CPRMethicillin resistant coagulase-negative staphylococci isolated from South Korean ducks exhibiting tremor

Coagulase-negative staphylococci are the main causes of bacterial meningitis in duck

Since September 2018, serious meningitis has been found on some breeding-duck farms in Shandong Province, China. A large number of ducks exhibit severe neurological symptoms. The ducks were randomly selected for laboratory testing. Duck brain samples were collected using standard sterile techniques, and the staphylococci isolates were detected in 404 (70.14%) out of 576 brain samples. A total of 525 coagulase-negative staphylococci (CoNS) strains were isolated, including 6 species: Staphylococcus sciuri (S. sciuri) (67.24%, 353/525), Staphylococcus epidermidis (S. epidermidis) (9.71%, 51/525), Staphylococcus saprophyticus (S. saprophyticus) (8.38%, 44/525), Staphylococcus lentus (S. lentus) (7.62%, 40/525), Staphylococcus haemolyticus (S. haemolyticus) (2.48%, 13/525), and Staphylococcus xylosus (S. xylosus) (4.57%, 24/525). Mixed strain infections were detected in 121 (29.95%) infected presentations. The antimicrobial susceptibility testing indicated that 40.38% of the isolates exhibited multi-drug resistance, and 53.90% of the strains were methicillin-resistant strains by amplification of the methicillin resistance gene (mecA) gene. Through experimental reproduction of the disease, we determined that the CoNS strains were the leading pathogens causing bacterial meningitis in ducks. Although these CoNS strains does not directly cause the death of sick ducks, they still cause large economic losses due to the retarded growth and development of the sick ducks, lower feed returns, and lower grades of processed duck products. The results of this study will contribute to our understanding of the epidemiology and pathogenesis of CoNS and be helpful in the prevention and treatment of the infection.

Genomic and biological characteristics of a novel lytic phage, vB_MscM-PMS3, infecting the opportunistic zoonotic pathogen Mammaliicoccus sciuri

Mammaliicoccus sciuri is an opportunistic zoonotic pathogen in humans and animals. We isolated the Mammaliicoccus phage vB_MscM-PMS3, which was also able to infect and lyse M. sciuri and M. lentus. The phage genome is a linear dsDNA that is 147,811 bp in length and contains 206 ORFs and three tRNA genes. It showed low genome coverage (< 17%) and sequence identity (< 91.3%) to other phage genomes. Phylogenetic analysis based on the whole genome and major capsid protein revealed that this phage clustered with members of the subfamily Twortvirinae of the family Herelleviridae, but it was distinctly separated from the other members, indicating its uniqueness.

The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed

Methicillin-resistant Staphylococcus sciuri (MRSS) strain C2865 from a stranded dog in Nigeria was trimethoprim (TMP) resistant but lacked formerly described staphylococcal TMP-resistant dihydrofolate reductase genes (dfr). Whole-genome sequencing, comparative genomics, and pan-genome analyses were pursued to unveil the molecular bases for TMP resistance via resistome and mobilome profiling. MRSS C2865 comprised a species subcluster and positioned just above the intraspecies boundary. Lack of species host tropism was observed. S. sciuri exhibited an open pan-genome, while MRSS C2865 harbored the highest number of unique genes (75% associated with mobilome). Within this fraction, we discovered a transferable TMP resistance gene, named dfrE, which confers high-level TMP resistance in Staphylococcus aureus and Escherichia coli. dfrE was located in a novel multidrug resistance mosaic plasmid (pUR2865-34) encompassing adaptive, mobilization, and segregational stability traits. dfrE was formerly denoted as dfr_like in Exiguobacterium spp. from fish farm sediment in China but escaped identification in one macrococcal and diverse staphylococcal genomes in different Asian countries. dfrE shares the highest identity with dfr of soil-related Paenibacillus anaericanus (68%). Data analysis discloses that dfrE has emerged from a single ancestor and places S. sciuri as a plausible donor. C2865 unique fraction additionally enclosed novel chromosomal mobile islands, including a multidrug-resistant pseudo-SCCmec cassette, three apparently functional prophages (Siphoviridae), and an SaPI4-related staphylococcal pathogenicity island. Since dfrE seems not yet common in staphylococcal clinical specimens, our data promote early surveillance and enable molecular diagnosis. We evidence the genome plasticity of S. sciuri and highlight its role as a resourceful reservoir for adaptive traits.

IMPORTANCE The discovery and surveillance of antimicrobial resistance genes (AMRG) and their mobilization platforms are critical to understand the evolution of bacterial resistance and to restrain further expansion. Limited genomic data are available on Staphylococcus sciuri; regardless, it is considered a reservoir for critical AMRG and mobile elements. We uncover a transferable staphylococcal TMP resistance gene, named dfrE, in a novel mosaic plasmid harboring additional resistance, adaptive, and self-stabilization features. dfrE is present but evaded detection in diverse species from varied sources geographically distant. Our analyses evidence that the dfrE-carrying element has emerged from a single ancestor and position S. sciuri as the donor species for dfrE spread. We also identify novel mobilizable chromosomal islands encompassing AMRG and three unrelated prophages. We prove high intraspecies heterogenicity and genome plasticity for S. sciuri. This work highlights the importance of genome-wide ecological studies to facilitate identification, characterization, and evolution routes of bacteria adaptive features.

First Description in Greece of mphC-Positive Staphylococci Causing Subclinical Mastitis in Ewes

The aim of the present study was to describe the first mphC-positive staphylococci, including two Staphylococcus lentus (Sle-087lar and Sle-091lar) and one Staphylococcus xylosus (Sxy-228lar), isolated from samples of animal origin, in Greece. Isolates Sle-087lar and Sxy-228lar were resistant to erythromycin, whereas Sle-091lar was resistant to erythromycin and lincomycin. All three isolates were susceptible to the remaining antibiotics. PCR screening showed that isolate Sle-091lar carried also ermB. For Sxy-228lar, whole-genome sequencing (WGS) and de novo assembly obtained an mphC-positive contig of 57.3-kb exhibiting high similarity with the genome of mphC-negative S. xylosus S170. However, mphC of Sxy-228lar was 91% similar to that found in plasmid pJW2311 from S. xylosus JW2311. Additionally, WGS data showed that Sle-087lar and Sle-091lar harbored mphC-carrying sequences being highly similar to the recently announced genome of the mphC-carrying S. lentus isolate 050AP from Tanzania. However, differences were observed in the mphC environment, suggesting the independent acquisition of the gene by each isolate. Sle-091lar also harbored transposon Tn917, which carries ermB resistance gene, integrated into S. lentus chromosome. These findings indicated that acquisition of resistance genes can lead to the emergence of multiresistant staphylococci, causing animal infections with economic burden.

Complete Genome Sequence of the Novel Bacteriophage pSco-10 Infecting Staphylococcus cohnii

Herein, we report the complete genome sequence of the Staphylococcus Myoviridae phage pSco-10 infecting Staphylococcus cohnii. The phage pSco-10 was isolated from duck feces collected from four farms in South Korea. The current report provides valuable information for genomic study of phages.

Complete genome sequence of multidrug-resistant Staphylococcus sciuri strain SNUDS-18 isolated from a farmed duck in South Korea

OBJECTIVES

This study aimed to determine the complete genome sequence of multidrug-resistant Staphylococcus sciuri strain SNUDS-18 isolated from a farmed duck in South Korea.

METHODS

Genomic DNA was sequenced using a PacBio RS II system. The obtained genome was annotated and antimicrobial resistance and virulence genes were identified.

RESULTS

The sequenced genome possessed a mecA homologue (mecA1) that was almost identical to that of other oxacillin-susceptible S. sciuri strains, whereas the staphylococcal cassette chromosome mec (SCCmec) was not detected. Moreover, various antimicrobial resistance genes conferring resistance to β-lactams, aminoglycosides, phenicols, tetracycline and macrolide-lincosamide-streptogramin B (MLS_B) antimicrobials were identified.

CONCLUSIONS

The SNUDS-18 genome and its associated genomic data will provide important insights into the biodiversity of the S. sciuri group as well as valuable information for the control of this potential pathogen.

Complete genome sequence of multidrug-resistant Staphylococcus cohnii ssp. urealyticus strain SNUDS-2 isolated from farmed duck, Republic of Korea

OBJECTIVES

Staphylococcus cohnii has become increasingly recognized as a potential pathogen of clinically significant nosocomial and farm animal infections. This study was designed to determine the genome of a multidrug-resistant S. cohnii subsp. urealyticus strain SNUDS-2 isolated from a farmed duck in Korea.

METHODS

Genomic DNA was sequenced using the PacBio RS II system. The complete genome was annotated and the presence of antimicrobial resistance and virulence genes were identified.

RESULTS

The annotated 2,625,703 bp genome contained various antimicrobial resistance genes conferring resistance to β-lactam, aminoglycosides, fluoroquinolones, phenicols and trimethoprim. The virulence-associated three synergistic hemolysins have been identified in the strain.

CONCLUSIONS

To the best of our knowledge, this is the first complete genome of S. cohnii, and will provide important insights into the biodiversity of CoNS and valuable information for the control of this emerging pathogen.

Antimicrobial resistance in coagulase-negative staphylococci from Nigerian traditional fermented foods

Background

Coagulase-negative staphylococci have become increasingly recognized as the etiological agent of some infections. A significant characteristic of coagulase-negative staphylococci especially strains isolated from animals and clinical samples is their resistance to routinely used antibiotics although, resistant strains isolated from fermented foods have not been fully reported.

Methods

A total of two hundred and fifty-five CoNS isolates were subjected to antimicrobial susceptibility test using the disc diffusion technique. The minimum inhibitory concentration of the isolates to the tested antibiotics was determined using the microbroth dilution method. Methicillin resistant strains were confirmed by detection of methicillin resistant genes (mecA) and also employing cefoxitin screening test.

Results

The isolates were confirmed to be methicillin resistant by the detection of mecA genes and the cefoxitin screening test. The isolates demonstrated appreciable resistance to ampicillin (86.7%), sulfomethoxazole–trimethoprim (74.9%), amoxicillin–clavulanic acid (52.5%) and oxacillin (35.7%). Methicillin resistance was exhibited by 13 out of the 255 isolates although no mecA gene was detected. It was also observed that the methicillin resistant isolates were prevalent in these traditional foods; iru, kindirmo, nono and wara.

Conclusion

This study has ameliorated the incidence of multiple antibiotic resistant coagulase-negative staphylococci in Nigerian fermented foods and if not tackled adequately might lead to horizontal transfer of antibiotic resistance from food to man.

Prevalence of the Antibiotic Resistance Genes in Coagulase-Positive-and Negative-Staphylococcus in Chicken Meat Retailed to Consumers

The use of antibiotics in farm management (growing crops and raising animals) has become a major area of concern. Its implications is the consequent emergence of antibiotic resistant bacteria (ARB) and accordingly their access into the human food chain with passage of antibiotic resistance genes (ARG) to the normal human intestinal microbiota and hence to other pathogenic bacteria causative human disease. Therefore, we pursued in this study to unravel the frequency and the quinolone resistance determining region, mecA and cfr genes of methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), methicillin-resistant coagulase-negative staphylococci (MRCNS) and methicillin-susceptible coagulase-negative staphylococci (MSCNS) isolated from the retail trade of ready-to-eat raw chicken meat samples collected during 1 year and sold across the Great Cairo area. The 50 Staphylococcus isolated from retail raw chicken meat were analyzed for their antibiotic resistance phenotypic profile on 12 antibiotics (penicillin, oxacillin, methicillin, ampicillin-sulbactam, erythromycin, tetracycline, clindamycin, gentamicin, ciprofloxacin, chloramphenicol, sulfamethoxazole-trimethoprim, and vancomycin) and their endorsement of the quinolone resistance determining region, mecA and cfr genes. The isolation results revealed 50 isolates, CPS (14) and CNS (36), representing ten species (S. aureus, S. hyicus, S. epidermedius, S. lugdunensis, S. haemolyticus, S. hominus, S. schleiferi, S. cohnii, S. intermedius, and S. lentus). Twenty seven isolates were methicillin-resistant. Out of the characterized 50 staphylococcal isolates, three were MRSA but only 2/3 carried the mecA gene. The ARG that bestows resistance to quinolones, β-lactams, macrolides, lincosamides, and streptogramin B [MLS(_B)] in MRSA and MR-CNS were perceived. According to the available literature, the present investigation was a unique endeavor into the identification of the quinolone-resistance-determining-regions, the identification of MRSA and MR-CNS from retail chicken meat in Egypt. In addition, these isolates might indicate the promulgation of methicillin, oxacillin and vancomycin resistance in the community and imply food safety hazards.