Complete high-quality genome sequence of Clostridium limosum (Hathewaya limosa) isolate 14S0207, recovered from a cow with suspected blackleg in Germany

Clostridium limosum can be found in soil and the intestinal tract of animals. In 2014, C. limosum was isolated from a suspected blackleg outbreak in cattle in Schleswig-Holstein, Germany. We present a complete genome sequence of a C. limosum strain represented by a circular chromosome and three plasmids

Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential

Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains ' sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements. However, the position and order of the local collinear blocks on the chromosome showed a considerable degree of preservation. The strains were divided into five stable phylogroups (I-V). Phylogroup I contained human food poisoning strains with chromosomal enterotoxin (cpe) and a Darmbrand strain characterized by a high frequency of mobile elements, a relatively small genome size and a marked loss of chromosomal genes, including loss of genes encoding virulence traits. These features might correspond to the adaptation of these strains to a particular habitat, causing human foodborne illnesses. This contrasts strains that belong to phylogroup II where the genome size points to the acquisition of genetic material. Most strains of phylogroup II have been isolated from enteric lesions in horses and dogs. Phylogroups III, IV and V are heterogeneous groups containing a variety of different strains, with phylogroup III being the most abundant (65.5%). In conclusion, C. perfringens displays five stable phylogroups reflecting different disease involvements, prompting further studies on the evolution of this highly important pathogen

Presence of Clostridium difficile in poultry and poultry meat in Egypt

C. difficile has been recognized as a potential zoonotic agent encouraging investigations of C. difficile prevalence and ribotypes in animals. Here we report the prevalence and diversity of Egyptian C. difficile in I) samples from healthy poultry (n = 50), II) samples from diseased poultry (n = 54), and III) poultry meat (n = 150). Thirteen isolates were obtained from seven healthy and five diseased animals, but no C. difficile was cultured from poultry meat. The isolated C. difficile strains belonged to 3 different PCR-ribotypes (039/2, 205 and 001/FLI01). The detection of strains related to RT 001 known for its ability to cause disease in humans makes poultry a potential reservoir for pathogenic C. difficile

First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene

Clostridium septicum is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with C. perfringens, as the most important etiologic agent of progressive gas gangrene. Clostridium septicum infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of C. septicum. This study presents the complete genome sequence of C. septicum DSM 7534T type strain as well as the first comparative analysis of five C. septicum genomes. The taxonomy of C. septicum, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA–DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species Clostridium chauvoei. The restriction-modification (RM) systems between two C. septicum genomes were heterogeneous for the RM types they encoded. C. septicum has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all C. septicum genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to Clostridium chauvoei toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of C. septicum and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.Peer Reviewe

Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations

Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations

Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany

Campylobacter fetus subsp. venerealis (Cfv) causes bovine genital campylobacteriosis (BGC), a World Organization for Animal Health (WOAH)-listed trade-relevant disease characterized by severe reproductive losses, such as infertility, early embryonic death and abortion in cattle. BGC has significant economic implications that have prompted several countries to adopt stringent eradication and surveillance measures to contain the disease. In Germany, there has been a low incidence of BGC cases over the past 28 years. This study aimed to illustrate the genomic diversity of German Cfv strains isolated from different federal states in Germany. This study analyzed 63 Cfv strains, collected between 1985 and 2015, by whole-genome sequencing and compared them with genome data of 91 international Cfv isolates. The phylogenetic analysis showed that the Cfv population is genetically conserved and has geographic clusters. In Germany, one phylogenetic lineage comprising all strains was identified. This German lineage was part of a subclade that probably emerged in the nineteenth century and diversified over time. The results of this study point to a non-recurrent cross-border introduction of Cfv in Germany. The BGC control interventions in Germany can be considered successful as no outbreaks were reported since 2015

Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations

Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations.Peer Reviewe

In silico Genomanalyse und molekulare Typisierung von Clostridium perfringens

Main objectives of the thesis: 1. In silico investigation of the genomic variability, phylogenetic relatedness and virulence assessment of C. perfringens by means of comparative genome analysis employing publically available genomic data. 2. Isolation, characterization and genotyping of C. perfringens strains from healthy and diseased poultry collected from different farms and slaughterhouses in Egypt. 3. Development and application of a core genome-based multilocus sequence typing system for C. perfringens. 1. In silico analysis of the genomic variability, phylogenetic relatedness and virulence genes of C. perfringens The Gram-positive anaerobic spore forming bacterium C. perfringens is able to produce a large number of toxins by which it can cause various defined diseases in different hosts. With the aim to investigate its genomic diversity the publically available genome sequence data of 76 C. perfringens strains from diverse ecological, geographical and temporal niches were analyzed. Data analysis included 30 complete genomes which were composed of a circular chromosome (2.9 to 3.5Mbp) and up to six extrachromosomal elements. A substantial degree of genomic variability was detected in respect to episome content, chromosome size and mobile elements. Insertion sequences were identified and revealed abundance of their occurrence in certain genomes. Comparative alignment of complete genomes displayed a considerable degree of conservation in the order of genes in each chromosome except for three (out of the 30) genomes. The analyzed 76 C. perfringens strains were divided into three different phylogroups (I - III). Phylogroup I consisted of human food poisoning strains with chromosomal cpe as well as a Darmbrand (enteritis necroticans) strain. This phylogroup is characterized by a significant enrichment in mobile elements, relative small genome size and marked loss of chromosomal genes. Phylogroup I strains lack also two putative iron uptake systems as well as the pfoA gene. The genomic features of this phylogroup I (abundance of IS elements and genome reduction) provide indications that these strains adapt to a certain habitat causing human foodborne illnesses. Also, the absence of certain virulence genes (iron uptake systems and PFO) indicates the strains’ adaptation to less competitive environment (food) for replication. The loss of chromosomal genes in phylogroup I was in contrast to phylogroup II, in which the genome size indicates the addition of new genetic material. Phylogroup II strains carry also an additional putative iron uptake operon and an additional copy of the pfoA gene. Strains of this phylogroup were frequently reported in different animal hosts (equine and canine) in which they can cause enteric lesions. In sum, this study provides new insights into genomic variability and phylogenetic structure of C. perfringens. Phylogroup I (chromosomal cpe and Darmbrand strains) appears to be exposed to certain evolutionary mechanisms and displays characteristics that indicate speciation of these strains 2. Characterization and typing of C. perfringens isolates from healthy and diseased poultry in Egypt To investigate the diversity of poultry strains of C. perfringens isolated from Egypt, 54 birds from 27 farms suspected for necrotic enteritis (NE) as well as 50 healthy birds (10 ducks, 40 chickens) from eight slaughterhouses were sampled. C. perfringens was isolated from birds suspected of NE in 14 different farms (n = 51 isolates) as well as from apparently healthy poultry at slaughterhouses (n = 83 isolates). The C. perfringens isolates from suspected NE cases in Egypt were of toxin type A and netB negative, despite fact that NetB toxin was reported to play an important role in NE pathogenesis. The beta2 toxin gene was detected in both diseased and non-diseased birds. Ten isolates from five healthy ducks that did not produce the typical dual hemolysis on blood agar were identified. In addition, seven isolates from two cases suspected for NE were detected with an insertion of 834bp DNA segment within the amplicon of alpha toxin gene. The inserted DNA segment was identical to group II intron. C. perfringens strains that carry the group II intron were reported previously in Japan, Italy and Denmark. Interestingly, the insertion was detected so far within chicken isolates only. Additionally, a pilot investigation based on classical MLST was performed to determine the genetic relatedness of C. perfringens isolated in individual diseased birds. The investigated isolates of two birds (bird no. 1 and no. 2) belong to a single MLST sequence type each (ST45 and ST46) in concordance with various reports that described limited diversity of strains in NE affected birds. However, the isolates from bird no. 3 belonged to three different STs. Comparing MLST data for the 12 strains of this study and MLST data described in prior investigations revealed that the 12 strains were assigned to new STs and do not belong to the previously described “NE-associated” genotypes (ST31, CC-4). 3. Development and application of a core genome-based multilocus sequence typing system for C. perfringens Whole genome sequencing can provide a complete overview on organism genetic information but also represents a powerful molecular epidemiological tool for pathogen subtyping and outbreak investigations. In this study, a cgMLST scheme of 1,450 genes was developed for C. perfringens typing. The developed scheme was applied on a set of 160 genomes. An average of 99.5% of the cgMLST targets was found typeable per each genome. This scheme has a greater discriminatory power than the classical MLSTs methods. In addition, a whole genome based SNP typing was performed. The discriminatory power between the cgMLST and the whole genome SNP typing was comparable. The developed cgMLST scheme was applied using a cluster type (CT) threshold of 60 allelic differences to analyze 87 genomes of poultry strains of C. perfringens. Based on cgMLST results, most CTs comprised isolates derived from a single country only. However, few CTs harbor strains which were isolated in different countries. This could be due to the poultry commercial system which is likely maintained by few companies i.e. few sources worldwide. Compared to isolates from healthy birds and meat samples, a limited diversity was found in the suspected necrotic enteritis (NE) isolates from Egypt, supporting the hypothesis that distinct isolates cause NE. Isolates from diseased birds were found to group with isolates from healthy birds or meat samples highlighting the wide distribution of potentially virulent strains and the multifactorial character of the disease. Additionally, the 160 genomes investigated in this study were divided into four main phylogroups by hierBAPS. Whole genome SNP typing showed a superior applicability to delineate these phylogroups. A minimum SNP difference of ~ 40,000 SNPs was observed between the phylogroups. In sum, a useful cgMLST scheme for C. perfringens was developed that is applicable for broad and standardized epidemiological investigations. On the other hand, whole genome SNP typing can map the affiliation of individual isolates to the main phylogroups of C. perfringens in more detail.Hauptziele der Arbeit: 1. In silico-Untersuchung der genomischen Variabilität, phylogenetischen Verwandtschaft und Virulenzeinschätzung von C. perfringens mittels vergleichender Genomanalyse unter Verwendung öffentlich zugänglicher genomischer Daten. 2. Isolierung, Charakterisierung und Genotypisierung von C. perfringens Stämmen von gesundem und erkranktem Geflügel, die in verschiedenen landwirtschaftlichen Betrieben und Schlachthöfen in Ägypten gesammelt wurden. 3. Entwicklung und Anwendung eines Core-genom basierten Multilocus-Sequenz-Typisierungssystems für C. perfringens. 1. In silico-Untersuchung der genomischen Variabilität, phylogenetischen Verwandtschaft und Virulenzgene von C. perfringens Das Gram-positive, anaerobe, sporenbildende Bakterium C. perfringens ist in der Lage, eine große Anzahl von Toxinen zu produzieren, wodurch es bei verschiedenen Wirten unterschiedliche definierte Krankheiten verursachen kann. Mit dem Ziel die genomische Vielfalt von C. perfringens zu untersuchen, wurden öffentlich verfügbaren Genomsequenzdaten von 76 Stämmen verschiedener ökologischer, geographischer und zeitlicher Herkunft analysiert. Die Datenanalyse umfasste 30 vollständige Genome, die aus einem ringförmigen Chromosom (2,9 bis 3,5 Mbp) und bis zu sechs extrachromosomalen Elementen bestanden. Ein erhebliches Maß an genomischer Variabilität wurde in Bezug auf Episom, Chromosomengröße und mobile Elemente festgestellt. Insertionssequenzen wurden identifiziert und die Häufung ihres Auftretens in bestimmten Genomen aufgedeckt. Das vergleichende Alignement vollständiger Genome zeigte einen erheblichen Grad an Konservierung in der Anordnung der Gene in jedem Chromosom, mit Ausnahme von drei (von den 30) Genomen. Die analysierten 76 C. perfringens Stämme wurden in drei verschiedene Phylogruppen (I - III) unterteilt. Phylogruppe I bestand aus lebensmittelvergiftenden Stämmen mit chromosomalem cpe sowie einem Darmbrand (Enteritis necroticans) Stamm. Diese Phylogruppe zeichnet sich durch eine signifikante Anreicherung mobiler Elemente, eine relativ kleine Genomgröße und einen deutlichen Verlust chromosomaler Gene aus. Den Phylogruppe I-Stämmen fehlen zwei mutmaßliche Eisen-Aufnahmesysteme sowie das pfoA Gen. Die genomischen Merkmale dieser Phylogruppe I (Fülle von IS-Elementen und Genomreduktion) liefern Hinweise darauf, dass sich diese Stämme an einen bestimmten Lebensraum anpassen, in welchem sie lebensmittelbedingte Krankheiten beim Menschen verursachen. Auch das Fehlen bestimmter Virulenzgene (Eisenaufnahmesysteme und PFO) deutet auf die Anpassung der Stämme an ein weniger kompetitives Umfeld (Lebensmittel) für die Replikation hin. Der Verlust chromosomaler Gene in der Phylogruppe I stand im Gegensatz zur Phylogruppe II, bei der die Genomgröße auf die Hinzugewinnung neuen Erbmaterials hinweist. Phylogruppe II-Stämme enthalten ein zusätzliches mutmaßliches Operon für Eisenaufnahme und eine zusätzliche Kopie des pfoA Gens. Stämme dieser Phylogruppe wurden häufig in verschiedenen Wirten (Pferd und Hund) beobachtet, bei denen sie enterische Läsionen verursachen können. In Summe liefert diese Studie neue Erkenntnisse über die genomische Variabilität und phylogenetische Struktur von C. perfringens. Phylogruppe I (chromosomale cpe- und Darmbrand-Stämme) scheint bestimmten evolutionären Mechanismen ausgesetzt und weist Merkmale auf, die auf eine Artbildung dieser Stämme hinweisen. 2. Charakterisierung und Genotypisierung von C. perfringens Stämmen aus gesundem und erkranktem Geflügel in Ägypten Um die Vielfalt der C. perfringens Geflügelstämme in Ägypten zu untersuchen, wurden 54 Vögel aus 27 Betrieben mit Verdacht auf nekrotische Enteritis (NE), sowie 50 gesunde Vögel (10 Enten, 40 Hühner) aus acht Schlachthöfen untersucht. C. perfringens wurde aus NE-verdächtigen Vögeln von 14 verschiedenen Betrieben isoliert (n = 51 Isolate), sowie aus augenscheinlich gesundem Geflügel in Schlachthöfen (n = 83 Isolate). Die C. perfringens Isolate aus NE-Verdachtsfällen in Ägypten gehörten zum Toxin-Typ A und waren netB negativ, obwohl NetB-Toxin eine wichtige Rolle bei der NE-Pathogenese spielen soll. Das beta2-Toxin-Gen wurde sowohl bei kranken als auch bei gesunden Vögeln nachgewiesen. Zehn Isolate von fünf gesunden Enten, die auf Blutagar nicht die typische Doppelzonen-Hämolyse zeigten, wurden identifiziert. Darüaber hinaus wurde bei sieben Isolaten aus zwei NE-Verdachtsfällen die Insertion eines DNA-Segments von 834 bp im Amplikon des Alpha-Toxin-Gens nachgewiesen. Das inserierte DNA-Segment war identisch mit einem Gruppe II Intron. C. perfringens Stämme, die ein Intron der Gruppe II tragen, wurden zuvor in Japan, Italien und Dänemark gefunden. Interessanterweise wurde die Insertion bisher nur bei Hühnerisolaten nachgewiesen. Zusätzlich wurde eine Pilotuntersuchung basierend auf klassischer MLST durchgeführt, um die genetische Verwandtschaft von C. perfringens bei einzelnen erkrankten Vögeln zu bestimmen. Die untersuchten Isolate von zwei Vögeln (Vogel Nr. 1 und Nr. 2) gehören jeweils zu einem einzigen MLST-Sequenztyp (ST45 und ST46) in Übereinstimmung mit verschiedenen Berichten, die eine begrenzte Vielfalt von Stämmen bei von NE betroffenen Vögeln beschrieben. Allerdings gehörten die Isolate von Vogel Nr. 3 zu drei verschiedenen STs. Der Vergleich der MLST-Daten für die 12 Stämme dieser Studie mit den in früheren Untersuchungen beschriebenen MLST-Daten ergab, dass die 12 Stämme neuen STs zugeordnet wurden und nicht zu den zuvor beschriebenen "NE-assoziierten" Genotypen (ST31, CC-4) gehören. 3. Entwicklung und Anwendung eines Core-genom basierten Multilocus-Sequenz-Typisierungssystems für C. perfringens Die Ganzgenomsequenzierung kann einen vollständigen Überblick über die genetische Information eines Organismus geben, stellt aber auch ein leistungsfähiges molekularepidemiologisches Werkzeug für die Subtypisierung von Krankheitserregern und die Untersuchung von Ausbrüchen dar. In dieser Studie wurde ein cgMLST-Schema mit 1.450 Genen für die Typisierung von C. perfringens entwickelt. Das entwickelte Schema wurde auf ein Set von 160 Genomen angewendet. Durchschnittlich 99,5% der cgMLST-Ziele wurden pro Genom als typisierbar gewertet. Das Schema hat eine größere diskriminatroische Power als die klassischen MLST-Methoden. Darüber hinaus wurde eine Gesamt-Genom basierte SNPTypisierung durchgeführt. Die Trennschärfe zwischen der cgMLST und der Gesamt-Genom SNP-Typisierung war vergleichbar. Das entwickelte cgMLST-Schema wurde mit einem Clustertyp (CT)-Schwellenwert von 60 allelischen Differenzen angewendet, um 87 Genome von Geflügelstämmen von C. perfringens zu analysieren. Basierend auf den cgMLSTErgebnissen enthielten die meisten Clustertypen (CTs) Isolate, die nur aus einem einzigen Land stammen. Andererseits beherbergen nur wenige CTs Stämme, die in verschiedenen Ländern isoliert wurden. Dies könnte auf das Geflügelhandelssystem zurückzuführen sein, das wahrscheinlich von wenigen Unternehmen unterhalten wird, d.h. von wenigen Quellen weltweit. Im Vergleich zu Isolaten von gesunden Vögeln und aus Fleischproben, wurde bei den vermeintlichen nekrotische Enteritis (NE) Isolaten aus Ägypten eine begrenzte Vielfalt festgestellt, was die Hypothese stützt, dass bestimmte Isolate NE verursachen. Isolate von kranken Vögeln wurden mit Isolaten von gesunden Vögeln oder Fleischproben gruppiert, dies unterstreicht den multifaktoriellen Charakter der Krankheit und die weite Verbreitung potenziell virulenter Stämme. Zusätzlich konnten die 160 in dieser Studie untersuchten Genome mittels hierBAPS in vier Hauptphylogruppen eingeteilt werden. Die Gesamt-Genom SNP-Typisierung zeigte eine überlegene Eignung zur Abgrenzung dieser Phylogruppen. Zwischen den Phylogruppen wurde eine minimale SNP-Differenz von ~ 40.000 SNPs beobachtet. In Summe wurde ein gut anwendbares cgMLST-Schema für C. perfringens entwickelt, das für breite und standardisierte epidemiologische Untersuchungen verwendbar ist. Andererseits kann die Gesamt-Genom SNP-Typisierung die Zugehörigkeit einzelner Isolate zu den Hauptphylogruppen von C. perfringens detaillierter abbilden

First Description of <i>Mergibacter septicus</i> Isolated from a Common Tern (<i>Sterna hirundo</i>) in Germany

Mergibacter septicus (M. septicus), previously known as Bisgaard Taxon 40, is a recently described species within the Pasteurellaceae family. In this study, we present a M. septicus strain isolated from a common tern (Sterna hirundo) chick that died just after fledging from the Banter See in Wilhelmshaven, Germany. The recovered M. septicus strain underwent microbiological phenotypic characterization, followed by whole genome sequencing on Illumina and Nanopore platforms. Phenotypically, M. septicus 19Y0039 demonstrated resistance to colistin, cephalexin, clindamycin, oxacillin, and penicillin G. The genome analysis revealed a circular 1.8 Mbp chromosome without any extrachromosomal elements, containing 1690 coding DNA sequences. The majority of these coding genes were associated with translation, ribosomal structure and biogenesis, followed by RNA processing and modification, and transcription. Genetic analyses revealed that the German M. septicus strain 19Y0039 is related to the American strain M. septicus A25201T. Through BLAST alignment, twelve putative virulence genes previously identified in the M. septicus type strain A25201T were also found in the German strain. Additionally, 84 putative virulence genes distributed across nine categories, including immune modulation, effector delivery system, nutrition/metabolic factors, regulation, stress survival, adherence, biofilm, exotoxin, and motility, were also identified

Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance

Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases. The custom-made databases identified a large repertoire of potential resistance and virulence-associated genes. This study provides the first resistance and virulence determinants database for A. butzleri