Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus

Abstract

Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a dataset of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.

Methicillin-resistant and methicillin-sensitive Staphylococcus aureus isolates from skin and nares of Brazilian children with atopic dermatitis demonstrate high level of clonal diversity

“…Despite their reported beneficial role, it is worth noting that CoNS are notorious for their antimicrobial resistance and are considered reservoirs of transferable resistance genes, such as SCC mec [ 66 ]. Most of the isolates evaluated in our study were methicillin-resistant, mainly S .…”

Antimicrobial and Methicillin Resistance Pattern of Potential Mastitis-Inducing Staphylococcus aureus and Coagulase-Negative Staphylococci Isolates from the Mammary Secretion of Dairy Goats

“…Another important finding was that resistance to most of the above-mentioned antimicrobials was consistently at a higher prevalence in CoNS compared to S. aureus strains, a trend similar to previous studies [ 19 , 20 , 22 ]. It is worth noting that CoNS are considered an important AMR gene reservoir that contributes to the intra- and inter-species dissemination of resistance within the Staphylococcus genus, with animal hosts and their food products likely acting as major AMR gene exchange hubs [ 19 , 54 , 55 ]. To our knowledge, this is the first study that has provided evidence on resistant CoNS directly isolated from the udder of goats in Greece.…”

Multidrug-Resistant Methicillin-Resistant Coagulase-Negative Staphylococci in Healthy Poultry Slaughtered for Human Consumption

“…mecA 36 , ermA 8 , ermB 8 , ermC 28 , mphC 29 , aph(3′)-IIIa 9 , ant(4′)-Ia 12 , str 2 , tetL 19 , tetK 14 , tetO 1 , tetM 2 , catp194 1 , dfrK 6 , dfrD 2 S. urealyticus 21 PEN 21 , FOX 18 , CIP 3 , CN 4 , TOB 6 , KAN 5 , ERY 21 , CD 21 , TET 21 , C 3 , FD 17 mecA 21 , ermA 1 , ermB 7 , ermC 19 , mphC 16 , aph(3′)-IIIa 5 , ant(4′)-Ia 2 , str 2 , tetL 17 , tetK 18 , tetO 13 , tetM 4 S. sciuri 15 PEN 14 , FOX 6 , LNZ 1 , CIP 3 , TOB 8 , KAN 4 , ERY 14 , CD 14 , TET 15 , C 2 , FD 10 , SXT 2 mecA 15 , cfr 1 , ermB 9 , ermC 7 , mphC 9 , aph(3′)-IIIa 3 , ant(4′)-Ia 7 , str 1 , tetL 11 , tetK 12 , tetO 2 , tetM 3 , dfrK…”

“…mecA 3 , ermB 1 , ermC 2 , mphC 2 , aph(3′)-IIIa 2 , ant(4′)-Ia 1 , str 1 , tetL 3 , tetK 1 , dfrK 1…”

“…Staphylococci are divided into two groups, coagulasepositive (CoPS) and coagulase-negative staphylococci (CoNS), according to their ability to coagulate plasma. CoPS are pathogenic species which have the coagulase enzyme that converts plasma fibrinogen into fibrin [3]. CoNS lack this enzyme and were considered, until recently, to be minor pathogens or apathogenic [4].…”