽

Author(s):

Gizat Almaw ◽

Getnet Abie Mekonnen ◽

Adane Mihret ◽

Abraham Aseffa ◽

Hawult Taye ◽

...

Keyword(s):

Population Structure ◽

Mycobacterium Bovis ◽

Type Species ◽

Clonal Complex ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Good Representation ◽

Long Distance ◽

Content Type ◽

Link Type

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M . bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

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Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004699 ◽

2019 ◽

Vol 71 (3) ◽

Cited By ~ 3

Author(s):

Xue Zhang ◽

Lida Zhang ◽

XiaoYan Yu ◽

Jing Zhang ◽

Yanjie Jiao ◽

...

Keyword(s):

Type Species ◽

Cow Dung ◽

Rrna Gene ◽

Content Type ◽

Mycolic Acids ◽

Link Type ◽

Pr China ◽

Taxonomic Characterization ◽

Reference Strains

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia , with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia , for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).

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Streptomyces barkulensis sp. nov., isolated from an estuarine lake

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.056614-0 ◽

2014 ◽

Vol 64 (Pt_4) ◽

pp. 1365-1372 ◽

Cited By ~ 21

Author(s):

Lopamudra Ray ◽

Samir Ranjan Mishra ◽

Ananta Narayan Panda ◽

Gurdeep Rastogi ◽

Ajit Kumar Pattanaik ◽

...

Keyword(s):

Type Species ◽

Gene Sequence ◽

Novel Species ◽

Threshold Value ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Phyletic Line ◽

Actinomycete Strain ◽

Reference Strains

The taxonomic position of a novel actinomycete, strain RC 1831T, isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Streptomyces . The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with Streptomyces glaucosporus DSM 41689T (98.22 % similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065T (98.40 %), Streptomyces radiopugnans R97 DSM 41901T (98.27 %), Streptomyces fenghuangensis GIMN4.003T (98.33 %), Streptomyces nanhaiensis DSM 41926T (98.13 %), Streptomyces megasporus NBRC 14749T (97.37 %) and Streptomyces macrosporus NBRC 14748T (98.22 %). However, the levels of DNA–DNA relatedness between strain RC 1831T and phylogenetically related strains Streptomyces atacamensis DSM 42065T (28.75±3.25 %) and Streptomyces glaucosporus DSM 41689T (15±2.40 %) were significantly lower than the 70 % threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831T is therefore considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces barkulensis sp. nov. is proposed. The type strain is RC 1831T ( = JCM 18754T = DSM 42082T).

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Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016

Journal of Medical Microbiology ◽

10.1099/jmm.0.001443 ◽

2021 ◽

Vol 70 (11) ◽

Author(s):

Mark Philip Bugayong ◽

Hidemasa Izumiya ◽

Josie M. Bilar ◽

Masatomo Morita ◽

Eiji Arakawa ◽

...

Keyword(s):

Vibrio Cholerae ◽

Type Species ◽

Variable Number Tandem Repeat ◽

The Philippines ◽

Large Chromosome ◽

Content Type ◽

Link Type ◽

Mlva Type ◽

El Tor

Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies. Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines. Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping. Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries. Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.

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Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Microbial Genomics ◽

10.1099/mgen.0.000326 ◽

2020 ◽

Vol 6 (2) ◽

Cited By ~ 1

Author(s):

Ammar Aziz ◽

Bart J. Currie ◽

Mark Mayo ◽

Derek S. Sarovich ◽

Erin P. Price

Keyword(s):

Primary Culture ◽

Type Species ◽

Sputum Sample ◽

Phylogenomic Analysis ◽

Content Type ◽

Transmission Event ◽

Bioinformatic Tools ◽

Link Type ◽

Sequence Types ◽

Polyclonal Infection

Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei , is exceedingly rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing (WGS) to characterize one such unusual B. pseudomallei transmission event, which occurred between a breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types (STs)-259 and -261 were identified in the mother’s sputum from both the primary culture sweep and in purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture sweeps of the mother’s breast milk and the child’s cerebrospinal fluid and blood samples contained only ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no genetic variation between mother and baby isolates, providing the strongest possible evidence of B. pseudomallei human-to-human transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, including the mother’s mixed ST-259/ST-261 sputum sample, was performed to investigate the effects of mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for bacterial mixture identification and strain parsing that avoids these pitfalls.

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Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004413 ◽

2020 ◽

Vol 70 (10) ◽

pp. 5296-5303 ◽

Cited By ~ 4

Author(s):

Kenika Lipun ◽

Wee Fei Aaron Teo ◽

Paweena Suksaard ◽

Wasu Pathom-aree ◽

Kannika Duangmal

Keyword(s):

Dna Hybridization ◽

Type Species ◽

Sequence Similarity ◽

Diaminopimelic Acid ◽

Rrna Gene ◽

Whole Cell ◽

Content Type ◽

Link Type ◽

Diamino Acid ◽

Reference Strains

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).

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Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population

Microbial Genomics ◽

10.1099/mgen.0.000708 ◽

2021 ◽

Vol 7 (11) ◽

Author(s):

Ka Lip Chew ◽

Sophie Octavia ◽

Roland Jureen ◽

Oon Tek Ng ◽

Kalisvar Marimuthu ◽

...

Keyword(s):

Virulence Factors ◽

Type Species ◽

Asian Population ◽

Bioinformatic Analysis ◽

Mycobacterium Abscessus ◽

Phylogenomic Analysis ◽

Pathogenic Potential ◽

Content Type ◽

Link Type ◽

Sequence Types

Mycobacterium abscessus comprises three subspecies: M. abscessus subsp. abscessus , M. abscessus subsp. bolletii , and M. abscessus subsp. massiliense . These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global M. abscessus isolates. Whole-genome-sequencing was performed on M. abscessus isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) M . abscessus subsp. massiliense , 67 (31.9 %) M . abscessus subsp. abscessus, and three (1.4 %) M . abscessus subsp. bolletii . Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 M. abscessus subsp. massiliense , but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.

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gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae

Microbial Genomics ◽

10.1099/mgen.0.000594 ◽

2021 ◽

Vol 7 (6) ◽

Author(s):

Thea G. Fennell ◽

Grace A. Blackwell ◽

Nicholas R. Thomson ◽

Matthew J. Dorman

Keyword(s):

Vibrio Cholerae ◽

Metabolic Pathway ◽

Type Species ◽

Gene Encoding ◽

Natural Competence ◽

Content Type ◽

Metabolic Substrate ◽

Link Type ◽

Reference Strains ◽

Present Experimental Evidence

Members of the bacterial genus Vibrio utilize chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae . We show that the gene encoding GbpA, known to be an important colonization and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae . We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within V. cholerae is more complex than previously thought, and emphasize the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.

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Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000079 ◽

2015 ◽

Vol 65 (Pt_4) ◽

pp. 1193-1198 ◽

Cited By ~ 24

Author(s):

Yanwei Wang ◽

Jinlong Song ◽

Yi Zhai ◽

Chi Zhang ◽

Jacoline Gerritsen ◽

...

Keyword(s):

Cell Wall ◽

Type Species ◽

Saline Lake ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Pr China ◽

Method Analysis ◽

Reference Strains ◽

The 16S Rrna Gene

A Gram-stain-positive, spore-forming, obligately anaerobic bacterium, designated LAM201T, was isolated from sediment samples from an alkaline-saline lake located in Daqing oilfield, Daqing City, PR China. Cells of strain LAM201T were non-motile and straight or spiral rod-shapes. Strain LAM201T was able to utilize glucose, fructose, maltose, trehalose and sorbitol as the sole carbon source. Acetic acid, ethanol, iso-butanoic acid and iso-valeric acid were the main products of glucose fermentation. The major fatty acids of LAM201T were C16 : 0 (26.7 %) and C18 : 0 (11.2 %). The main polar lipids were four unknown glycolipids and five unknown phospholipids. The predominant cell-wall sugars were ribose and galactose. The cell-wall peptidoglycan of strain LAM201T contained alanine, glycine, glutamic acid and aspartic acid. Sodium sulfite was used as the electron acceptor. The G+C content of the genomic DNA was 32±0.8 mol%, as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Romboutsia and was most closely related to Romboutsia lituseburensis DSM 797T and Romboutsia ilealis CRIBT with 97.3 % and 97.2 % similarities, respectively. The DNA–DNA hybridization values between strain LAM201T and the two reference strains were 37 % and 31 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM201T is suggested to represent a novel species within the genus Romboutsia , for which the name Romboutsia sedimentorum sp. nov. is proposed. The type strain is LAM201T ( = ACCC 00717T = JCM 19607T).

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Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population

Microbial Genomics ◽

10.1099/mgen.0.000579 ◽

2021 ◽

Vol 7 (5) ◽

Author(s):

Frédéric Auvray ◽

Alexandre Perrat ◽

Yoko Arimizu ◽

Camille V. Chagneau ◽

Nadège Bossuet-Greif ◽

...

Keyword(s):

Escherichia Coli ◽

Type Species ◽

Whole Genome Sequence ◽

Active Metabolites ◽

Content Type ◽

E Coli ◽

Link Type ◽

Sequence Types ◽

Trna Locus ◽

Integrative And Conjugative Element

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.

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