Diversity of methicillin-resistant coagulase-negative Staphylococcus spp. and methicillin-resistant Mammaliicoccus spp. isolated from ruminants and New World camelids

Information about livestock carrying methicillin-resistant coagulase-negative staphylococci and mammaliicocci (MRCoNS/MRM) is scarce. The study was designed to gain knowledge of the prevalence, the phenotypic and genotypic antimicrobial resistance and the genetic diversity of MRCoNS/MRM originating from ruminants and New World camelids. In addition, a multi-locus sequence typing scheme for the characterization of Mammaliicoccus (formerly Staphylococcus) sciuri was developed. The study was conducted from April 2014 to January 2017 at the University Clinic for Ruminants and the Institute of Microbiology at the University of Veterinary Medicine Vienna. Seven hundred twenty-three nasal swabs originating from ruminants and New World camelids with and without clinical signs were examined. After isolation, MRCoNS/MRM were identified by MALDI-TOF, rpoB sequencing and typed by DNA microarray-based analysis and PCR. Antimicrobial susceptibility testing was conducted by agar disk diffusion. From all 723 nasal swabs, 189 MRCoNS/MRM were obtained. Members of the Mammaliicoccus (M.) sciuri group were predominant (M. sciuri (n = 130), followed by M. lentus (n = 43), M. fleurettii (n = 11)). In total, 158 out of 189 isolates showed phenotypically a multi-resistance profile. A seven-loci multi-locus sequence typing scheme for M. sciuri was developed. The scheme includes the analysis of internal segments of the house-keeping genes ack, aroE, ftsZ, glpK, gmk, pta1 and tpiA. In total, 28 different sequence types (STs) were identified among 92 selected M. sciuri isolates. ST1 was the most prevalent ST (n = 35), followed by ST 2 (n = 15), ST3 and ST5 (each n = 5), ST4 (n = 3), ST6, ST7, ST8, ST9, ST10 and ST11 (each n = 2)

Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile

Abstract While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.1 Introduction 2 Methods 2.1 Sampling and ethics 2.2 Isolation and identification of Clostridioides difficile 2.3 Antimicrobial susceptibility testing 2.4 Whole-genome sequencing and comparative genomic analysis 2.5 Statistical analysis 3 Results 3.1 Prevalence of Clostridioides difficile and risk factors for shedding 3.2 Antimicrobial susceptibility testing and detection of antimicrobial resistance determinants 3.3 Genomic characterization of canine Clostridioides difficile 3.4 Genome annotation and comparison 4 Discussio

Herd-Level Risk Factors for the Seropositivity to Mycoplasma hyopneumoniae and the Occurrence of Enzootic Pneumonia Among Fattening Pigs in Areas of Endemic Infection and High Pig Density

The aim of the present study was to identify potential risk factors for the occurrence of enzootic pneumonia (EP) in herds situated in a region of high pig density, where a majority of herds is endemically infected with Mycoplasma hyopneumoniae. Between 2006 and 2010, overall 100 herds were enrolled in a case–control study. Data were collected through personal interview with the farmers, clinical examination of pigs and their environments, and serological testing for M. hyopneumoniae, swine influenza virus and porcine reproductive and respiratory syndrome virus. There were 40 case herds (coughing index high, seroprevalence high) with a mean coughing index of 4.3 and a seroprevalence of 86.6%. There were two control groups. Control group I consisted of 25 herds (coughing index low, seroprevalence low) with mean values of 0.7 and 11.2%, and 35 herds were allocated to control group II (coughing index low, seroprevalence high) where the mean coughing index was 0.9 and seroprevalence 86.3%. Case herds and control II herds had an increased age of piglets at weaning compared to control I herds. Any contact between fattening pigs of different age during restocking of compartments increased the risk for the occurrence of EP in a herd. Finally, farms that use living animals for the exposure to gilts during the acclimatization and farms that had increased number of weaned piglets per sow and year were less likely to test positive for M. hyopneumoniae and less likely to develop clinical symptoms of EP in fattening pigs

Erratum to "First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarod is sp. nov" [Syst. Appl. Microbiol. 42 (2019) 457-467].

Erratum for: First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. [Syst Appl Microbiol. 2019

First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov

Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 degrees C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated. A genome search against all available marine metagenomes and 16S rRNA gene databases indicated that these two species represent a novel non-free-living marine lineage of Mollicutes, specifically associated with marine animals. Morphology and physiology were compatible with other members of this group, and genomic and phenotypic analyses demonstrated that these organisms represent two novel species of the genus Mycoplasma, for which the names Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. are proposed; the type strains are PET (DSM 105487(T), CIP 111404(T)) and 5H(T) (DSM 105,488(T), CIP 111405(T)), respectively. (C) 2019 Elsevier GmbH. All rights reserved

Mycoplasma taxonomy: what’s in a name and where to submit?

The International Committee on Systematics of Prokaryotes (ICSP) oversees the nomenclature of prokaryotes, naming rules and issues Judicial Commission Opinions concerning taxonomy, Bacteriological Code revisions, etc. Mycoplasmology is represented by a subcommittee of experts on behalf of the International Organization for Mycoplasmology (IOM). Taxonomy of Mollicutes standards (Brown et al., 2007) include deposition: (i) type strains into two culture collections; (ii) 16S rRNA gene sequences with phylogenetic analysis; (iii) demonstration type strains differ from known valid species; (iv) assignment to an order, family and genus in the class. (v) description of novel Mollicutes species should also follow the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes in which genome sequence (complete or draft) the proposed type strain is required (this is not required for Candidatus assignment) (Chun et al., 2018). Antiserum is no longer required (Firrao and Brown 2012); Submission of Mollicutes to culture collections is imperative to assist the community longer term by accessing strains, retaining them for future work and is required when describing a new species. In 2021 the ICSP reviewed international culture collections accepting depositions of Mollicutes. The following collections indicated they accept strains (*with no charge for deposition, shipping fees apply): USA: ATCC* (https://www.lgcstandards-atcc.org/?geo_country=es) France: CIP* (https://catalogue-crbip.pasteur.fr/resultatRecherche.xhtml) Germany: DSMZ* (https://www.dsmz.de/search?tx_kesearch_pi1[sword]=mycoplasma&cHash=e52a26740bdd69d3bf55a6bca2fe6d74) Japan: NBRC (https://www.nite.go.jp/nbrc/catalogue/NBRCDispSearchServlet?lang=en) UK: NCTC* (https://www.phe-culturecollections.org.uk/) Taiwan: BCRC (https://catalog.bcrc.firdi.org.tw/Welcome) (case by case review) Taxonomic naming of new species: Recent publications suggest renaming of species to unusual/unconventional names (Gupta and Oren, 2020). The ICSP Mollicutes Subcommittee is committed to retaining nomenclature aligned to the agreed code and existing scientific/clinical practice, retaining standards for authors naming Mollicutes. Balish et al., 2020 recommended rejection of published names within the class Mollicutes. When considering naming new species, we recommend contacting the committee for advice prior to publication, engage with the Mollicute community prior to publication of controversial changes, especially impacting pathogenic relevant bacteria

Recommended rejection of the names<em> Malacoplasma</em> gen. nov., <em>Mesomycoplasma</em> gen. nov., <em>Metamycoplasma</em> gen. nov., <em>Metamycoplasmataceae</em> fam. nov.,<em> Mycoplasmoidaceae</em> fam. nov., <em>Mycoplasmoidales</em> ord. nov., <em>Mycoplasmoides</em> gen. nov., <em>Mycoplasmopsis</em> gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein.

The consensus of the members of the International Committee on Systematics of Prokaryotes' Subcommittee on the taxonomy of Mollicutes is that recently proposed sweeping changes to nomenclature of members of the Mycoplasmatales, specifically involving introduction of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceaefam. nov., Mycoplasmoidaceaefam. nov., Mycoplasmoidalesord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov., and all proposed species or subspecies comb. nov. placed therein, should be rejected because they violate one or more essential points of the International Code of Nomenclature of Prokaryotes

Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals