Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

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Kerstersia similis sp. nov., isolated from human clinical samples

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.037887-0 ◽

2012 ◽

Vol 62 (Pt_9) ◽

pp. 2156-2159 ◽

Cited By ~ 20

Author(s):

Peter Vandamme ◽

Evie De Brandt ◽

Kurt Houf ◽

Thierry De Baere

Keyword(s):

Type Strain ◽

Type Species ◽

Gene Sequence ◽

Clinical Samples ◽

Content Type ◽

Biochemical Characteristics ◽

Link Type ◽

Gene Sequence Analysis ◽

The Usa ◽

Kerstersia Gyiorum

Analysis of gyrB gene sequences, (GTG)5-primed PCR fingerprinting and biochemical characteristics determined in the Biolog GEN III microtest system were used to differentiate an unnamed Kerstersia species from Kerstersia gyiorum , the type and only named species in this genus. The inability to oxidize d-galacturonic and d-glucuronic acids and the ability to oxidize d-serine, along with gyrB gene sequence analysis and (GTG)5-PCR fingerprints, readily differentiated the unnamed taxon from the type species. Therefore, we propose to formally classify this unnamed taxon as Kerstersia similis sp. nov. with strain LMG 5890T ( = CCUG 46999T), isolated from a leg wound in the USA in 1983, as the type strain.

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Sneathia amnii bacteraemia and chorioamnionitis leading to second trimester abortion: a case report

Access Microbiology ◽

10.1099/acmi.0.000290 ◽

2021 ◽

Vol 3 (12) ◽

Author(s):

Lien Gruwier ◽

Aaron Sprenkels ◽

Sofie Hulsbosch ◽

Anne Vankeerberghen ◽

Reinoud Cartuyvels

Keyword(s):

Type Species ◽

Culture Broth ◽

Second Trimester ◽

Trimester Abortion ◽

Content Type ◽

Link Type ◽

First Case ◽

Gene Sequence Analysis ◽

The Usa ◽

Septic Abortion

Background. Sneathia amnii (formerly designated as Leptotrichia amnionii ) was first described in 2002 in the USA. Members of the genus Sneathia can be part of the normal flora of the genitourinary tract, but have been implicated in invasive (mostly gynaecological) infections. Case presentation. To the best of our knowledge, here we present the first case of S. amnii infection in Belgium, in a young woman presenting with fever leading to second trimester septic abortion. Conclusions. Despite its pathogenicity, S. amnii remains an underrated cause of infections due to inherent difficulties with conventional laboratory methods. By extracting the bacterial DNA directly from the blood culture broth and performing a 16S ribosomal RNA gene sequence analysis we succeeded in identifying S. amnii as the most probable cause of the septic abortion in our patient.

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Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Microbial Genomics ◽

10.1099/mgen.0.000495 ◽

2020 ◽

Vol 6 (12) ◽

Author(s):

Siew Woh Choo ◽

Shusruto Rishik ◽

Wei Yee Wee

Keyword(s):

Type Species ◽

Genomic Structure ◽

Phylogenetic Analyses ◽

Opportunistic Pathogen ◽

Genomic Islands ◽

Comparative Genome ◽

Content Type ◽

Link Type ◽

Defence Genes ◽

Genome Analyses

Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum . Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum , supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

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Hybrid genome assembly of Shigella sonnei reveals the novel finding of chromosomal integration of an IncFII plasmid carrying a mphA gene

Access Microbiology ◽

10.1099/acmi.0.000189 ◽

2020 ◽

Author(s):

Dhiviya Prabaa Muthuirulandi Sethuvel ◽

Shalini Anandan ◽

Dhivya Murugan ◽

Kalaiarasi Asokan ◽

Karthick Vasudevan ◽

...

Keyword(s):

Resistance Genes ◽

Genome Analysis ◽

Complete Genome ◽

Type Species ◽

Shigella Sonnei ◽

Diffusion Method ◽

The Novel ◽

Content Type ◽

Link Type ◽

Complete Genome Analysis

Azithromycin is increasingly being used for the treatment of shigellosis despite a lack of interpretative guidelines and with limited clinical evidence. The present study determined azithromycin susceptibility and correlated this with macrolide-resistance genes in Shigella spp. isolated from stool specimens in Vellore, India. The susceptibility of 332 Shigella isolates to azithromycin was determined using the disc diffusion method. Of these, 31 isolates were found to be azithromycin resistant. The azithromycin minimum inhibitory concentration (MIC) was determined using the broth microdilution method. In addition, isolates were screened for mphA and ermB genes using conventional PCR. Furthermore, an isolate that was positive for resistance genes was subjected to complete genome analysis, and was analysed for mobile genetic elements. The azithromycin MIC for the 31 resistant Shigella isolates ranged between 2 and 16 mg l−1. PCR results showed that a single isolate of Shigella sonnei carried a mphA gene. Complete genome analysis revealed integration of an IncFII plasmid into the chromosome of S. sonnei , which was also found to carry the following resistance genes: sul1, bla DHA1, qnrB4, mphA, tetR. Mutations in the quinolone-resistance-determining region (QRDR) were also observed. Additionally, prophages, insertion sequences and integrons were identified. The novel finding of IncFII plasmid integration into the chromosome of S. sonnei highlights the potential risk of Shigella spp. becoming resistance to azithromycin in the future. These suggests that it is imperative to monitor Shigella susceptibility and to study the resistance mechanism of Shigella to azithromycin considering the limited treatment choices for shigellosis.

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Bacterial gastroenteritis caused by the putative zoonotic pathogen Campylobacter lanienae: First reported case in Germany

Access Microbiology ◽

10.1099/acmi.0.000199 ◽

2021 ◽

Author(s):

Juliane Fornefett ◽

Anne Busch ◽

Sandra Döpping ◽

Helmut Hotzel ◽

Dagmar Rimek

Keyword(s):

Type Species ◽

Campylobacter Coli ◽

Pathogenic Potential ◽

Content Type ◽

Link Type ◽

First Case ◽

Strain Collection ◽

Causative Agents ◽

Bacterial Gastroenteritis ◽

Abattoir Workers

Foodborne campylobacteriosis is the most common cause of human bacterial enteritis in Germany. Campylobacter jejuni and Campylobacter coli are the main causative agents for enteric disease, but a number of other species are involved, including rare ones. These rare Campylobacter spp. are emerging zoonotic pathogens in humans due to increasing international movement of supplies, livestock and people. Campylobacter lanienae was first isolated from healthy abattoir workers in Switzerland and at first its pathogenic potential for humans was considered to be low. Recently, the first case of Campylobacter lanienae -associated human enteritis was reported in Canada. Here, we describe a case of mild Campylobacter lanienae -associated enteritis with subsequent asymptomatic excretion in a butcher. The isolate is available at the TLV strain collection (no. TP00333/18). This first reported case of human Campylobacter lanienae campylobacteriosis in Germany demonstrates the agent’s likely zoonotic pathogenicity.

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A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

Microbial Genomics ◽

10.1099/mgen.0.000690 ◽

2021 ◽

Vol 7 (11) ◽

Author(s):

Aysun Urhan ◽

Thomas Abeel

Keyword(s):

Acinetobacter Baumannii ◽

Type Species ◽

Variant Calling ◽

Reference Sequence ◽

Beta Lactam ◽

Final Size ◽

Content Type ◽

Pan Genome ◽

Link Type ◽

Microbial Organisms

Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many successful applications and a rapid increase in the number of methods available in the literature. Despite this enthusiasm, there has been no attempt at exploring these graph construction methods in depth, demonstrating their practical use. In this study, we aim to develop a general guide to help researchers who may want to incorporate pan-genomes in their analyses of microbial organisms. We evaluated the state-of-the art pan-genome construction tools to model a collection of 70 Acinetobacter baumannii strains. Our results suggest that all tools produced pan-genome graphs conforming to our expectations based on previous literature, and that their approach to homologue detection is likely to be the most influential in determining the final size and complexity of the pan-genome. The graphs overlapped most in the core pan-genome content while the cloud genes varied significantly among tools. We propose an alternative approach for pan-genome construction by combining two of the tools, Panaroo and Ptolemy, to further exploit them in downstream analyses, and demonstrate the effectiveness of our pipeline for structural variant calling in beta-lactam resistance genes in the same set of A. baumannii isolates, identifying various transposon structures for carbapenem resistance in chromosome, as well as plasmids. We identify a novel plasmid structure in two multidrug-resistant clinical isolates that had previously been studied, and which could be important for their resistance phenotypes.

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Analysis of the antimicrobial resistance gene frequency in whole-genome sequenced Vibrio from Latin American countries

Journal of Medical Microbiology ◽

10.1099/jmm.0.001428 ◽

2021 ◽

Vol 70 (9) ◽

Author(s):

Felipe Pinheiro Vilela ◽

Juliana Pfrimer Falcão

Keyword(s):

Antimicrobial Resistance ◽

Latin American ◽

Resistance Genes ◽

Vibrio Parahaemolyticus ◽

Type Species ◽

Contaminated Water ◽

Content Type ◽

Link Type ◽

Antimicrobial Resistance Gene ◽

Latin American Countries

Vibrio species are important environmental-related bacteria responsible for diverse infections in humans due to consumption of contaminated water and seafood in underdeveloped areas of the world. This study aimed to investigate the frequency of antimicrobial resistance genes in 577 sequenced Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated in Latin American countries available at the NCBI Pathogen Detection database and to determine the sequence type (ST) of the strains. Almost all strains studied (99.8%) carried at least one antimicrobial resistance gene, while 54.2 % presented a multidrug-resistance profile. The Vibrio strains exhibited genotypic resistance to 11 antimicrobial classes and almG, varG, and catB9, which confer resistance to antibiotic peptides, β-lactams and amphenicols, respectively, were the most detected genes. Vibrio parahaemolyticus and V. vulnificus showed a broad diversity of STs. Vibrio cholerae strains isolated in Haiti after 2010’s earthquake presented the highest diversity and amount of resistance genes in the set of strains analysed and mostly belonged to ST69. In conclusion, the detection of resistance genes from 11 antimicrobial classes and the high number of multidrug-resistant Vibrio species strains emphasize that Latin American public health authorities should employ more efficient control measures and that special attention should be given for the rational use of antimicrobials in human therapy and aquaculture, since the consumption of contaminated water and seafood with resistant Vibrio may result in human infections difficult to be treated.

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Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

Journal of Clinical Microbiology ◽

10.1128/jcm.00582-20 ◽

2020 ◽

Vol 58 (9) ◽

Author(s):

Austin Wesevich ◽

Granger Sutton ◽

Felicia Ruffin ◽

Lawrence P. Park ◽

Derrick E. Fouts ◽

...

Keyword(s):

Clinical Outcome ◽

Hospital Mortality ◽

Clinical Outcomes ◽

Genome Analysis ◽

Enterobacter Aerogenes ◽

Genomic Islands ◽

Klebsiella Aerogenes ◽

Poor Clinical Outcome ◽

Content Type ◽

Pan Genome

ABSTRACT Enterobacter aerogenes was recently renamed Klebsiella aerogenes. This study aimed to identify differences in clinical characteristics, outcomes, and bacterial genetics among patients with K. aerogenes versus Enterobacter species bloodstream infections (BSI). We prospectively enrolled patients with K. aerogenes or Enterobacter cloacae complex (Ecc) BSI from 2002 to 2015. We performed whole-genome sequencing (WGS) and pan-genome analysis on all bacteria. Overall, 150 patients with K. aerogenes (46/150 [31%]) or Ecc (104/150 [69%]) BSI were enrolled. The two groups had similar baseline characteristics. Neither total in-hospital mortality (13/46 [28%] versus 22/104 [21%]; P = 0.3) nor attributable in-hospital mortality (9/46 [20%] versus 13/104 [12%]; P = 0.3) differed between patients with K. aerogenes versus Ecc BSI, respectively. However, poor clinical outcome (death before discharge, recurrent BSI, and/or BSI complication) was higher for K. aerogenes than Ecc BSI (32/46 [70%] versus 42/104 [40%]; P = 0.001). In a multivariable regression model, K. aerogenes BSI, relative to Ecc BSI, was predictive of poor clinical outcome (odds ratio 3.3; 95% confidence interval 1.4 to 8.1; P = 0.008). Pan-genome analysis revealed 983 genes in 323 genomic islands unique to K. aerogenes isolates, including putative virulence genes involved in iron acquisition (n = 67), fimbriae/pili/flagella production (n = 117), and metal homeostasis (n = 34). Antibiotic resistance was largely found in Ecc lineage 1, which had a higher rate of multidrug resistant phenotype (23/54 [43%]) relative to all other bacterial isolates (23/96 [24%]; P = 0.03). K. aerogenes BSI was associated with poor clinical outcomes relative to Ecc BSI. Putative virulence factors in K. aerogenes may account for these differences.

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Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

Microbial Genomics ◽

10.1099/mgen.0.000727 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Andreina I. Castillo ◽

Chi-Wei Tsai ◽

Chiou-Chu Su ◽

Ling-Wei Weng ◽

Yu-Chen Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Type Species ◽

Xylella Fastidiosa ◽

Content Type ◽

Link Type ◽

Genome Recombination ◽

Haplotype Networks ◽

The Usa ◽

Multiple Regions ◽

Central Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis , which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.

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The open pan-genome architecture and virulence landscape of Mycobacterium bovis

Microbial Genomics ◽

10.1099/mgen.0.000664 ◽

2021 ◽

Vol 7 (10) ◽

Author(s):

Ana C. Reis ◽

Mónica V. Cunha

Keyword(s):

Mycobacterium Bovis ◽

Type Species ◽

Genome Structure ◽

Genome Architecture ◽

Evolutionary Potential ◽

Content Type ◽

Accessory Genome ◽

Pan Genome ◽

Link Type ◽

Clusters Of Orthologous Groups

Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis , one of the animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work, whole-genome comparative analyses of 70 M . bovis were performed to gain insights into the pan-genome architecture. The comparison across M. bovis predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete M. bovis subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, n=258), ‘lipid metabolism and transport’ (n=242), ‘energy production and conversion’ (n=214) and ‘unknown function’ (n=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of M. bovis from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of M. bovis encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that M. bovis can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.

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