Phenotypic and genotypic characterization of coagulase-negative staphylococci isolated in blood cultures from patients with haematological malignancies

Prevalence, biofilm formation, and mass spectrometric characterization of linezolid-resistant Staphylococcus capitis isolated from a tertiary hospital in China

OBJECTIVES

Linezolid-resistant Staphylococcus capitis (LRSC) has become a new challenge for clinical anti-infective therapy. The present study aimed to investigate the trends of LRSC prevalence in a tertiary hospital of China 2017-2020. The resistance mechanisms, virulence genes, biofilm formation, and mass spectrometric characteristics of LRSC isolates were also analysed.

METHODS

This study retrospectively analysed the antibiotic resistance trends of coagulase negative staphylococci (CoNS) isolated from clinical samples collected between 2017-2020. Antimicrobial resistance profiles were tested by micro-broth dilution and the E-test method. Antimicrobial resistance genes and virulence genes were detected by polymerase chain reaction, and dru-typing sequences were obtained by Sanger sequencing. Crystal violet staining in 96-well plates was used to detect biofilm formation ability. Mass spectrometric characterization of LRSC was analysed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) coupled with ClinProTools.

RESULTS

The linezolid resistance rate in 3575 CoNS clinical strains was 1.6%, wherein the great majority of was LRSC (91.1%, n = 51/56), with a resistant rate of 15.5% (n = 51/328) in all S. capitis isolates. In this study, 48 out of the 51 LRSC strains and 54 of 277 linezolid-susceptible S. capitis (LSSC) strains were enrolled. G2576T, C2104T, T2130A, C2163T, and T2319C mutations in the 23S rRNA V region and acquisition of cfr were the main linezolid resistant mechanisms in LRSC. The biofilm-forming ability of LRSC was more potent than LSSC, with a higher detection rate of bap (P < 0.05). Eleven mass spectrometric peaks of interest were identified by using MALDI-TOF MS and ClinProTools, which were differently distributed between LRSC and LSSC strains, with the area under the receiver operating characteristic curve of more than 0.8, especially for 5465.37 m/z.

CONCLUSIONS

Linezolid resistance was mediated by mutations in the 23S rRNA V region and presence of the cfr gene in LRSC strains. LRSC strains have stronger biofilm-forming ability than LSSC strains, which maybe associated with the adhesion-related gene of bap. Further, linezolid-resistant and linezolid-susceptible S. capitis could be rapidly identified with mass spectrometric characterization. To the best of our knowledge, this study is the first to document the biofilm formation ability of LRSC and the potential usefulness of MALDI-TOF MS for the discrimination of LRSC and LSSC.

Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden

Emergence of a genetically distinct, multidrug-resistant Staphylococcus capitis clone (NRCS-A) present in neonatal intensive care units has recently been extensively reported. The aims of the present study were to investigate which clones of S. capitis isolated from blood in a Swedish neonatal intensive care unit (NICU) have been present since 1987 and to investigate whether the NRCS-A clone has disseminated in Sweden. All S. capitis isolates from blood cultures of neonates (≤ 28 days of age) between 1987 and 2017 (n = 46) were whole-genome sequenced, and core genome multilocus sequence typing (cgMLST) was performed. Single-nucleotide polymorphism (SNP)-based phylogenetic relationships between the S. capitis isolates and in silico predictions of presence of genetic traits specific to the NRCS-A clone were identified. Furthermore, antibiotic susceptibility testing, including screening for heterogeneous glycopeptide-intermediate resistance, was performed. Thirty-five isolates clustered closely to the isolates previously determined as belonging to the NRCS-A clone and had fewer than 81 core genome loci differences out of 1063. Twenty-one of these isolates were multidrug resistant. The NRCS-A clone was found in 2001. Six pairs of isolates had differences of fewer than two SNPs. Genetic traits associated with the NRCS-A clone such as nsr, ebh, tarJ, and CRISPR were found in all 35 isolates. The increasing incidence of S. capitis blood cultures of neonates is predominantly represented by the NRSC-A clone at our NICU in Sweden. Furthermore, there were indications of transmission between cases; adherence to basic hygiene procedures and surveillance measures are thus warranted.

Different Genotypes of Adhesion Operon Genes in Staphylococcus epidermidis Isolates From Various Ocular Infections

BACKGROUND

Staphylococcus epidermidis is one of the common causes of bacterial keratitis and post-operation infections. One of the most important virulence factors of S. epidermidis is biofilm formation. Poly-N-acetylglucosamine (PNAG) production is critical for biofilm formation in S. epidermidis. The intercellular adhesion (ica) operon is formed by icaA, icaD, icaB, and icaC genes, which participate in the biosynthesis of PNAG. Strains of S. epidermidis from different infections show different genotypes in relation to adhesion operon genes. Therefore, regarding the fact that the pathogenic strain in each community has unique genotypes, this study investigated the relation between ica operon genotypes and various ocular infections. However, the correlation between the ica operon genes and the mecA gene was analyzed in the isolates.

METHODS

For this study, samples of the conjunctiva, cornea, and intraocular fluid of patients with ocular infection were collected. After culture and incubation, detection of S. epidermidis was performed using biochemical and coagulase tests. The antibiotic susceptibility of the bacteria was evaluated by the disk diffusion method. After this, DNA was extracted from the bacteria and the presence of icaA, icaD, is256, and mecA genes was analyzed using polymerase chain reaction.

RESULTS

All 50 coagulase-negative Staphylococcus samples isolated from different eye infections were characterized as S. epidermidis. Most of the samples (36%) were isolated from the cornea and the others were, respectively, from the conjunctiva (24%), vitreous (20%), anterior chamber (8%), eyelid (6%), and nasolacrimal duct (6%). The icaA, icaD, and is256 genes were detected with different genotypes in isolates from keratitis and endophthalmities compared with conjunctivitis. Overall, the most isolated genotype from ocular infections was icaA+. icaD+. is256+. (46%). Most of the isolates (82.60%) had mecA, icaA, and icaD genes simultaneously, which indicates a strong relationship between the adhesion genes and the antibiotic resistance gene.

CONCLUSIONS

The adhesion operon genes were observed with different genotypes in S. epidermidis samples isolated from various ocular infections.

Biochemical Fingerprinting of Methicillin-Resistant Staphylococcus aureus Isolated From Sewage and Hospital in Iran

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is known as a common pathogen in nosocomial and community-acquired infections. Sewage acts as an environmental reservoir and may have a significant role in development and dissemination of antibiotic resistance.

OBJECTIVES

This study was undertaken to determine the epidemiological relatedness between the MRSA isolated from sewage and human infections.

MATERIALS AND METHODS

Samples were collected from a referral hospital and also a sewage treatment plant in Tehran, Iran, during 2010. All the MRSA isolates were identified at the species level and typed using Phene plate (PhP) system and SCCmec typing. Antibiotic susceptibility tests were also performed.

RESULTS

Of the 1142 isolates, 200 MRSA strains from the sewage (n = 100) and the clinic (n = 100) were isolated. Distinct PhP types, consisting of 16 common types and 13 single types, and also 3 different staphylococcal cassette chromosome mec (SCCmec) types (III, IVa and IVc) were found amongst the MRSA isolated from the two different sources. The results of antibiotic susceptibility testing showed an increased resistance to penicillin, ciprofloxacin, erythromycin, clindamycin and tetracycline. In addition, none of the isolates showed resistance to vancomycin, quinupristin -dalfopristin and linezolid.

CONCLUSIONS

The presence of common PhP types and also SCCmec type III, as an indicator for hospital strains, among the isolates, may indicate an epidemiological link between clinical and sewage MRSA isolates in Tehran.

Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies

Staphylococcus epidermidis is an important cause of bloodstream infections in patients with hematological malignancies. Knowledge of the long-term epidemiology of these infections is limited. We surveyed all S. epidermidis blood culture isolates from patients treated for hematological malignancies at the University Hospital of Örebro, Sweden from 1980 to 2009. A total of 373 S. epidermidis isolates were identified and multilocus sequence typing, staphylococcal chromosome cassette mec (SCCmec) typing and standard antibiotic susceptibility testing were employed to characterize these isolates. The majority of the isolates 361/373 (97%) belonged to clonal complex 2, and the 373 isolates were divided into 45 sequence types (STs); Simpson's Diversity Index was 0.56. The most prevalent STs were ST2 (243/373, 65%) and ST215 (28/373, 8%). Ninety three percent (226/243) of the ST2 isolates displayed either SCCmec type III or IV. ST2 and 215 were isolated during the entire study period, and together these STs caused temporal peaks in the number of positive blood cultures of S. epidermidis. Methicillin resistance was detected in 213/273 (78%) of all isolates. In the two predominating STs, ST2 and ST215, methicillin resistance was detected in 256/271 isolates (95%), compared with 34/100 (34%) in other STs (p<0.001). In conclusion, in this long-term study of patients with hematological malignancies, we demonstrate a predominance of methicillin-resistant ST2 among S. epidermidis blood culture isolates.

Characteristics of hospital- and community-acquired meticillin-resistant Staphylococcus aureus in Tehran, Iran

Staphylococcus aureus is a leading cause of hospital-acquired (HA) and community-acquired (CA) infections worldwide. Recently, S. aureus strains resistant to meticillin (MRSA) have become established within both communities. We isolated 314 isolates of MRSA from hospitalized patients in a referral hospital (HA isolates) and 268 isolates from its outpatient clinic (CA isolates) in Tehran, Iran, between February 2008 and December 2010. These isolates were tested for their susceptibility to 17 antibiotics and typed using the PhPlate system. The diversity in the structures of staphylococcal cassette chromosome mec (SCCmec) elements and ccr types was also detected using a multiplex-PCR assay and isolates were examined for the presence of different classes of prophages. Whilst all isolates were resistant to penicillin, the HA isolates were significantly more resistant to all other antibiotics tested than the CA isolates. Isolates carrying only SCCmec type III and ccr type 3 were dominant (91 %), but 20 % of the CA isolates belonging to less prevalent types carried only SCCmec types IVa, c and ccr type 2. These isolates also carried pvl genes and contained SGA prophage type. Our results indicate that whilst the dominant clonal groups of HA- and CA-MRSA belong to SCCmec type III and carry ccr type 3 genes, several distinct but less prevalent types of CA-MRSA carrying SCCmec type IVa, c and type 2 ccr are also found in Tehran. These strains carry pvl genes and the SGA prophage type, a characteristic that might be used as a marker for detection of CA-MRSA in this country.

Alteration of the colonization pattern of coagulase-negative staphylococci in patients undergoing treatment for hematological malignancy

The aim was to prospectively describe the colonization pattern of coagulase-negative staphylococci (CoNS) and the relationship between colonizing and invasive CoNS isolates among patients undergoing treatment for hematological malignancy. Fourteen newly diagnosed patients were included with either multiple myeloma or acute leukemia. Patients were repeatedly sampled from nares, throat, axillae, and perineum, and the CoNS isolates obtained were phenotypically characterized together with blood isolates of CoNS using the PhenePlate system (PhP). During the treatment a gradual reduction in the heterogeneity of colonizing CoNS was observed as well as an inter-patient accumulation of phenotypically related and multi-drug-resistant CoNS. These clusters of CoNS persisted for 2-3 months after the end of therapy. Ten positive blood cultures of CoNS were obtained and in the majority of these cases CoNS of the same PhP type were found in superficial cultures collected prior to the blood culture sampling. In conclusion, the study shows that therapy for hematological malignancy is associated with a homogenization of colonizing CoNS isolates and that this acquired flora of CoNS is persistent several months after the end of therapy. Furthermore, the results suggest that the source of bloodstream infections of CoNS in hematological patients is colonizing CoNS of the skin and mucosa.

Coagulase-negative staphylococci from non-mastitic bovine mammary gland: characterization of Staphylococcus chromogenes and Staphylococcus haemolyticus by antibiotic susceptibility testing and pulsed-field gel electrophoresis

During routine microbiological examination of milk samples from dairy cows without clinical signs of mastitis, quarter milk samples of 231 dairy cows from 12 herds were investigated for the presence of coagulase-negative staphylococci (CNS). The isolates were identified on the basis of colony morphology, Gram staining, catalase and coagulase test and the commercial kit, API Staph. CNS was detected in 29% (67/231) of the cows. A total of seven CNS species were identified with the most prevalent being Staphylococcus (Staph.) chromogenes (30%) and Staph. haemolyticus (28·8%), followed by Staph. simulans (11·2%), Staph. xylosus (11·2%), Staph. epidermidis (7·5%), Staph. hyicus (6·3%) and Staph. sciuri (5%). The predominant species, Staph. chromogenes and Staph. haemolyticus, were further characterized by antibiotic susceptibility testing using the agar disc diffusion method (Kirby-Bauer) and by pulsed-field gel electrophoresis (PFGE). Considerable resistance to ampicillin and penicillin was observed in both species. Isolates with identical or highly similar PFGE profiles were detected at the herd level despite a marked heterogeneity seen for both species. On the basis of somatic cell count, absence of clinical signs of inflammation and heterogeneity of genotypes, we assume that CNS isolated in this study could not be considered as important causative agents of the bovine mammary gland inflammation.

Clinical implications of icaA and icaD genes in coagulase negative staphylococci and Staphylococcus aureus bacteremia in febrile neutropenic pediatric cancer patients

BACKGROUND

Staphylococci are the most frequently isolated organisms from blood cultures of febrile neutropenic (FN) cancer patients. We aimed to define the nature of these isolates by studying the prevalence of icaA and icaD genes in coagulase-negative staphylococci (CoNS) and Staphylococcus aureus isolates in relation to clinical and microbiological features.

PROCEDURE

Fifty-five CoNS and S. aureus isolates from blood cultures of FN pediatric patients receiving chemotherapy were tested for slime production using Congo red agar plate test (CRA test), and for the presence of icaA and icaD genes by PCR.

RESULTS

Of the CoNS isolates, eight were positive for ica genes, and three were slime positive/ica negative. A total of 11 (24.4%) cases of CoNS bacteremia were either ica genes or CRA test positive. There was a concordance between ica genes and CRA test positivity (P < 0.001). S. aureus isolates exhibited icaA and icaD genes more than CoNS isolates (P = 0.03). Vancomycin was significantly more prescribed in episodes of ica-positive cases (P = 0.029).

CONCLUSIONS

The results of the present study support the hypothesis that the ica genes are important virulence markers for clinically significant CoNS isolates, indicating their ability to produce slime. This could be used to assign a group with higher risk FN. On the other hand, absence of these genes may permit, along with other clinical criteria, the consideration of a low-risk FN episode and allow for safe early discharge.

Partial atlE sequencing of Staphylococcus epidermidis strains from prosthetic joint infections

Partial atlE sequencing (atlE nucleotides 2782 to 3114 [atlE(2782-3114)]) was performed in 41 Staphylococcus epidermidis isolates from prosthetic joint infections (PJIs) and 44 isolates from skin as controls. The atlE(2782-3114) allele 1 (type strain sequence) was significantly more frequent in PJI strains (38/41 versus 29/44 in controls; P = 0.0023). Most PJI strains were positive for mecA, icaA/icaD, and IS256, and most belonged to the sequence type 27 subgroup, suggesting the involvement of few related clones.

Clonal dissemination of Staphylococcus epidermidis in an oncology ward

Coagulase-negative staphylococci (CoNS) are the main cause of catheter-related infections, especially among immunosuppressed and neutropenic patients, as well as a source of bacterial contamination in blood cultures. Using biochemical identification and pulsed-field gel electrophoresis (PFGE), we sought to identify possible clonal isolates of bacteremia in patients with central lines in an oncology ward (OW), with comparison to isolates that were recovered by venipuncture from an adult emergency room (ER). A total of 243 CoNS isolates were identified to species level from the OW (126) and ER (117), with Staphylococcus epidermidis isolates being the most common (OW, 79.4%; ER, 45.3%). PFGE demonstrated a predominant clone of S. epidermidis (major subtype A) which was 35.5 times more likely (odds ratio [OR] = 35.5; 95% confidence interval [CI] = 4.7 to 267.0; P < 0.00001) to be present in the OW versus the ER. These (CoNS or major subtype A) isolates were more frequently resistant to gentamicin (OR = 2.83; 95% CI = 1.23 to 6.53; P = 0.016) and less frequently resistant to trimethoprim-sulfamethoxazole (OR = 0.38; 95% CI = 0.18 to 0.80; P = 0.013). Subset analysis of S. epidermidis isolates 2 years after the study period showed the persistence of the clone of major subtype A within the OW. This study demonstrates the presence of a predominant clone among central line isolates from an OW that is not present in CoNS venipuncture isolates from an ER.

Genotypic diversity of coagulase-negative staphylococci causing endocarditis: a global perspective

Coagulase-negative staphylococci (CNS) are important causes of infective endocarditis (IE), but their microbiological profiles are poorly described. We performed DNA target sequencing and susceptibility testing for 91 patients with definite CNS IE who were identified from the International Collaboration on Endocarditis-Microbiology, a large, multicenter, multinational consortium. A hierarchy of gene sequences demonstrated great genetic diversity within CNS from patients with definite endocarditis that represented diverse geographic regions. In particular, rpoB sequence data demonstrated unique genetic signatures with the potential to serve as an important tool for global surveillance.