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Pathogenicity and phylogenetic analysis of ovine contagious ecthyma virus isolated during a sheeppox outbreak in Morocco

Bamouh Z, Tifrouin I, Elkarhat Z, Abid L, Fellahi S, Elharrak M

Microb Pathog, 2024 Dec;197:107023.
PMID: 39423917 DOI: 10.1016/j.micpath.2024.107023

Contagious ecthyma (CE), also known as ORF is a highly contagious zoonotic viral skin disease that affects humans, sheep, goats and other domesticated and wild animals. As reported here-in, the objective of this study was to investigate a suspected outbreak of both sheeppox and ORF diseases in a sheep herd during the winter of 2020 in Northwest Morocco. The affected sheep showed nodules and proliferative scabby skin lesions around the mouth and hairless area of the body. Samples of skin crust were collected for virus identification and isolation. A virus was isolated in Vero cells, lamb testis and heart cells and the cytopathic effect was characterized by cells aggregation, ballooning, and detachment. Initially, the suspensions of skin crust were positive for sheeppox virus (SPPV) by PCR. Subsequent testing of the isolated virus from skin crust of affected animals indicated that the virus was SPPV-negative and ORFV-positive by PCR. Furthermore, nucleotide sequences of the B2L aligned with reference ORFV isolates for genetic analysis. Phylogenetic analyses results confirmed that the isolated virus was ORFV and that the virus was closely related to ORFV strains isolated in Sudan and Malaysia. In conclusion, this study is the first reported detection of ORFV in Morocco, and therefore, poses as an imminent threat to the health of humans, domestic and wild animals.

Matched MeSH terms: Phylogeny*
Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation

Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM

J Mol Evol, 2024 Dec;92(6):944-963.
PMID: 39549052 DOI: 10.1007/s00239-024-10219-3

Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.

Matched MeSH terms: Phylogeny*
Molecular identification and phylogenetic analysis of Anaplasma marginale and Anaplasma centrale isolated from commercial Mafriwal cattle in Johor, Malaysia

Nur-Amalina N, Nur-Sabrina AM, Muhamad-Ali HAM, Mohammad-Sabri AR, Nor-Azlina AA, Basripuzi NH

Trop Biomed, 2024 Dec 01;41(4):385-391.
PMID: 39876493 DOI: 10.47665/tb.41.S.001

Bovine anaplasmosis is a tick-borne disease in cattle which is mainly caused by Anaplasma marginale and Anaplasma centrale. It poses significant economic burdens and threat on livestock industries worldwide. This study aimed to identify Anaplasma spp. infecting the commercial Mafriwal cattle in Johor, Malaysia and investigate their phylogenetic relationship in the population. In this study, polymerase chain reaction (PCR) targeting the MSP4 gene for A. marginale and the 16s rRNA gene for A. centrale were performed. These assays were conducted on blood samples collected from 242 Mafriwal cattle. BLAST analysis and phylogenetic trees were constructed to analyze the genetic relationships between the Anaplasma spp. The results revealed 57.85% of the sampled population were infected with Anaplasma spp., 21.90% with A. marginale, 9.50% with A. centrale and 26.45% with both A. marginale and A. centrale. BLAST analysis showed 100% similarities between A. marginale sequences from this study and the sequence from a goat in Brazil. Similarly, A. centrale sequences were closely related to strains from tick vector, Rhipicephalus (Boophilus) microplus in Panama with 100% similarity. Phylogenetic analysis confirmed distinct clades for A. marginale and A. centrale, indicating genetic diversity and specific species differentiation. The findings highlight the endemicity of bovine anaplasmosis in Malaysian cattle populations and potential cross-border transmission routes. Moreover, this study provides the first report of A. centrale prevalence in Malaysia, emphasizing the importance of ongoing surveillance and management efforts. Understanding the genetic diversity and species differentiation of these pathogens is crucial for designing effective control strategies and vaccine development. In conclusion, this study enhances our understanding of the prevalence and genetic dynamics of bovine anaplasmosis among Mafriwal cattle in its largest population in Malaysia for better diagnosis and effective control measures.

Matched MeSH terms: Phylogeny*
Fulltext Emergence of non-classical genotype constellations of G9P[8] rotavirus strains in diarrheic children in Sabah, Malaysia

Fong SY, Akari Y, Amit LN, John JL, Chin AZ, Komoto S, et al.

Infect Genet Evol, 2024 Nov;125:105685.
PMID: 39461399 DOI: 10.1016/j.meegid.2024.105685

G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.

Matched MeSH terms: Phylogeny*
Fulltext A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples

Kuo LY, Tang SK, Huang YH, Xie PJ, Chen CW, Chang ZX, et al.

Sci Data, 2024 Dec 02;11(1):1314.
PMID: 39622837 DOI: 10.1038/s41597-024-04161-8

Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.

Matched MeSH terms: Phylogeny*
Eco-phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont

Medeiros ID, Ibáñez A, Arnold AE, Hedderson TA, Miadlikowska J, Flakus A, et al.

Am J Bot, 2024 Dec;111(12):e16441.
PMID: 39639425 DOI: 10.1002/ajb2.16441

PREMISE: Southern Africa is a biodiversity hotspot rich in endemic plants and lichen-forming fungi. However, species-level data about lichen photobionts in this region are minimal. We focused on Trebouxia (Chlorophyta), the most common lichen photobiont, to understand how southern African species fit into the global biodiversity of this genus and are distributed across biomes and mycobiont partners.
METHODS: We sequenced Trebouxia nuclear ribosomal ITS and rbcL of 139 lichen thalli from diverse biomes in South Africa and Namibia. Global Trebouxia phylogenies incorporating these new data were inferred with a maximum likelihood approach. Trebouxia biodiversity, biogeography, and mycobiont-photobiont associations were assessed in phylogenetic and ecological network frameworks.
RESULTS: An estimated 43 putative Trebouxia species were found across the region, including seven potentially endemic species. Only five clades represent formally described species: T. arboricola s.l. (A13), T. cf. cretacea (A01), T. incrustata (A06), T. lynniae (A39), and T. maresiae (A46). Potential endemic species were not significantly associated with the Greater Cape Floristic Region or desert. Trebouxia species occurred frequently across multiple biomes. Annual precipitation, but not precipitation seasonality, was significant in explaining variation in Trebouxia communities. Consistent with other studies of lichen photobionts, the Trebouxia-mycobiont network had an anti-nested structure.
CONCLUSIONS: Depending on the metric used, ca. 20-30% of global Trebouxia biodiversity occurs in southern Africa, including many species yet to be described. With a classification scheme for Trebouxia now well established, tree-based approaches are preferable over "barcode gap" methods for delimiting new species.

Matched MeSH terms: Phylogeny*
Complete genome sequence analysis of the novel bacteriophage PA-1 infecting phytopathogenic Pantoea ananatis in Malaysia

Singh PSS, Toh WK, Lim BH, Wong HL, Loh PC

Arch Virol, 2025 Feb 17;170(3):60.
PMID: 39961917 DOI: 10.1007/s00705-025-06239-z

A novel bacteriophage, PA-1, was isolated using Pantoea ananatis, a bacterium that is responsible for rice leaf blight worldwide, as the host. PA-1 has a linear genome of 46,332 bp with a GC content of 50.55%. It contains 83 protein-encoding genes, and no tRNA-encoding genes were detected. The genome is densely organized, with an average CDS size of 516 bp, and 92.38% of the genome consists of protein-coding regions. Whole-genome sequencing and phylogenetic and morphological analysis showed that PA-1 is a novel phage that is phylogenetically distinct, suggesting that it may represent a new genus within the class Caudoviricetes..

Matched MeSH terms: Phylogeny*
Genetic profile of the whole genome sequence of African swine fever virus from the first outbreak in Malaysian Borneo

Azami MM, Pauzi NAS, Hamdan N, Sidik MR, Tulis AN, Hassan R, et al.

Vet Res Commun, 2025 Jan 15;49(2):77.
PMID: 39809923 DOI: 10.1007/s11259-025-10645-8

African swine fever (ASF), a severe and highly contagious haemorrhagic viral disease of pigs, is becoming a major threat not only in Malaysia but around the world. The first confirmed case of ASF in Malaysia was reported in February 2021. Despite the emergence of ASF in Malaysia, genetic information on this causative pathogen for the local livestock is still limited. This study aimed to genetically characterize the African swine fever virus (ASFV) responsible for the 2021 outbreak in Malaysia. The genome of the ASFV isolated during the first outbreak in Malaysia was analysed as ASFV/Sabah/Malaysia/1160/21 which has 190,594 base pairs, with a nitrogenous bases (GC) content of 40.33% and 195 predicted Open Reading Frames (ORF). The complete genome sequence was compared with other annotated ASFV genomes retrieved from database of National Center for Biotechnology Information (NCBI) to obtain information based on target gene B646L, E183L, intergenic region (IGR) between I73R and I329L (IGRI73R-I329L), EP402R and B602L. The ASFV/Sabah/Malaysia/1160/21 genome had a high similarity percentage to the reference genome, Georgia 2007 and all Southeast Asian strains. Phylogenetic analysis revealed that the ASFV strain belonged to genotype II, serogroup 8, CVR1 and showed high characteristics of IGR variant II based on IGRI73R-I329L. This study expands our understanding of genetic diversity and provides significant insights into the genomic characteristics and variation of ASFV strains that are circulating in Malaysia.

Matched MeSH terms: Phylogeny*
Island geography drives evolution of rattan palms in tropical Asian rainforests

Kuhnhäuser BG, Bates CD, Dransfield J, Geri C, Henderson A, Julia S, et al.

Science, 2025 Mar 14;387(6739):1204-1209.
PMID: 40080567 DOI: 10.1126/science.adp3437

Distributed across two continents and thousands of islands, the Asian tropics are among the most species-rich areas on Earth. The origins of this diversity, however, remain poorly understood. Here, we reveal and classify contributions of individual tropical Asian regions to their overall diversity by leveraging species-level phylogenomic data and new fossils from the most species-rich Asian palm lineage, the rattans and relatives (Arecaceae, Calamoideae). Radiators (Borneo) generate and distribute diversity, incubators (Indochina, New Guinea, and Sulawesi) produce diversity in isolation, corridors (Java, Maluku, Sumatra, and the Thai-Malay Peninsula) connect neighboring regions, and accumulators (Australia, India, Palawan, and the Philippines) acquire diversity generated elsewhere. These contrasting contributions can be explained by differences in region size and isolation, elucidating how the unique island-dominated geography of the Asian tropics drives their outstanding biodiversity.

Matched MeSH terms: Phylogeny*
Fulltext Genome sequence of the hepatitis C virus subtype 6n isolated from malaysia

Ng KT, Lee YM, Al-Darraji HA, Xia X, Takebe Y, Chan KG, et al.

Genome Announc, 2013 Jan;1(1).
PMID: 23409272 DOI: 10.1128/genomeA.00168-12

We report the full genome sequence of hepatitis C virus (HCV) subtype 6n from Kuala Lumpur, Malaysia. Phylogenetic analysis of the isolate 10MYKJ032 suggests that Southeast Asia might be the origin for the HCV subtype 6n and highlights the possible spread of this lineage from Southeast Asia to other regions.

Matched MeSH terms: Phylogeny
Fulltext A taxonomic study on the genus Ettchellsia Cameron, with descriptions of three new species (Hymenoptera, Megalyridae, Dinapsini)

Mita T, Shaw SR

Zookeys, 2012.
PMID: 23378818 DOI: 10.3897/zookeys.254.4182

Three new species of Ettchellsia Cameron, namely, Ettchellsia ignitasp. n. from Peninsular Malaysia and Borneo, Ettchellsia nigripessp. n. from Sulawesi and Ettchellsia reidisp. n. from Borneo are described and illustrated. A key to the species of Ettchellsia is provided based on females.

Matched MeSH terms: Phylogeny
Fulltext A glance at molecular identification of bamboo (poaceae: bambusoideae)

Nabilah Mohamad Khairi, Wilson Thau Lym Yong, Julius Kulip, Kenneth Francis Rodrigues

Borneo International Journal of Biotechnology, 2020;1(1):19-33.
MyJurnal

Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.

Matched MeSH terms: Phylogeny
On the taxonomic status of Asthenodipsas vertebralis (Boulenger, 1900) (Squamata: Pareidae) in Borneo with the description of a new species

Quah ESH, Lim KKP, Grismer LL

Zootaxa, 2021 Mar 24;4949(1):zootaxa.4949.1.2.
PMID: 33756993 DOI: 10.11646/zootaxa.4949.1.2

The taxonomic status of Asthenodipsas vertebralis in Borneo has been plagued with uncertainty over the last eighty years. An examination of museum collections resulted in the discovery of a voucher specimen of A. vertebralis from Sarawak, East Malaysia that confirms the presence of the species in Borneo and a previously unrecognised species, Asthenodipsas ingeri sp. nov. from Mount Kinabalu, Sabah. Asthenodipsas ingeri sp. nov. can be differentiated from its congeners by the combination of an absence of preoculars and suboculars, 1st and 3rd pair of infralabials in contact, two pairs of posterior inframaxillaries, supralabials 3-5 (sometimes 3 4) in contact with orbit, 15/15/15 rows of dorsal scales, presence of sharp vertebral keel, and divided subcaudals. This study highlights the importance of careful re-examination of museum collections that could potentially harbour new species hiding in plain sight. These discoveries also add to the growing number of reptile and amphibian species being described from Borneo that shows no signs of abating but are already potentially threatened by the continued deforestation and developments on the island.

Matched MeSH terms: Phylogeny
A new Occidozyga from Sarawak, Malaysian Borneo (Anura: Dicroglossidae)

Matsui M, Nishikawa K, Eto K, Hamidy A, Hossman Y, Fukuyama I

Zootaxa, 2021 Feb 10;4926(4):zootaxa.4926.4.4.
PMID: 33756730 DOI: 10.11646/zootaxa.4926.4.4

We found a uniquely colored dicroglossid frog of the genus Occidozyga from western Sarawak, East Malaysia. It is divergent from other congeners in morphology and mtDNA sequences. In a molecular phylogeny, this species is the sister lineage to the continental species O. lima and O. martensii with weak support. The species is small with SVL 16-18 mm in males and 18-19 mm in females, without dorsolateral fold but with transverse wrinkles on dorsum, tips of fingers lacking disks but of toes with disks, only first and second toes webbed to disks, and orange-brown dorsum with dark brown band. We thus describe it as a new species.

Matched MeSH terms: Phylogeny
Purification, biochemical characterisation and bioinformatic analysis of recombinant farnesol dehydrogenase from Theobroma cacao

Satyaveanthan MV, Suhaimi SA, Ng CL, Muhd-Noor ND, Awang A, Lam KW, et al.

Plant Physiol Biochem, 2021 Apr;161:143-155.
PMID: 33588320 DOI: 10.1016/j.plaphy.2021.01.050

The juvenile hormones (JH) in plants are suggested to act as a form of plant defensive strategy especially against insect herbivory. The oxidation of farnesol to farnesoic acid is a key step in the juvenile hormone biosynthesis pathway. We herein present the purification and characterisation of the recombinant Theobroma cacao farnesol dehydrogenase enzyme that catalyses oxidation of farnesol to farnesal. The recombinant enzyme was purified to apparent homogeneity by affinity chromatography. The purified enzyme was characterised in terms of its deduced amino acid sequences, phylogeny, substrate specificity, kinetic parameters, structural modeling, and docking simulation. The phylogenetic analysis indicated that the T. cacao farnesol dehydrogenase (TcFolDH) showed a close relationship with A. thaliana farnesol dehydrogenase gene. The TcFolDH monomer had a large N-terminal domain which adopted a typical Rossmann-fold, harboring the GxxGxG motif (NADP(H)-binding domain) and a small C-terminal domain. The enzyme was a homotrimer comprised of subunits with molecular masses of 36 kDa. The TcFolDH was highly specific to NADP+ as coenzyme. The substrate specificity studies showed trans, trans-farnesol was the most preferred substrate for the TcFolDH, suggesting that the purified enzyme was a NADP+-dependent farnesol dehydrogenase. The docking of trans, trans-farnesol and NADP+ into the active site of the enzyme showed the important residues, and their interactions involved in the substrate and coenzyme binding of TcFolDH. Considering the extensive involvement of JH in both insects and plants, an in-depth knowledge on the recombinant production of intermediate enzymes of the JH biosynthesis pathway could help provide a potential method for insect control.

Matched MeSH terms: Phylogeny
Fulltext An Overview of the Genetic Variations of the SARS-CoV-2 Genomes Isolated in Southeast Asian Countries

Yap PSX, Tan TS, Chan YF, Tee KK, Kamarulzaman A, Teh CSJ

J Microbiol Biotechnol, 2020 Jul 28;30(7):962-966.
PMID: 32627759 DOI: 10.4014/jmb.2006.06009

Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.

Matched MeSH terms: Phylogeny
Precipitation Impacts Dissemination of Three Sooty Blotch and Flyspeck Taxa on Apple Fruit

Rosli H, Batzer JC, Hernández E, Beruski G, Dixon PM, Gleason ML

Plant Dis, 2020 Sep;104(9):2398-2405.
PMID: 32689919 DOI: 10.1094/PDIS-11-19-2340-RE

The spatial dissemination of three prevalent taxa of sooty blotch and flyspeck (SBFS) fungi under several levels of precipitation was compared during 2015 and 2016 in an Iowa apple orchard. Overhead irrigation was used to supplement ambient precipitation in order to insure SBFS spore dissemination and colony development. There were five irrigation levels, involving 1-min-long periods of irrigation that were imposed either once or twice per hour at intervals of 3, 6, or 12 h, as well as a nonirrigated control. Preselected apple fruit were inoculated with one of the three SBFS taxa to serve as sources of inoculum. Dissemination from these inoculated apple fruit was assessed at harvest by counting SBFS colonies on water-sprayed and nontreated fruit. As a further control, additional fruit were enclosed in fruit bags throughout the fruit development period. In both 2015 and 2016, the number of colonies of the SBFS fungus Peltaster gemmifer per apple increased sharply as the duration of irrigation increased, whereas the number of colonies of Microcyclosporella mali increased to a lesser extent and Stomiopeltis sp. RS1 showed no increase. In 2015, the linear relationship between the duration of irrigation-imposed precipitation levels and the number of colonies on the water-sprayed apple fruit was similar for P. gemmifer (slope = 0.09), Stomiopeltis sp. RS1 (slope = 0.07), and Microcyclosporella mali (slope = 0.13); whereas, in 2016, the slope was higher for P. gemmifer (0.28) than for Stomiopeltis sp. RS1 (-0.09) or M. mali (0.06). The results indicated that dissemination of P. gemmifer increased sharply in response to increased irrigation-imposed precipitation, and that dissemination patterns differed considerably among the three SBFS taxa. The apparent advantage of P. gemmifer in precipitation-triggered dissemination may stem from its ability to produce spores rapidly by budding. To our knowledge, this is the first article to assess splash dispersal by SBFS fungi in the field and the first to document taxon-specific patterns of dissemination in this pathogen complex.

Matched MeSH terms: Phylogeny
Fulltext Mitochondrial genomes and phylogenetic relationships of Lates japonicus, Lates niloticus, and Psammoperca waigiensis (Perciformes: Latidae)

Gan HM, Takahashi H, Hammer MP, Tan MH, Lee YP, Voss JM, et al.

Mitochondrial DNA B Resour, 2017 Feb 06;2(1):73-75.
PMID: 33473721 DOI: 10.1080/23802359.2017.1285206

The complete mitochondrial genomes of four fish species of the commercially important family Latidae were sequenced using the Illumina MiSeq, thereby significantly increasing the mitogenomic resources for the family. Whole mitogenome-based phylogenetic analysis supports the monophyly of the genus Lates and more generally the family Latidae. The mitogenome sequences from this study will be useful for future assessments of the diversity within and between Lates species and studies of phylogenetic relationships within the diverse and taxonomically challenging perciform fishes.

Matched MeSH terms: Phylogeny
Phylogenomic Analysis Supports Two Possible Origins for Latin American Strains of Vibrio parahaemolyticus Associated with Acute Hepatopancreatic Necrosis Disease (AHPND)

González-Gómez JP, Soto-Rodriguez S, López-Cuevas O, Castro-Del Campo N, Chaidez C, Gomez-Gil B

Curr Microbiol, 2020 Dec;77(12):3851-3860.
PMID: 32959087 DOI: 10.1007/s00284-020-02214-w

Acute hepatopancreatic necrosis disease (AHPND) is a severe disease affecting recently stocked cultured shrimps. The disease is mainly caused by V. parahaemolyticus that harbors the pVA1 plasmid; this plasmid contains the pirA and pirB genes, which encode a delta-endotoxin. AHPND originated in China in 2009 and has since spread to several other Asian countries and recently to Latin America (2013). Many Asian strains have been sequenced, and their sequences are publicly accessible in scientific databases, but only four strains from Latin America have been reported. In this study, we analyzed nine pVA1-harboring V. parahaemolyticus sequences from strains isolated in Mexico along with the 38 previously available pVA1-harboring V. parahaemolyticus sequences and the reference strain RIMD 2210633. The studied sequences were clustered into three phylogenetic clades (Latin American, Malaysian, and Cosmopolitan) through pangenomic and phylogenomic analysis. The nucleotide sequence alignment of the pVA1 plasmids harbored by the Asian and Latin American strains confirmed that the main structural difference in the plasmid between the Asian and Latin American strains is the absence of the Tn3 transposon in the Asian strains; in addition, some deletions in the pirAB region were found in two of the Latin American strains. Our study represents the most robust and inclusive phylogenomic analysis of pVA1-harboring V. parahaemolyticus conducted to date and provides insight into the epidemiology of AHPND. In addition, this study highlights that disease diagnosis through the detection of the pirA and pirB genes is an inadequate approach due to the instability of these genes.

Matched MeSH terms: Phylogeny
Fulltext Whole genome analysis of multidrug-resistant Citrobacter freundii B9-C2 isolated from preterm neonate's stool in the first week

Yap PSX, Ahmad Kamar A, Chong CW, Yap IKS, Teh CSJ

J Glob Antimicrob Resist, 2020 06;21:246-251.
PMID: 32304769 DOI: 10.1016/j.jgar.2020.03.024

BACKGROUND: Resistance to colistin, the last line therapy for infections caused by multidrug-resistant Gram-negative bacteria, represents a major public health threat. Citrobacter freundii B9-C2 which was isolated from the stool of preterm neonate on the first week of life, displayed resistance to almost all major antibiotics, including colistin. Through whole genome sequencing (WGS), we characterised the genome features that underline the antibiotic-resistance phenotype of this isolate.
METHODS: Genome of C. freundii B9-C2 was sequenced on an Illumina MiSeq platform. The assembled genome was annotated and deposited into GenBank under the accession number CP027849.
RESULTS: Multiple antimicrobial resistance genes including blaCMY-66 were identified. Further, the presence of 15 antibiotic efflux pump-encoding resistance genes, including crp, baeR, hns, patA, emrB, msbA, acrA, acrB, emrR, mdtC, mdtB, mdtG, kdpE, mdfA and msrB, were detected and likely to account for the observed cephalosporins, carbapenems, aminoglycosides and monobactams resistance in C. freundii B9-C2. The isolate also presented unique virulence genes related to biofilm formation, motility and iron uptake. The genome was compared to publicly available genomes and it was closely related to strains with environmental origins.
CONCLUSION: To the best of our knowledge, this is the first report of intestinal carriage of colistin-resistant C. freundii from the stool of a neonate in Malaysia. Using genomic analysis, we have contributed to the understanding of the potential mechanism of resistance and the phylogenetic relationship of the isolates with draft genomes available in the public domain.

Matched MeSH terms: Phylogeny

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