Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis

Staphylococcus borealis - A newly identified pathogen of bovine mammary glands

Twelve Staphylococcus borealis strains, isolated in Canada and Poland from milk of cows with intramammary infections, were characterized phenotypically (biochemical reactions on ID 32 STAPH and Biolog Phenotype MicroArrays™ PM1 and PM2A, ability of biofilm production) and genotypically (random amplified polymorphic DNA). In addition, a genomic comparison was done with S. borealis strains of human and porcine origin using the multilocus sequence typing (MLST) technique. The bovine isolates showed a high degree of phenotypic and genotypic diversity, however, they could be differentiated from human strains by the negative test for urease (found in all but one bovine isolate examined with ID 32 STAPH) and positive reaction for D-galactose (on Biolog phenotype microarray PM1) and D-lactose (on both commercial systems). The MLST method, utilizing six concatenated genes of the total length of ∼2930 bp, revealed that bovine strains (irrespective of the country of origin) show a distinctly greater degree of mutual relationship than to the strains of human and porcine origin, suggesting that S. borealis has evolved independently in these hosts. In conclusion, bovine-specific S. borealis can be involved in intramammary infections in cattle.

Spontaneous Genomic Variation as a Survival Strategy of Nosocomial Staphylococcus haemolyticus

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.

Evaluation of the antimicrobial function of Ginkgo biloba exocarp extract against clinical bacteria and its effect on Staphylococcus haemolyticus by disrupting biofilms

ETHNOPHARMACOLOGICAL RELEVANCE

The fruit of Ginkgo biloba L. (Ginkgo nuts) has been used for a long time as a critical Chinese medicine material to treat cough and asthma, as well as a disinfectant. Similar records were written in the Compendium of Materia Medica (Ben Cao Gang Mu, pinyin in Chinese) and Sheng Nong's herbal classic (Shen Nong Ben Cao Jing, pinyin in Chinese). Recent research has shown that Ginkgo biloba exocarp extract (GBEE) has the functions of unblocking blood vessels and improving brain function, as well as antitumour activity and antibacterial activity. GBEE was shown to inhibit methicillin-resistant Staphylococcus aureus (MRSA) biofilm formation as a traditional Chinese herb in our previous report in this journal. AIM OF THE STUD: yThe antibiotic resistance of clinical bacteria has recently become increasingly serious. Thus, this study aimed to investigate the Ginkgo biloba exocarp extract (GBEE) antibacterial lineage, as well as its effect and mechanism on S. haemolyticus biofilms. This study will provide a new perspective on clinical multidrug resistant (MDR) treatment with ethnopharmacology herbs.

METHODS

The microbroth dilution assay was carried out to measure the antibacterial effect of GBEE on 13 types of clinical bacteria. Bacterial growth curves with or without GBEE treatment were drawn at different time points. The potential targets of GBEE against S. haemolyticus were screened by transcriptome sequencing. The effects of GBEE on bacterial biofilm formation and mature biofilm disruption were determined by crystal violet staining and scanning electron microscopy. The metabolic activity of bacteria inside the biofilm was assessed by colony-forming unit (CFU) counting and (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2HY-tetrazolium bromide (MTT) assay. Quantitative polymerase chain reaction (qPCR) was used to measure the gene expression profile of GBEE on S. haemolyticus biofilm-related factors.

RESULTS

The results showed that GBEE has bacteriostatic effects on 3 g-positive (G⁺) and 2 g-negative (G^-) bacteria among 13 species of clinical bacteria. The antibacterial effect of GBEE supernatant liquid was stronger than the antibacterial effect of GBEE supernviaould-like liquid. GBEE supernatant liquid inhibited the growth of S. epidermidis, S. haemolyticus, and E. faecium at shallow concentrations with minimum inhibitory concentrations (MICs) of 2 μg/ml, 4 μg/ml and 8 μg/ml, respectively. Genes involved in quorum sensing, two-component systems, folate biosynthesis, and ATP-binding cassette (ABC) transporters were differentially expressed in GBEE-treated groups compared with controls. Crystal violet, scanning electron microscopy (SEM) and MTT assays showed that GBEE suppressed S. haemolyticus biofilm formation in a dose-dependent manner. Moreover, GBEE supernatant liquid downregulated cidA, cidB and atl, which are involved in cell lysis and extracellular DNA (eDNA) release, as well as downregulated the cbp, ebp and fbp participation in encoding cell-surface binding proteins.

CONCLUSIONS

GBEE has an excellent antibacterial effect on gram-positive bacteria and also inhibits the growth of gram-negative bacteria, such as A. baumannii (carbapenem-resistant Acinetobacter baumannii) CRABA and S. maltophilia. GBEE inhibits the biofilm formation of S. haemolyticus by altering the regulation and biofilm material-related genes, including the release of eDNA and cell-surface binding proteins.

Influence of Sub-Inhibitory Dosage of Cefotaxime on Multidrug Resistant Staphylococcus haemolyticus Isolated from Sick Neonatal Care Unit

Staphylococcus haemolyticus has emerged to be a frequently encountered late-onset sepsis pathogen among newborn infants. Critical care of neonates involves substantial usage of antibiotics and these pathogens are often exposed to sub-optimal doses of antibiotics which can augment maintenance of selection determinants and a range of physiological effects, prime among them being biofilm formation. Therefore, in this study, the outcome of a sub-inhibitory dosage of a commonly prescribed third-generation antibiotic, cefotaxime (CTX), on multidrug resistant (MDR) S. haemolyticus, was investigated. A total of 19 CTX-resistant, MDR and 5 CTX-susceptible strains isolated from neonates were included. Biofilm-forming abilities of S. haemolyticus isolates in the presence of sub-optimal CTX (30 μg/mL) were determined by crystal violet assays and extracellular DNA (eDNA) quantitation. CTX was found to significantly enhance biofilm production among the non-susceptible isolates (p-valueWilcoxintest—0.000008) with an increase in eDNA levels (p-valueWilcoxintest—0.000004). Further, in the absence of antibiotic selection in vitro, populations of MDR isolates, JNM56C1 and JNM60C2 remained antibiotic non-susceptible after >500 generations of growth. These findings demonstrate that sub-optimal concentration of CTX induces biofilm formation and short-term non-exposure to antibiotics does not alter non-susceptibility among S. haemolyticus isolates under the tested conditions.

Characterization of New Staphylococcus haemolyticus ST42 Populations in Northern Taiwan

Introduction: Staphylococcus haemolyticus is an acquired opportunistic pathogen causing nosocomial infections. Our previous studies of S. haemolyticus showed a group of isolates that produced a significantly higher disease severity than the others. Further molecular typing showed that the sequence type (ST) 42 was the major clone among the isolates. The main aim of this study was to characterize ST42. Materials and Methods: Sixty-one and 36 isolates were collected from burn and nonburn patients, respectively. Molecular typing, antibiotic susceptibility assays, and phenotypic characterizations were performed. Results: Thirteen STs, including seven new STs, were established (ST42 to ST48). ST42 was prevalent in burn and nonburn patients, and all the pulsotype C isolates were ST42. Four of the novel STs originated from ST3, suggesting that these clonal lineages evolved locally. ST3 and ST42 showed a significant difference in clindamycin susceptibility; molecular typing showed only one MLST locus variation among seven loci in SH1431, which has been reportedly involved in the regulation of biofilm formation through Zn ²⁺ binding affinities. Conclusions: Seven novel S. haemolyticus STs were identified; phylogenetic analysis suggested the presence of locally evolved clonal lineages. The predominant ST42 showed weak biofilm formation abilities; other factors that cause the clonal lineage change still need further investigation.

Vancomycin heteroresistance in Staphylococcus haemolyticus: elusive phenotype

Aim

To determine the presence of vancomycin heteroresistance in Staphylococcus haemolyticus.

Materials & methods

A total of 48 rifampicin-resistant S. haemolyticus isolates from bloodstream infections were included. Vancomycin heteroresistance was determined using the population analysis profile-area under curve (PAP-AUC) method. All the isolates were screened for the presence of mecA gene, mutations in the rpoB gene, staphylococcal cassette chromosome mec and multilocus sequence types.

Results

Fifteen isolates were identified as heteroresistant vancomycin-intermediate S. haemolyticus using PAP-AUC method. Dual rpoB mutations (D471E and I527M) contributed for the rifampicin resistance. The sequence types of heteroresistant vancomycin-intermediate S. haemolyticus were highly diverse.

Conclusion

These findings illustrate the potential of S. haemolyticus to develop heteroresistance, which emphasizes the need for routine surveillance of S. haemolyticus isolated from intensive care units for infection control practices.

First Case of Staphylococci Carrying Linezolid Resistance Genes from Laryngological Infections in Poland

Linezolid is currently used to treat infections caused by multidrug-resistant Gram-positive cocci. Both linezolid-resistant S. aureus (LRSA) and coagulase-negative staphylococci (CoNS) strains have been collected worldwide. Two isolates carrying linezolid resistance genes were recovered from laryngological patients and characterized by determining their antimicrobial resistance patterns and using molecular methods such as spa typing, MLST, SCCmec typing, detection of virulence genes and ica operon expression, and analysis of antimicrobial resistance determinants. Both isolates were multidrug resistant, including resistance to methicillin. The S. aureus strain was identified as ST-398/t4474/SCCmec IVe, harboring adhesin, hemolysin genes, and the ica operon. The S. haemolyticus strain was identified as ST-42/mecA-positive and harbored hemolysin genes. Linezolid resistance in S. aureus strain was associated with the mutations in the ribosomal proteins L3 and L4, and in S. haemolyticus, resistance was associated with the presence of cfr gene. Moreover, S. aureus strain harbored optrA and poxtA genes. We identified the first case of staphylococci carrying linezolid resistance genes from patients with chronic sinusitis in Poland. Since both S. aureus and CoNS are the most common etiological factors in laryngological infections, monitoring of such infections combined with surveillance and infection prevention programs is important to decrease the number of linezolid-resistant staphylococcal strains.

Genomic investigation of clinically significant coagulase-negative staphylococci

Introduction. Coagulase-negative staphylococci have been recognized both as emerging pathogens and contaminants of clinical samples. High-resolution genomic investigation may provide insights into their clinical significance.Aims. To review the literature regarding coagulase-negative staphylococcal infection and the utility of genomic methods to aid diagnosis and management, and to identify promising areas for future research.Methodology. We searched Google Scholar with the terms (Staphylococcus) AND (sequencing OR (infection)). We prioritized papers that addressed coagulase-negative staphylococci, genomic analysis, or infection.Results. A number of studies have investigated specimen-related, phenotypic and genetic factors associated with colonization, infection and virulence, but diagnosis remains problematic.Conclusion. Genomic investigation provides insights into the genetic diversity and natural history of colonization and infection. Such information allows the development of new methodologies to identify and compare relatedness and predict antimicrobial resistance. Future clinical studies that employ suitable sampling frames coupled with the application of high-resolution whole-genome sequencing may aid the development of more discriminatory diagnostic approaches to coagulase-staphylococcal infection.

Staphylococcus borealis sp. nov., isolated from human skin and blood

When analysing a large cohort of Staphylococcus haemolyticus, using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as S. haemolyticus based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to S. haemolyticus, these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA-DNA hybridization <70  %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus Staphylococcus and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48^T, is deposited in the Culture Collection University of Gothenburg (CCUG 73747^T) and in the Spanish Type Culture Collection (CECT 30011^T).

Influence of antibiotics on biofilm formation by different clones of nosocomial Staphylococcus haemolyticus

Staphylococcus haemolyticus is the most common organism among clinical isolatesof methicillin-resistant staphylococci. Aim: This study evaluated the ability to produce biofilm with the presence of the antibiotics (1/4 minimum inhibitory concentrations) of S. haemolyticus strains isolated from blood culture. Methods: Clonal distribution was assessed in pulsed-field gel electrophoresis. PCR assays were performed to detect mecA, icaA, aap, atlE, atl, fbp genes. S. haemolyticus strains grown in the presence of the antibiotics were investigated for biofilm formation on glass, polystyrene and catheter surfaces. Results: Biofilm formation was independent of the presence of the icaA and mecA genes, pulsed-field gel electrophoresis type. Vancomycin, oxacillin, moxifloxacin, rifampicin, teicoplanin, tigecycline and linezolid did not inhibit biofilm formation on abiotic surfaces. Conclusion: This study demonstrated that the biofilm formation process is complex and may not be related to ica gene carriage. Furthermore, in this study the biofilm formation was increased in the presence of antimicrobial agents.

Genetic Relatedness of Staphylococcus haemolyticus in Gut and Skin of Preterm Neonates and Breast Milk of Their Mothers

BACKGROUND

Staphylococcus haemolyticus is a common colonizer and cause of late-onset sepsis (LOS) in preterm neonates. By describing genetic relatedness, we aimed to determine whether mother's breast milk (BM) is a source of S. haemolyticus colonizing neonatal gut and skin and/or causing LOS.

METHODS

S. haemolyticus was isolated from stool and skin swabs of 49 BM-fed preterm neonates admitted to neonatal intensive care unit, 20 healthy BM-fed term neonates and BM of mothers once a week and typed by multilocus variable number tandem repeat analysis and multilocus sequence typing. Virulence-related genes were determined by polymerase chain reaction.

RESULTS

Compared with term neonates, S. haemolyticus colonized more commonly gut (35% vs. 89.9%; P < 0.001) and skin (50% vs. 91.8%; P < 0.001) of preterm neonates and mothers' BM (15% vs. 38.8%). Isolates from preterm compared with term neonates and their mothers carried more commonly the mecA gene (83.5% vs. 5.4%; P < 0.001) and IS256 (52.4% vs. 2.7%; P < 0.001) and belonged to clonal complex 29 (89.1% vs. 63%; P = 0.014). Only 7 (14.3%) preterm and 3 (15%) term neonates were colonized in gut or on skin with multilocus variable number tandem repeat analysis types indistinguishable from those in BM. Most frequent multilocus variable number tandem repeat analysis types belonged to sequence type 3 or 42, comprised 71.1%-78.4% of isolates from preterm neonates/mothers and caused all 7 LOS episodes. LOS-causing strain colonized the gut of 4/7 and the skin of 5/7 neonates, but not BM, before onset of LOS.

CONCLUSIONS

S. haemolyticus colonizing gut and skin or causing LOS in preterm neonates rarely originate from BM but are mecA-positive strains adapted to hospital environment.

A Comprehensive Multilocus Sequence Typing Scheme for Identification and Genotyping of Staphylococcus Strains

Increasing clinical significance of coagulase-negative staphylococci requires effective methods for species identification and genotyping. In this study, six housekeeping genes (femA, ftsZ, gap, pyrH, rpoB, and tuf) with extensive allelic polymorphisms were identified and evaluated to develop a comprehensive multilocus sequence typing (MLST) scheme. Selected primers were capable of amplification of the six loci from all of the 180 Staphylococcus strains belonging to 18 different species. Sequence analysis of each locus (44-63 alleles) revealed higher nucleotide diversity than 16S rRNA (28 alleles). Phylogenetic analysis of the concatenated sequences (3054 bp) of the six loci provided accurate species identification and highly discriminatory typing for all the strains. Multilocus allelic analysis of the 180 Staphylococcus strains generated 103 different sequence profiles, suggesting high genetic diversity of the strains. For example, 30 S. aureus, 37 S. epidermidis, 32 S. haemolyticus, and 14 S. hominis strains were typed into 15, 21, 11, and 10 sequence profiles, respectively. Compared with published MLST schemes that restrict on a few particular species, this new scheme both achieved similar discrimination for typing S. aureus, S. epidermidis, S. haemolyticus, and S. hominis and provided sufficient discriminatory power for typing additional opportunistic species, such as S. cohnii, S. capitis, and S. warneri. Importantly, the comprehensive MLST scheme for Staphylococcus strains provides a better genotyping tool for understanding the phylogeny of coagulase-positive Staphylococcus aureus strains.

Higher intake of coagulase-negative staphylococci from maternal milk promotes gut colonization with mecA-negative Staphylococcus epidermidis in preterm neonates

OBJECTIVE

We aimed to determine factors associated with gut colonization of preterm neonates with coagulase-negative staphylococci (CoNS) from maternal milk (MM).

STUDY DESIGN

CoNS isolated from weekly collected stool and MM of hospitalized preterm (n = 49) and healthy term neonates (n = 20) were genotyped. Colonization-related factors were determined by Cox proportional hazards regression.

RESULT

Gut colonization with mecA-negative Staphylococcus epidermidis from MM was less prevalent (40.8% vs. 95%) and delayed (median age 15.5 vs. 2 days) in preterm compared with term neonates. Enhanced colonization was associated with higher intake of CoNS from MM (hazard ratio (95% confidence interval) 1.006 (1.00-1.01) for 10⁶ colony-forming units), lower proportion of mecA-positive predominant NICU strains in gut (0.09 (0.01-0.49) for 1%) and lower incidence of late-onset CoNS sepsis (5% vs. 34% in those without colonization).

CONCLUSION

Enteral feeding with larger proportion of unpasteurized MM and limiting spread of predominant strains may promote colonization with CoNS from MM.

Clinical features, outcomes, and molecular characteristics of an outbreak of Staphylococcus haemolyticus infection, among a mass-burn casualty patient group, in a tertiary center in northern Taiwan

BACKGROUND/PURPOSE

We reported an outbreak of Staphylococcus haemolyticus (SH) infection in a group of young patients (mean age 21.6) simultaneously hospitalized due to a mass-burn incident. This study analyzed the clinical features of these patients and the microbiological characteristics of the outbreak.

METHODS

All 50 patients hospitalized for burns were enrolled, and their clinical differences were analyzed based on culture results. A drug sensitivity test and pulsed-field gel electrophoresis (PFGE) were conducted to analyze the microbiological difference between SH isolates from the mass-burn casualty patients (the study group) and SH isolates from other patients hospitalized during the same period (the control group) with the intention of identifying the strain of SH outbreak.

RESULTS

Patients with isolated SH (N = 36) had a significantly higher disease severity (higher revised Baux score, APACHE II score, and concurrent bacteremia rate), and a significantly poorer clinical outcome (longer ICU and hospital stay, and longer MV usage). Significant differences in the phenotype (antibiotics drug sensitivity test) and genotype (PFGE typing) were observed between the study and control groups. The dominant PFGE type C identified among the study group was related to poorer outcomes in a subgroup analysis.

CONCLUSION

A dominant PFGE type of SH infection was found in these mass-burn casualty patients. Pathogenesis or virulence factors may have contributed to our results. Further study of isolated SH should be conducted.

High diversity in SCCmec elements among multidrug-resistant Staphylococcus haemolyticus strains originating from paediatric patients; characterization of a new composite island

PURPOSE

Staphylococcus haemolyticus has emerged as a highly antimicrobial-resistant healthcare-associated pathogen, in particular for patients admitted to neonatal intensive care. The objective of this study was to study the nature of SCCmec types among MDR-SH strains isolated from paediatric patients.

METHODOLOGY

S. haemolyticus strains (n=60) were isolated from paediatric patients. Antibiotic resistance patterns were established using the disk agar diffusion and micro-broth dilution methods. SCCmec typing was performed using whole-genome sequencing (WGS) and an additional PCR analysis.

RESULTS

All S. haemolyticus isolates demonstrated multidrug resistance. Using WGS, various novel mec types and combinations of SCCmec types were found, including a new composite island [SCCmec type V (Vd)+SCC cad/ars/cop] comprising 30 % of the strains. SCCmec type V was identified in 23 % of the isolates. A combination of the mecA gene enclosed by two copies of IS431 and absence of the mecRI and ccr genes was identified in 11 strains. In total, mecA regulatory genes were absent in all SH isolates used in this study.

CONCLUSION

A high diversity of SCCmec elements with the prevalence of a new composite island was determined among MRSH strains. The structure of the composite island represented by MDR-SH strains in this study, in combination with the presence of a restriction-modification system type III, is described for the first time in this study. The presence of an 8 bp direct repeat (DR) and the sequences flanking the DR may support the integration of the mecA gene complex as a composite transposon (IS431-mecA-IS431) independently from recombinase genes.

Coagulase-Negative Staphylococci in Human Milk From Mothers of Preterm Compared With Term Neonates

BACKGROUND

Human milk is the preferred nutrition for neonates and a source of bacteria. Research aim: The authors aimed to characterize the molecular epidemiology and genetic content of staphylococci in the human milk of mothers of preterm and term neonates.

METHODS

Staphylococci were isolated once per week in the 1st month postpartum from the human milk of mothers of 20 healthy term and 49 preterm neonates hospitalized in the neonatal intensive care unit. Multilocus variable-number tandem-repeats analysis and multilocus sequence typing were used. The presence of the mecA gene, icaA gene of the ica-operon, IS 256, and ACME genetic elements was determined by PCR.

RESULTS

The human milk of mothers of preterm compared with term neonates had higher counts of staphylococci but lower species diversity. The human milk of mothers of preterm compared with term neonates more often contained Staphylococcus epidermidis mecA (32.7% vs. 2.6%), icaA (18.8% vs. 6%), IS 256 (7.9% vs. 0.9%), and ACME (15.4% vs. 5.1%), as well as Staphylococcus haemolyticus mecA (90.5% vs. 10%) and IS 256 (61.9% vs. 10%). The overall distribution of multilocus variable-number tandem-repeats analysis (MLVA) types and sequence types was similar between the human milk of mothers of preterm and term neonates, but a few mecA-IS 256-positive MLVA types colonized only mothers of preterm neonates. Maternal hospitalization within 1 month postpartum and the use of an arterial catheter or antibacterial treatment in the neonate increased the odds of harboring mecA-positive staphylococci in human milk.

CONCLUSION

Limiting exposure of mothers of preterm neonates to the hospital could prevent human milk colonization with more pathogenic staphylococci.

Genetic diversity and population structure of food-borne Staphylococcus carnosus strains

The species Staphylococcus carnosus is a non-pathogenic representative of the coagulase negative staphylococci. Specific strains are applied as meat starter cultures. The species consists of two subspecies, S. carnosus ssp. carnosus and S. carnosus ssp. utilis. In order to place S. carnosus strains, characterized in former studies, in a genetic background that allows a typing of candidates for starter cultures, a Multilocus Sequence Typing (MLST) scheme was developed. Internal fragments of the genes tpiA, xprT, dat, gmk, glpK, narG, cstA, encoding triosephosphate isomerase, xanthine phosphoribosyltransferase, d-amino acid aminotransferase, guanylate kinase, glycerol kinase, the α-chain of the respiratory nitrate reductase, and a carbon starvation protein where chosen. Genes were selected based on their equal distribution in the genome, taxonomic value in subspecies differentiation and metabolic function. This MLST was applied to 44 S. carnosus strains, most of them previously analyzed for their suitability as starter cultures. The number of alleles varied between zero (tpiA) and five (cstA) and allowed the definition of nine sequence types (ST). ST1 was most abundant (18 strains), followed by ST2 (8) and ST4 (6). The nine STs confirmed a close relationship of all strains despite their isolation source and year, but lacked correlation with physiological activities relevant for starter cultures. The low amount of STs in the strain set lets us suggest that recombination between strains is rare. Thus, it is hypothesized that evolutionary events seem to be due to single point mutations rather than intrachromosomal recombination, and that the species possesses a clonal population structure.

Identification of Novel Sequence Types among Staphylococcus haemolyticus Isolated from Variety of Infections in India

The aim of this study was to determine sequence types of 34 S. haemolyticus strains isolated from a variety of infections between 2013 and 2016 in India by MLST. The MEGA5.2 software was used to align and compare the nucleotide sequences. The advanced cluster analysis was performed to define the clonal complexes. MLST analysis showed 24 new sequence types (ST) among S. haemolyticus isolates, irrespective of sources and place of isolation. The finding of this study allowed to set up an MLST database on the PubMLST.org website using BIGSdb software and made available at http://pubmlst.org/shaemolyticus/. The data of this study thus suggest that MLST can be used to study population structure and diversity among S. haemolyticus isolates.

Multidrug-resistant Staphylococcus haemolyticus isolates from infected eyes and healthy conjunctivae in India

This study aimed to determine the presence of antibiotic resistance genes (ARGs), SCCmec elements and genetic relatedness among Staphylococcus haemolyticus isolated from patients with a variety of eye infections (n=11) and from healthy conjunctiva (n=7). Minimum inhibitory concentrations were determined for 14 antimicrobials according to BSAC guidelines. PCR was used to identify the presence of mecA, mecC, SCCmec type and ARGs. Sequencing was used to determine mutations in gyrA, gyrB, topoisomerase IVA and IVB genes. Genetic relatedness was determined by PFGE. Of the 18 isolates, 17 showed resistance to at least one antibiotic, but none showed resistance to vancomycin or rifampicin. Ten isolates were oxacillin-resistant and carried the mecA gene, eight of which belonged to SCCmec type V. The presence of non-mec SCC elements in two meticillin-susceptible isolates and untypeable SCC elements in meticillin-resistant isolates suggests the involvement of S. haemolyticus in the diversification of SCC elements. Sequence analysis revealed point mutations in gyrA (Ser-84→Leu) and topoisomerase IVA genes (Ser-80→Leu) in 13 isolates, and additional variation in the QRDR (Asp-84→Asn) of two isolates, showing good correlation between mutations in gyrA and topoisomerase IV genes and the level of resistance to fluoroquinolones. PFGE analysis showed distinct pulsotypes forming two major clusters, indicating the existence of diversity among isolates, irrespective of the source of isolation. This study suggests that S. haemolyticus isolates from infected eyes and healthy conjunctivae invariably carried ARGs and SCCmec elements and showed diversity in their genomic content, irrespective of the source of isolation.

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.

Variable number of tandem repeat profiles and antimicrobial resistance patterns of Staphylococcus haemolyticus strains isolated from blood cultures in children

Staphylococcus haemolyticus is a healthcare-associated pathogen and can cause a variety of lifethreatening infections. Additionally, multi-drug resistance (MDR), in particular methicillin-resistant S. haemolyticus (MRSH) isolates, have emerged. Dissemination of such strains can be of great concern in the hospital environment. A total number of 20S. haemolyticus isolates from blood cultures obtained from children were included in this study. A high prevalence of MDR-MRSH isolates with high MIC values to vancomycin was found and 35% of the isolates were intermediate resistant to vancomycin. Multilocus variable number of tandem repeats analysis (MLVF) revealed 5 MLVF types among 20 isolates of S. haemolyticus. Twelve isolates shared the same MLVF type and were isolated from different wards in a pediatric hospital in Iran. This is a serious alarm for infection control; i.e. in the absence of adequate infection diagnostics and infection control guidelines, these resistant strains can spread to other sectors of a hospital and possibly among the community.

Comparative Genotypes, Staphylococcal Cassette Chromosome mec (SCCmec) Genes and Antimicrobial Resistance amongst Staphylococcus epidermidis and Staphylococcus haemolyticus Isolates from Infections in Humans and Companion Animals

This study compares the characteristics of Staphylococcus epidermidis (SE) and Staphylococcus haemolyticus (SH) isolates from epidemiologically unrelated infections in humans (Hu) (28 SE-Hu; 8 SH-Hu) and companion animals (CpA) (12 SE-CpA; 13 SH-CpA). All isolates underwent antimicrobial susceptibility testing, multilocus sequence typing and DNA microarray profiling to detect antimicrobial resistance and SCCmec-associated genes. All methicillin-resistant (MR) isolates (33/40 SE, 20/21 SH) underwent dru and mecA allele typing. Isolates were predominantly assigned to sequence types (STs) within a single clonal complex (CC2, SE, 84.8%; CC1, SH, 95.2%). SCCmec IV predominated among MRSE with ST2-MRSE-IVc common to both Hu (40.9%) and CpA (54.5%). Identical mecA alleles and nontypeable dru types (dts) were identified in one ST2-MRSE-IVc Hu and CpA isolate, however, all mecA alleles and 2/4 dts detected among 18 ST2-MRSE-IVc isolates were closely related, sharing >96.5% DNA sequence homology. Although only one ST-SCCmec type combination (ST1 with a non-typeable [NT] SCCmec NT9 [class C mec and ccrB4]) was common to four MRSH-Hu and one MRSH-CpA, all MRSH isolates were closely related based on similar STs, SCCmec genes (V/V_T or components thereof), mecA alleles and dts. Overall, 39.6% of MR isolates harbored NT SCCmec elements, and ACME was more common amongst MRSE and CpA isolates. Multidrug resistance (MDR) was detected among 96.7% of isolates but they differed in the prevalence of specific macrolide, aminoglycoside and trimethoprim resistance genes amongst SE and SH isolates. Ciprofloxacin, rifampicin, chloramphenicol [fexA, cat-pC221], tetracycline [tet(K)], aminoglycosides [aadD, aphA3] and fusidic acid [fusB] resistance was significantly more common amongst CpA isolates. SE and SH isolates causing infections in Hu and CpA hosts belong predominantly to STs within a single lineage, harboring similar but variable SCCmec genes, mecA alleles and dts. Host and staphylococcal species-specific characteristics were identified in relation to antimicrobial resistance genes and phenotypes, SCCmec and ACME.

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

OBJECTIVES

Staphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation.

METHODS

Whole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny.

RESULTS

SNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A-G), of which four (A-D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication.

CONCLUSIONS

The presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.

Multilocus sequence typing and further genetic characterization of the enigmatic pathogen, Staphylococcus hominis

Staphylococcus hominis is a commensal resident of human skin and an opportunistic pathogen. The species is subdivided into two subspecies, S. hominis subsp. hominis and S. hominis subsp. novobiosepticus, which are difficult to distinguish. To investigate the evolution and epidemiology of S. hominis, a total of 108 isolates collected from 10 countries over 40 years were characterized by classical phenotypic methods and genetic methods. One nonsynonymous mutation in gyrB, scored with a novel SNP typing assay, had a perfect association with the novobiocin-resistant phenotype. A multilocus sequence typing (MLST) scheme was developed from six housekeeping gene fragments, and revealed relatively high levels of genetic diversity and a significant impact of recombination on S. hominis population structure. Among the 40 sequence types (STs) identified by MLST, three STs (ST2, ST16 and ST23) were S. hominis subsp. novobiosepticus, and they distinguished between isolates from different outbreaks, whereas 37 other STs were S. hominis subsp. hominis, one of which was widely disseminated (ST1). A modified PCR assay was developed to detect the presence of ccrAB4 from the SCCmec genetic element. S. hominis subsp. novobiosepticus isolates were oxacillin-resistant and carriers of specific components of SCCmec (mecA class A, ccrAB3, ccrAB4, ccrC), whereas S. hominis subsp. hominis included both oxacillin-sensitive and -resistant isolates and a more diverse array of SCCmec components. Surprisingly, phylogenetic analyses indicated that S. hominis subsp. novobiosepticus may be a polyphyletic and, hence, artificial taxon. In summary, these results revealed the genetic diversity of S. hominis, the identities of outbreak-causing clones, and the evolutionary relationships between subspecies and clones. The pathogenic lifestyle attributed to S. hominis subsp. novobiosepticus may have originated on more than one occasion.

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology

Multi-locus sequence typing (MLST) is a high-resolution genetic typing approach to identify species and strains of pathogens impacting human health, agriculture (animals and plants), and biosafety. In this review, we outline the general concepts behind MLST, molecular approaches for obtaining MLST data, analytical approaches for MLST data, and the contributions MLST studies have made in a wide variety of areas. We then look at the future of MLST and their relative strengths and weaknesses with respect to whole genome sequence typing approaches that are moving into the research arena at an ever-increasing pace. Throughout the paper, we provide exemplar references of these various aspects of MLST. The literature is simply too vast to make this review comprehensive, nevertheless, we have attempted to include enough references in a variety of key areas to introduce the reader to the broad applications and complications of MLST data.