Molecular Epidemiology of Methicillin-Resistant Staphylococcus hominis (MRSHo): Low Clonality and Reservoirs of SCCmec Structural Elements

BACKGROUND: Methicillin resistant Staphylococcus hominis (MRSHo) are important human pathogens in immunocompromised patients. However, little is known regarding its population structure and staphylococcal chromosomal cassette mec (SCCmec) content. METHODOLOGY/PRINCIPAL FINDINGS: To assess the population structure and the SCCmec content of S. hominis, 34 MRSHo and 11 methicillin-susceptible S. hominis (MSSHo) from neutropenic patients collected over a 3-year period were studied. The genetic backgrounds of S. hominis isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and SCCmec types were determined by PCR. Cassette chromosome recombinases (ccr) were characterized by PCR and ccrB sequencing. The 34 S. hominis isolates were classified into as many as 28 types and 32 subtypes (SID = 99.82%); clonal dissemination was occasionally observed. The main SCCmec structures identified were SCCmec type VI (4B) (20%), SCCmec VIII (4A) (15%), and a new SCCmec composed of mec complex A in association with ccrAB1 (38%); 27% of the isolates harbored non-typeable SCCmec. Overall, a high prevalence of mec complex A (73.5%), ccrAB1 (50%) and ccrAB4 (44%) were found. Importantly, ccrB1 and ccrB4 from both MRSHo and MSSHo showed a high nucleotide sequence homology with those found in S. aureus SCCmec I, VI and VIII respectively (>95%). CONCLUSIONS/SIGNIFICANCE: The S. hominis population showed a limited clonality and a low genetic diversity in the allotypes of ccr and classes of mec complex. Moreover, our data suggest that S. hominis might have been a privileged source of mec complex A, ccrB1 and ccrB4, for the assembly of primordial SCCmec types

Staphylococcus saprophyticus causing infections in humans is associated with high resistance to heavy metals

Research Areas: Microbiology ; Pharmacology & PharmacyStaphylococcus saprophyticus is a common pathogen of the urinary tract, a heavy metal-rich environment, but information regarding its heavy metal resistance is unknown. We investigated 422 S. saprophyticus isolates from human infection and colonization/contamination, animals, and environmental sources for resistance to copper, zinc, arsenic, and cadmium using the agar dilution method. To identify the genes associated with metal resistance and assess possible links to pathogenicity, we accessed the wholegenome sequence of all isolates and used in silico and pangenome-wide association approaches. The MIC values for copper and zinc were uniformly high (1,600mg/liter). Genes encoding copper efflux pumps (copA, copB, copZ, mco, and csoR) and zinc transporters (zinT, czrAB, znuBC, and zur) were abundant in the population (20 to 100%). Arsenic and cadmium showed various susceptibility levels. Genes encoding the ars operon (arsRDABC), an ABC transporter and a two-component permease, were linked to resistance to arsenic (MICs$1,600mg/liter; 14or cadC and cadD-cadX or czrC) and genes encoding multidrug efflux pumps and hyperosmoregulation in acidified conditions were associated with resistance to cadmium (MICs$ 200mg/liter; 20% [85/422]; P, 0.05). These resistance genes were frequently carried by mobile genetic elements. Resistance to arsenic and cadmium were linked to human infection and a clonal lineage originating in animals (P, 0.05). Altogether, S. saprophyticus was highly resistant to heavy metals and accumulated multiple metal resistance determinants. The highest arsenic and cadmium resistance levels were associated with infection, suggesting resistance to these metals is relevant for S. saprophyticus pathogenicityinfo:eu-repo/semantics/publishedVersio

Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections

Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997-2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016-2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive generic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors

High Genetic Diversity among Community-Associated Staphylococcus aureus in Europe: Results from a Multicenter Study

Background: Several studies have addressed the epidemiology of community-associated Staphylococcus aureus (CA-SA) in Europe; nonetheless, a comprehensive perspective remains unclear. In this study, we aimed to describe the population structure of CA-SA and to shed light on the origin of methicillin-resistant S. aureus (MRSA) in this continent. Methods and Findings: A total of 568 colonization and infection isolates, comprising both MRSA and methicillin-susceptible S. aureus (MSSA), were recovered in 16 European countries, from community and community-onset infections. The genetic background of isolates was characterized by molecular typing techniques (spa typing, pulsed-field gel electrophoresis and multilocus sequence typing) and the presence of PVL and ACME was tested by PCR. MRSA were further characterized by SCCmec typing. We found that 59 % of all isolates were associated with community-associated clones. Most MRSA were related with USA300 (ST8-IVa and variants) (40%), followed by the European clone (ST80-IVc and derivatives) (28%) and the Taiwan clone (ST59-IVa and related clonal types) (15%). A total of 83 % of MRSA carried Panton-Valentine leukocidin (PVL) and 14 % carried the arginine catabolic mobile element (ACME). Surprisingly, we found a high genetic diversity among MRSA clonal types (ST-SCCmec), Simpson’s index of diversity = 0.852 (0.788–0.916). Specifically, about half of the isolates carried novel associations between genetic background and SCCmec. Analysis by BURP showed that some CA-MSSA and CA-MRS

Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus.

Staphylococcus haemolyticus is one of the most common pathogens associated with medical-device related infections, but its molecular epidemiology is poorly explored. In the current study, we aimed to better understand the genetic mechanisms contributing to S. haemolyticus diversity in the hospital environment and their impact on the population structure and clinical relevant phenotypic traits. The analysis of a representative S. haemolyticus collection by multilocus sequence typing (MLST) has identified a single highly prevalent and diverse genetic lineage of nosocomial S. haemolyticus clonal complex (CC) 29 accounting for 91% of the collection of isolates disseminated worldwide. The examination of the sequence changes at MLST loci during clonal diversification showed that recombination had a higher impact than mutation in shaping the S. haemolyticus population. Also, we ascertained that another mechanism contributing significantly to clonal diversification and adaptation was mediated by insertion sequence (IS) elements. We found that all nosocomial S. haemolyticus, belonging to different STs, were rich in IS1272 copies, as determined by Southern hybridization of macrorestriction patterns. In particular, we observed that the chromosome of a S. haemolyticus strain within CC29 was highly unstable during serial growth in vitro which paralleled with IS1272 transposition events and changes in clinically relevant phenotypic traits namely, mannitol fermentation, susceptibility to beta-lactams, biofilm formation and hemolysis. Our results suggest that recombination and IS transposition might be a strategy of adaptation, evolution and pathogenicity of the major S. haemolyticus prevalent lineage in the hospital environment

Spontaneous Genomic Variation as a Survival Strategy of Nosocomial Staphylococcus haemolyticus

Funding Information: This work was funded by project PTDC/CVT-CVT/29510/2017 from Fundação para a Ciência e a Tecnologia (awarded to M.Miragaia); Projects LISBOA-01-0145-FEDER007660 (Microbiologia Molecular, Estrutural e Celular) and UID/Multi/04378/2019 funded by FEDER funds through COMPETE2020—Programa Operacional de Competitividade e Internacionalização (POCI); and by ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI—“Fundos Europeus Estruturais e de Investimento” from “Programa Operacional Regional Lisboa2020” and by national funds through FCT. Publisher Copyright: Copyright © 2023 Bouchami et al.Staphylococcus haemolyticus is one of the most important nosocomial human pathogens frequently isolated in bloodstream and medical device-related infections. However, its mechanisms of evolution and adaptation are still poorly explored. To characterize the strategies of genetic and phenotypic diversity in S. haemolyticus, we analyzed an invasive strain for genetic and phenotypic stability after serial passage in vitro in the absence and presence of beta-lactam antibiotics. We performed pulsed-field gel electrophoresis (PFGE) of the culture and analyzed five colonies at seven time points during stability assays for beta-lactam susceptibility, hemolysis, mannitol fermentation, and biofilm production. We compared their whole genomes and performed phylogenetic analysis based on core single-nucleotide polymorphisms (SNPs). We observed a high instability in the PFGE profiles at the different time points in the absence of antibiotic. Analysis of WGS data for individual colonies showed the occurrence of six large-scale genomic deletions within the oriC environ, smaller deletions in non-oriC environ regions, and nonsynonymous mutations in clinically relevant genes. The regions of deletion and point mutations included genes encoding amino acid and metal transporters, resistance to environmental stress and beta-lactams, virulence, mannitol fermentation, metabolic processes, and insertion sequence (IS) elements. Parallel variation was detected in clinically significant phenotypic traits such as mannitol fermentation, hemolysis, and biofilm formation. In the presence of oxacillin, PFGE profiles were overall stable over time and mainly corresponded to a single genomic variant. Our results suggest that S. haemolyticus populations are composed of subpopulations of genetic and phenotypic variants. The maintenance of subpopulations in different physiological states may be a strategy to adapt rapidly to stress situations imposed by the host, particularly in the hospital environment. IMPORTANCE The introduction of medical devices and antibiotics into clinical practice have substantially improved patient quality of life and contributed to extended life expectancy. One of its most cumbersome consequences was the emergence of medical device-associated infections caused by multidrug-resistant and opportunistic bacteria such as Staphylococcus haemolyticus. However, the reason for this bacterium’s success is still elusive. We found that in the absence of environmental stresses, S. haemolyticus can spontaneously produce subpopulations of genomic and phenotypic variants with deletions/mutations in clinically relevant genes. However, when exposed to selective pressures, such as the presence of antibiotics, a single genomic variant will be recruited and become dominant. We suggest that the maintenance of these cell subpopulations in different physiological states is an extremely effective strategy to adapt to stresses imposed by the host or the infection environment and might contribute for S. haemolyticus survival and persistence in the hospital.publishersversionpublishe

Phylogenetic analysis.

<p>(A) Identification and characterization of a major genetic lineage. Application of eBURST algorithm to MLST data for the collection of 109 <i>S</i>. <i>haemolyticus</i> isolates obtained in this study and that of Cavanagh [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156653#pone.0156653.ref011" target="_blank">11</a>]. The relatedness between STs and clonal complexes was displayed as an eBURST diagram. Each ST is represented by a number and a node, and each line links STs that are single locus variants (SLVs). Bleu node corresponds to the founder (ST29). The size of the node corresponds to the frequency of the isolates. Clusters of linked STs correspond to clonal complexes. (B-C) Phylogenetic trees inferred from the concatenated sequences of the seven MLST loci. Maximum likelihood (ML) Phylogenetic tree was constructed based on concatenated sequences of 7 housekeeping loci for 26 STs obtained in the present study and 17 STs identified in Cavanagh study [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156653#pone.0156653.ref011" target="_blank">11</a>]. The trees were drawn to scale using MEGA 6. The ML analysis identified two groups one containing the great majority of STs that corresponded to CC29 identified by eBURST analysis, and the other containing only four STs. Asterisks indicate the STs identified in this study. STs of CC29 are underlined with red. Each red circle on phylogenetic tree (C) corresponds to an ST [The same ST in ML tree (B)].</p

Molecular characterization of 65 MRSHae and MSSHae isolates.

<p>Molecular characterization of 65 MRSHae and MSSHae isolates.</p

Phenotypic and genotypic <i>In vitro</i> stability.

<p>(A) <i>In vitro</i> stability over time of SmaI PFGE profiles. (B) <i>In vitro</i> stability over time of IS<i>1272</i>-hybridization patterns. Lane M: λ ladder used as a size marker. The positions of molecular markers (in kilobase pairs) are indicated by black lines. The white arrows indicates band loss/gain in PFGE and SmaI-IS<i>1272</i> profiles. The arrowheads on the right of each lane correspond to the appearance of a band. The arrowheads on the left of each lane correspond to the disappearance of a band. At the top of each lane the day that the MRSHae HSM742 isolate was collected is indicated in relation to the first isolate (day 0). (C) Stability over time of phenotypic traits. Oxa, oxacillin; Fox, cefoxitin; empty set (Ø), hemolysis zone diameter; a plus sign indicates fermentation of mannitol; a minus sign indicates no fermentation of mannitol; V, variable. The asterisks indicate days that showed alteration. The presence (dark gray) and absence (light gray) of alteration are indicated by filled rectangles.</p