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Fulltext Identification and characterization of Burkholderia multivorans CCA53

Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T

BMC Res Notes, 2017 Jul 06;10(1):249.
PMID: 28683814 DOI: 10.1186/s13104-017-2565-1

OBJECTIVE: A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53.
RESULTS: Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

Matched MeSH terms: Multilocus Sequence Typing/methods*
Fulltext Multilocus Sequence Typing Analysis of Invasive and Non-Invasive Group B Streptococcus of Hospital Origin in Malaysia

Ezhumalai M, Muthanna A, Suhaili Z, Dzaraly ND, Amin-Nordin S, Amal MNA, et al.

Malays J Med Sci, 2020 Feb;27(1):134-138.
PMID: 32158353 MyJurnal DOI: 10.21315/mjms2020.27.1.14

The aim of this study was to study the genotype of a hospital collection of Group B Streptococcus (GBS) from invasive and non-invasive sites. Fifty-one pre-characterised human of GBS were re-identified and further analysed by multilocus sequence typing (MLST) in relation to previously published serotypes. Fifteen sequence types (ST) were found with ST1 being the most predominant. ST1 was also associated with majority of the invasive isolates. The genotypic distribution patterns of GBS in this study were largely in agreement with previous reports from other countries indicating the tendency of certain genotypes to prevail in human infection settings.

Matched MeSH terms: Multilocus Sequence Typing
Fulltext Multilocus sequence typing of clinical Burkholderia pseudomallei isolates from Cambodia

Gyamfi E, Delvallez G, Cheng S, Meng S, Oeurn K, Sam C, et al.

PLoS Negl Trop Dis, 2024 Nov;18(11):e0012652.
PMID: 39541393 DOI: 10.1371/journal.pntd.0012652

Melioidosis is a neglected tropical disease caused by Burkholderia pseudomallei, endemic to Southeast Asia and Northern Australia. Despite its increasing global public health and clinical significance, the molecular epidemiology of melioidosis and genetic diversity of B. pseudomallei in Cambodia remains poorly understood. This study aims to elucidate the genetic diversity and antibiotic susceptibility profiles of B. pseudomallei isolates responsible for melioidosis in humans. For this purpose, 14 clinical isolates cryopreserved at the Medical Biology Laboratory at Institut Pasteur du Cambodge from 2016 to 2020 were subjected to antimicrobial susceptibility testing and Multilocus Sequence Typing (MLST). Phenotypic testing revealed that 92.86% (13/14) of the isolates were sensitive to all tested antibiotics, while one isolate exhibited resistance to trimethoprim-sulfamethoxazole. MLST analysis resolved our isolates into 14 unique Sequence Types (STs), including 10 previously documented in Southeast Asia. Notably, ST1858, ST2064, ST2065, and ST2066 were identified as novel STs, while ST54, ST99, ST211, and ST1359 were reported in Cambodia for the first time in this study. Comparing our MLST data with available sequences on PubMLST (n = 165), our study unveiled a high genetic diversity of B. pseudomallei in Cambodia. The identified STs were closely associated with isolates from other Southeast Asian countries, particularly Thailand, Vietnam, and Malaysia. In conclusion, this study provided insight into the genetic diversity among B. pseudomallei clinical isolates in Cambodia and their close genetic association with Southeast Asian isolates. To further our understanding, a One Health approach, incorporating human, environmental (mainly soil), and animal compartments, is essential to decipher the epidemiology of B. pseudomallei in Cambodia.

Matched MeSH terms: Multilocus Sequence Typing*
Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains

Mat Ghani N, Hong KW, Liew YJM, Lau YY, Yong HS, Tee KK, et al.

Pathog Glob Health, 2025;119(1-2):10-21.
PMID: 39699991 DOI: 10.1080/20477724.2024.2442194

Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.

Matched MeSH terms: Multilocus Sequence Typing*
Fulltext Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal Pathogen Scedosporium aurantiacum

Harun A, Kan A, Schwabenbauer K, Gilgado F, Perdomo H, Firacative C, et al.

Front Cell Infect Microbiol, 2021;11:761596.
PMID: 35024355 DOI: 10.3389/fcimb.2021.761596

Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on "Scedosporium/Pseudallescheria Infections" and "Fungal Respiratory Infections in Cystic Fibrosis".

Matched MeSH terms: Multilocus Sequence Typing
Phylogenetic relationship of non-typeable Haemophilus influenzae isolated in Malaysia

Mohd-Zain Z, Kamsani NH, Ahmad N, Clarke SC

Infect Genet Evol, 2015 Dec;36:240-3.
PMID: 26394107 DOI: 10.1016/j.meegid.2015.09.017

The epidemiology of non-typeable Haemophilus influenzae (NTHi) remains poorly understood. We therefore sought to determine the genetic relationship of 25 NTHi isolated from various states in Malaysia using multilocus sequence typing (MLST). The majority of isolates were obtained from sputum. There were 24 novel sequence types (STs). Eight isolates were single-locus variants, the remainder being singletons. Clustering was not based on clinical site of isolation or geographical origin. Despite the limited number of isolates examined in this study, we demonstrate that NTHi isolates in Malaysia are diverse and warrant further investigation.

Matched MeSH terms: Multilocus Sequence Typing
Fulltext In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas

Tran PN, Savka MA, Gan HM

Front Microbiol, 2017;8:1296.
PMID: 28747902 DOI: 10.3389/fmicb.2017.01296

The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans-P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.

Matched MeSH terms: Multilocus Sequence Typing
Distribution of sasX, qacA/B and mupA genes and determination of genetic relatedness of methicillin-resistant Staphylococcus aureus among clinical isolates and nasal swab samples from the same patients in a hospital in Malaysia

Nurhafiza NNBA, Siti Asma H, Azian H, Foo PC, Yasmin KMI, Chan YY

Singapore Med J, 2020 12 02.
PMID: 33264563 DOI: 10.11622/smedj.2020166

INTRODUCTION: This study determined the distribution of sasX, qacA/B and mupA genes from methicillin-resistant Staphylococcus aureus (MRSA) isolated from clinical samples and nasal swab samples of the same patients and analysed their genetic relatedness.
METHODS: Polymerase chain reaction (PCR) was used to detect the presence of sasX, qacA/B and mupA genes from 47 paired MRSA isolates. A paired isolate was defined as one nasal swab (colonising) isolate and clinical isolate that caused infection in the same patient. 22 selected paired isolates were subjected to multilocus sequence typing (MLST). The genetic relatedness among the isolates and association between the putative genes with epidemic sequence types (STs) were investigated.
RESULTS: 7 (14.9%, n = 14) paired isolates were positive for the sasX gene. qacA/B genes were positive in 7.4% (n = 7) of the isolates, from three paired isolates and one clinical isolate whose paired colonising isolate was negative. The paired sample of three patients were positive for both genes. The mupA gene was not detected in all the isolates. MLST revealed two epidemic STs, ST22 and ST239, and a novel ST4649. sasX and qacA/B genes were found in ST239 in 29.5% (n = 13) and 13.6% (n = 6) of cases, respectively. Gene co-existence occurred in 13.6% (n = 6) of MRSA ST239 and 2.3% (n = 1) of MRSA ST4649.
CONCLUSION: sasX and qacA/B genes were present in the MRSA isolates, while the mupA gene was undetected. ST22 and ST239 were the major MRSA clones. The circulating MRSA genotypes conferred different virulence and resistance determinants in our healthcare settings.

Matched MeSH terms: Multilocus Sequence Typing
Overview of the distribution of Burkholderia pseudomallei Sequence Types and the Emergence of Sequence Type 1342 in Malaysia

Teh CSJ, Yap PSX, Zulkefli NJ, Subramaniam P, Sit PS, Kong ZX, et al.

Transbound Emerg Dis, 2021 Jan 27.
PMID: 33506647 DOI: 10.1111/tbed.14005

Burkholderia pseudomallei, a Gram-negative bacterial pathogen that causes melioidosis, is of public health importance in endemic areas including Malaysia. An investigation of the molecular epidemiology links of B. pseudomallei would contribute to better understanding of the clonal relationships, transmission dynamics and evolutionary change. Multi-locus sequence typing (MLST) of 45 clinical B. pseudomallei isolates collected from sporadic meliodosis cases in Malaysia was performed. In addition, a total of 449 B. pseudomallei Malaysian strains submitted to the MLST database from 1964 until 2019 were included in the temporal analysis to determine the endemic sequence types (STs), emergence and re-emergence of ST(s). In addition, strain-specific distribution was evaluated using BURST tool. Genotyping of 45 clinical strains were resolved into 12 STs and the majority were affiliated with ST46 (n=11) and ST1342 (n=7). Concomitantly, ST46 was the most prevalent ST in Malaysia which first reported in 1964. All the Malaysian B. pseudomallei strains were resolved into 76 different STs with 36 of them uniquely present only in Malaysia. ST1342 was most closely related to ST1034, in which both STs were unique to Malaysia and first isolated from soil samples in Pahang, a state in Malaysia. The present study revealed a high diversity of B. pseudomallei in Malaysia. Localised evolution giving rise to the emergence of new STs was observed, suggesting that host and environmental factors play a crucial role in the evolutionary changes of B. pseudomallei.

Matched MeSH terms: Multilocus Sequence Typing
25S rDNA genotyping and multi-locus sequence typing of Candida albicans of pathogenic and commensal origins in the Klang Valley, Malaysia

Illyaaseen Z, Ngeow YF, Yap SF, Ng HF

Malays J Pathol, 2021 Apr;43(1):55-61.
PMID: 33903306

Candida albicans is an important opportunistic fungal pathogen capable of causing fatal systemic infections in humans. Presently in Malaysia, there is little information available on the genetic diversity of this organism and trends in behavioural characteristics. In this project, three genotyping methods: 25S rDNA genotyping, Alternative Lengthening of Telomerase (ALT) sequence typing and Multi-Locus Sequence Typing (MLST) were applied to study the genetic diversity of strains from infected hospital in-patients and asymptomatic individuals in the community. The results showed that, with the 25S rDNA genotyping, as in other parts of the world, the most common genotype was type A which accounted for approximately 70% of the 111 isolates tested. Further typing with the ALT sequence showed type 3 to be the most common in the isolates tested. MLST analysis revealed many possibly novel sequence types, as well as a statistically significant association between pathogenicity and a group of closely related isolates, most of which were from hospital samples. Further work on genotypes associated with enhanced virulence will help to clarify the value of genotyping for clinical and epidemiological investigations.

Matched MeSH terms: Multilocus Sequence Typing
Fulltext Dormant phages of Helicobacter pylori reveal distinct populations in Europe

Vale FF, Vadivelu J, Oleastro M, Breurec S, Engstrand L, Perets TT, et al.

Sci Rep, 2015;5:14333.
PMID: 26387443 DOI: 10.1038/srep14333

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.

Matched MeSH terms: Multilocus Sequence Typing
Use of COI, CytB and ND5 genes for intra- and inter-specific differentiation of Haematobia irritans and Haematobia exigua

Low VL, Tan TK, Lim PE, Domingues LN, Tay ST, Lim YA, et al.

Vet Parasitol, 2014 Aug 29;204(3-4):439-42.
PMID: 24912955 DOI: 10.1016/j.vetpar.2014.05.036

A multilocus sequence analysis using mitochondria-encoded cytochrome c oxidase subunit I (COI), cytochrome B (CytB), NADH dehydrogenase subunit 5 (ND5); nuclear encoded 18S ribosomal RNA (18S) and 28S ribosomal RNA (28S) genes was performed to determine the levels of genetic variation between the closely related species Haematobia irritans Linnaeus and Haematobia exigua de Meijere. Among these five genes, ND5 and CytB genes were found to be more variable and informative in resolving the interspecific relationships of both species. In contrast, the COI gene was more valuable in inferring the intraspecific relationships. The ribosomal 18S and 28S sequences of H. irritans and H. exigua were highly conserved with limited intra- and inter-specific variation. Molecular evidence presented in this study demonstrated that both flies are genetically distinct and could be differentiated based on sequence analysis of mitochondrial genes.

Matched MeSH terms: Multilocus Sequence Typing/veterinary
Genetic variation analysis of Vibrio cholerae using multilocus sequencing typing and multi-virulence locus sequencing typing

Teh CS, Chua KH, Thong KL

Infect Genet Evol, 2011 Jul;11(5):1121-8.
PMID: 21511055 DOI: 10.1016/j.meegid.2011.04.005

This paper describes the development and application of multilocus sequencing typing (MLST) and multi-virulence locus sequencing typing (MVLST) methods in determining the genetic variation and relatedness of 43 Vibrio cholerae strains of different serogroups isolated from various sources in Malaysia. The MLST assay used six housekeeping genes (dnaE, lap, recA, gyrB, cat and gmd), while the MVLST assay incorporated three virulence genes (ctxAB, tcpA and tcpI) and three virulence-associated genes (hlyA, toxR and rtxA). Our data showed that the dnaE and rtxA genes were the most conserved genes in V. cholerae O1 strains. Among the 12 studied genes, transitional substitutions that led to silent mutations were observed in all, except for gmd and hlyA, while non-synonymous substitutions occurred more frequently in virulence and virulence-associated genes. Five V. cholerae O1 strains were found to be the El Tor variant O1 strains because they harboured the classical ctxB gene. In addition, the classical ctxB gene was also observed in O139 V. cholerae. A total of 29 MLST types were observed, and this assay could differentiate V. cholerae within the non-O1/non-O139 serogroups. A total of 27 MVLST types were obtained. MVLST appeared to be more discriminatory than MLST because it could differentiate V. cholerae strains from two different outbreaks and could separate the toxigenic from the non-toxigenic subtypes. Although the O1 V. cholerae strains were closely related, the combined MLST and MVLST analyses differentiated the strains isolated from different localities. In conclusion, sequence-based analysis in this study provided a better understanding of mutation points and the type of mutations in V. cholerae. The MVLST assay is useful to characterise O1 V. cholerae strains, while combined analysis may improve the discriminatory power and is suitable for the local epidemiological study of V. cholerae.

Matched MeSH terms: Multilocus Sequence Typing*
Emergence of ST119 Acinetobacter pittii co-harbouring NDM-1 and OXA-58 in Malaysia

Ang GY, Yu CY, Cheong YM, Yin WF, Chan KG

Int J Antimicrob Agents, 2016 Feb;47(2):168-9.
PMID: 26742728 DOI: 10.1016/j.ijantimicag.2015.11.008
Matched MeSH terms: Multilocus Sequence Typing*
Fulltext Whole genome sequencing and genomic characteristics analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates in two hospitals in China

Tian C, Di L, Dong S, Tian X, Huang D, Zhao Y, et al.

Infect Genet Evol, 2024 Sep;123:105642.
PMID: 39013496 DOI: 10.1016/j.meegid.2024.105642

Nosocomial outbreaks caused by carbapenem-resistant Acinetobacter baumannii (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The A. baumannii isolates were mainly collected from the ICU and isolated from the sputum (71.43%, 15/21), followed by urine (14.29%, 3/21). Twenty-one A. baumannii strains possessed a multidrug-resistant (MDR) profile, and whole-genome sequencing showed that they all carried blaOXA-23. Based on the Pasteur multilocus sequence typing (MLST) scheme, all strains were typed into a sequence type 2 (ST2). Based on the Oxford MLST scheme, six strains belonged to ST540, three of which were ST208, and four strains were assigned to ST784. Kaptive showed most of the strains (38.10%, 8/21) contained KL93. As for the lipoolygosaccharide (OC locus) type, OCL1c and OCL1d were identified, accounting for 33.33% (7/21) and 66.67% (14/21), respectively. Based on the BacWGSTdb server, we found that the strains belonging to ST540 and ST784 were all collected from China. However, the ST938 strains were isolated from Malaysia and Thailand. Comparative genomics analysis showed that the AB10 strain had a closed relationship with SXAB10-SXAB13 strains, suggesting the transmission happened in these two hospitals and other hospital in China. In addition, the 4300STDY7045869 strain, which was collected from Thailand, possessed near genetic relationship with our isolates in this study, suggesting the possible spread among various countries. Additionally, 3-237 single nucleotide polymorphisms were observed among these strains. In conclusion, this study conducted a genome-based study for A. baumannii strains collected from two hospitals in China and revealed their epidemiological and molecular features. Clone spreading occurred in these two hospitals. Hence, there is an urgent need for increased surveillance in hospitals and other clinical settings to prevent and control CRAB spreading.

Matched MeSH terms: Multilocus Sequence Typing*
Genomic characterization and identification of multiple drug resistance genes in clinical isolates of Acinetobacter baumannii through whole genome sequencing

Habibi N, Mustafa AS, Nasser K, Al-Obaid I, Alfouzan W, Uddin S, et al.

Mol Biol Rep, 2025 Feb 15;52(1):233.
PMID: 39954144 DOI: 10.1007/s11033-025-10353-1

BACKGROUND: Acinetobacter baumannii is a notorious nosocomial pathogen universally in healthcare settings. Its natural competent characteristics for genetic recombination are responsible for acquired antibiotic resistance and render it untreatable through commonly used antibiotics. Hence, characterizing the A. baumannii genomes for multidrug resistance carriage is of paramount importance. The study aimed to characterize the whole genome of clinical isolates of A. baumannii to identify specifically the types of antibiotic resistance genes, drug classes and mobile genetic elements. We also aimed to determine the significant multi-locus sequence tags (MLSTs). The phylogeny of the isolates was established with other clinical strains distributed globally.
METHODS AND RESULTS: Fifteen clinical isolates (isolated from tracheal secretion, urine and bronchoalveolar lavage) were subjected to whole genome sequencing. Raw sequences were assembled using SPAdes and species were identified using KmerFinder 3.2. The assembled genomes were annotated using the Prokka v1.14.6. Resfinder 4.6.0 was used to determine antibiotic resistance genes. The sequences were aligned against seven housekeeping genes aka sequence tags (STs) available within the MLST database (v 2.0.9). MobileGeneticElement finder (v1.0.3) were used for profiling mobile genetic elements associated with the antibiotic resistance genes. The genomes of nosocomial A. baumannii were assembled with an average N50 of 23,480 and GC content of 38%. There were approximately 3700 CDs, 53 tRNA and 3 rRNA. About 80% of the isolates were ST2 type. The genomes possessed antibiotic resistance genes (n = 24) belonging to 17 drug classes. The predicted phenotype was multidrug resistant. Among the mobile genetic elements, 12 insertion sequences and 2 composite transposons were also found. The mode of antibiotic resistance was mostly through antibiotic inactivation in all the isolates.
CONCLUSIONS: The results imply the occurrence of multidrug resistant genes in clinical isolates of A. baumannii strains in the healthcare settings of Kuwait. A more comprehensive survey should be undertaken for antimicrobial resistance monitoring on a regular basis for surveillance, contact tracing, and potential mitigation in clinical settings.

Matched MeSH terms: Multilocus Sequence Typing/methods
Fulltext First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia

Gan HM, Eng WWH, Dhanoa A

J Glob Antimicrob Resist, 2020 03;20:153-159.
PMID: 31325618 DOI: 10.1016/j.jgar.2019.07.008

OBJECTIVES: Despite the increasing reports of carbapenem-resistant Enterobacteriaceae in Malaysia, genomic resources for carbapenem-resistant clinical strains of Klebsiella pneumoniae (K. pneumoniae) remain unavailable. This study aimed to sequence the genomes of multiple carbapenem-resistant K. pneumoniae strains from Malaysia and to identify the genetic basis for their resistance.
METHODS: Illumina whole genome sequencing was performed on eight carbapenem-resistant K. pneumoniae isolated from a Malaysian hospital. Genetic diversity was inferred from the assembled genomes based on in silico multilocus sequence typing (MLST). In addition, plasmid-derived and chromosome-derived contigs were predicted using the machine learning approach. After genome annotation, genes associated with carbapenem resistance were identified based on similarity searched against the ResFinder database.
RESULTS: The eight K. pneumoniae isolates were grouped into six different sequence types, some of which were represented by a single isolate in the MLST database. Genomic potential for carbapenem-resistance was attributed to the presence of plasmid-localised blaNDM (blaNDM-1/blaNDM-5) or blaKPC (blaKPC-2/blaKPC-6) in these sequenced strains. The majority of these carbapenem resistance genes was flanked by repetitive (transposase or integrase) sequences, suggesting their potential mobility. This study also reported the first blaKPC-6-harbouring plasmid contig to be assembled for K. pneumoniae, and the second for the genus Klebsiella.
CONCLUSION: This study reported the first genomic resources for carbapenem-resistant K. pneumoniae from Malaysia. The high diversity of carbapenem resistance genes and sequence types uncovered from eight isolates from the same hospital is worrying and indicates an urgent need to improve the genomic surveillance of clinical K. pneumoniae in Malaysia.

Matched MeSH terms: Multilocus Sequence Typing
Fulltext Molecular Characteristics of Burkholderia pseudomallei Collected From Humans in Hainan, China

Zhu X, Chen H, Li S, Wang LC, Wu DR, Wang XM, et al.

Front Microbiol, 2020;11:778.
PMID: 32457710 DOI: 10.3389/fmicb.2020.00778

Melioidosis is a common infectious disease in Southeast Asia and Northern Australia. In Hainan, several cases have been reported, but no systematic study has yet been done on the molecular epidemiology profiles of the organism. An investigation of the molecular epidemiology links and population structure of Burkholderia pseudomallei would help to better understand the clonally of the isolates and differences among them. In this study, multilocus variable-number tandem repeat analysis (MLVA), and multilocus sequence typing (MLST) were applied to examine the epidemiological relatedness and population structure of 166 B. pseudomallei isolates obtained during 2002-2014 in Hainan, China. Both the MLVA_4 and MLST approaches had high discriminatory power for this population, with diversity indices of 0.9899 and 0.9457, respectively. However, the MLVA_4 assay showed a higher discriminatory power than the MLST approach, and a variable-number tandem repeat (VNTR3 933) found by the MLVA approach was the most useful in discriminating strains from this province. A total of 166 strains yielded 99 MLVA_4 genotypes, of which 34 genotypes were shared by 101 isolates, for a clustering rate of 60.8% (101/166), which suggested that some cases may have a common source. Additionally, 65 isolates showed distinct genotypes, indicating that more than 39.2% (65/166) of melioidosis cases in Hainan had epidemiologically unrelated or sporadic characteristics. The 166 isolates were resolved into 48 STs, of which five STs (ST55, -70, -46, -50, and -58) were here found to be predominant. Phylogenetic analysis of 116 isolates conducted using the eBURST v3 segregated the 48 STs into eight groups with ST50 as predicted founder, and 21 STs were found to be singletons, which suggest that the strains in the Hainan region represent a high diversity of ST clones, indicating that many B. pseudomallei clone groups are endemic to this region. Moreover, ST50 had 5 SLV, 7 DLV, 6 TLV, and 29 satellite STs and formed a radial expansion pattern, suggesting that the melioidosis epidemic in this study was mainly caused by the clonal expansion of ST 50. Phylogenetic analysis on global scale suggests that China's isolates are closely related to isolates from Southeast Asia, particularly from Thailand and Malaysia.

Matched MeSH terms: Multilocus Sequence Typing
Characterization of Campylobacter jejuni and Campylobacter coli isolates from chicken offal in Metro Manila, Philippines: Insights from virulence gene prevalence and multilocus sequence typing analysis

Subejano MSE, Penuliar G

Trop Biomed, 2023 Dec 01;40(4):422-429.
PMID: 38308829 DOI: 10.47665/tb.40.4.007

Campylobacteriosis is a human infection primarily caused by Campylobacter jejuni and Campylobacter coli. Consumption of contaminated chicken and poultry products is the main mode of transmission. These bacteria possess virulence factors, including adhesins and toxins, which contribute to their pathogenesis. Moreover, their large genomes undergo frequent genetic recombination, resulting in a high degree of genetic diversity. However, limited information is available regarding the virulence and genotypic diversity profiles of these microorganisms in the Philippines. The objective of this study was to address this knowledge gap by characterizing Campylobacter isolates obtained from chicken offal sold in wet markets in Metro Manila, Philippines. Multilocus Sequence Typing (MLST) analysis was performed to determine the sequence types, resulting in the identification of 13 unique sequence types, including nine previously unreported ones, and three clonal complexes. Notably, the widespread sequence type ST-305 was found in samples from different markets. Furthermore, six isolates deposited in the Campylobacter PubMLST database were identified as C. coli based on allele profiles. Profiling using 10 selected virulence genes revealed that more than half of the isolates carried these genes. The most prevalent virulence gene was cadF (100%), followed by flaA (95%), racR, cdtA, cdtB, and cdtC (85%). The genes dnaJ and ceuE were also present in 75% of the isolates. Despite the limited sample size, the findings of this study reveal a significant level of genotypic diversity among the Campylobacter isolates. This diversity has important implications for source attribution studies and the identification of strains involved in campylobacteriosis outbreaks. Furthermore, the investigation of virulence factors associated with colonization and invasion of the avian gut can provide insights for the development of practical applications in Campylobacter control strategies. Understanding and addressing these factors are crucial steps toward mitigating the risk of Campylobacter infections and enhancing public health efforts.

Matched MeSH terms: Multilocus Sequence Typing
Fulltext Multigene Phylogeography of Bactrocera caudata (Insecta: Tephritidae): Distinct Genetic Lineages in Northern and Southern Hemispheres

Yong HS, Lim PE, Tan J, Song SL, Suana IW, Eamsobhana P

PLoS One, 2015;10(6):e0129455.
PMID: 26090853 DOI: 10.1371/journal.pone.0129455

Bactrocera caudata is a pest of pumpkin flower. Specimens of B. caudata from the northern hemisphere (mainland Asia) and southern hemisphere (Indonesia) were analysed using the partial DNA sequences of the nuclear 28S rRNA and internal transcribed spacer region 2 (ITS-2) genes, and the mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and 16S rRNA genes. The COI, COII, 16S rDNA and concatenated COI+COII+16S and COI+COII+16S+28S+ITS-2 nucleotide sequences revealed that B. caudata from the northern hemisphere (Peninsular Malaysia, East Malaysia, Thailand) was distinctly different from the southern hemisphere (Indonesia: Java, Bali and Lombok), without common haplotype between them. Phylogenetic analysis revealed two distinct clades (northern and southern hemispheres), indicating distinct genetic lineage. The uncorrected 'p' distance for the concatenated COI+COII+16S nucleotide sequences between the taxa from the northern and southern hemispheres ('p' = 4.46-4.94%) was several folds higher than the 'p' distance for the taxa in the northern hemisphere ('p' = 0.00-0.77%) and the southern hemisphere ('p' = 0.00%). This distinct difference was also reflected by concatenated COI+COII+16S+28S+ITS-2 nucleotide sequences with an uncorrected 'p' distance of 2.34-2.69% between the taxa of northern and southern hemispheres. In accordance with the type locality the Indonesian taxa belong to the nominal species. Thus the taxa from the northern hemisphere, if they were to constitute a cryptic species of the B. caudata species complex based on molecular data, need to be formally described as a new species. The Thailand and Malaysian B. caudata populations in the northern hemisphere showed distinct genetic structure and phylogeographic pattern.

Matched MeSH terms: Multilocus Sequence Typing

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