Coagulase-negative staphylococci: update on the molecular epidemiology and clinical presentation, with a focus on Staphylococcus epidermidis and Staphylococcus saprophyticus

Bacteriuria and antibiotic use during the third wave of COVID-19 intensive care in Sweden

BACKGROUND

Urinary tract infections (UTIs) are prevalent among patients carrying indwelling catheters in the intensive care unit (ICU). This study investigates antibiotic use and bacterial colonisation among ICU patients during the third wave of the COVID-19 pandemic, building on our prior discovery of increased Enterococcus colonisation associated with increased cephalosporin use in early COVID-19.

METHODS

Longitudinal urine samples from COVID-19 patients (n = 109) with transurethral catheterisation were analysed for bacterial prevalence, further identified via MALDI-TOF. Microbiological results were combined with clinical data obtained daily, assessed and compared with COVID-19 waves 1 and 2.

RESULTS

Patients in wave 3 exhibited improved outcomes compared to those in waves 1 and 2, alongside a decrease in antibiotic use. Staphylococcus emerged as the primary bacterium and early colonizer of the urinary tract, potentially due to the absence of antibiotic treatment. Our results imply that length of stay (LOS) correlates solely with enteric pathogens and that antibiotic treatment correlates with colonisation by certain uropathogens, whereas the absence of antimicrobial therapy is associated with rapid colonisation of skin flora. Polymicrobial colonisation was common, predominantly involving Gram-positive bacteria.

CONCLUSION

Our findings underscore the complexity of bacteriuria in ICU patients, advocating for targeted surveillance and tailored antibiotic approaches to mitigate UTI risk. Insights into antibiotic use and bacterial colonisation are vital for optimising stewardship practices, combating antimicrobial resistance, and enhancing ICU patient outcomes.

Comprehensive Approaches for the Search and Characterization of Staphylococcins

Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.

Effect of Long-Term Use of Alcohol-Containing Handwashing Gels on the Biofilm-Forming Capacity of Staphylococcus epidermidis

The spread of coronavirus disease 2019 (COVID-19) has promoted the use of hand sanitizers among the general population as recommended by health authorities. Alcohols, which are used in many hand sanitizers, have been shown to promotes the formation of biofilms by certain bacteria and to increase bacterial resistance to disinfection. We investigated the effect of continued use of alcohol-based gel hand sanitizer on biofilm formation by the Staphylococcus epidermidis resident strain isolated from the hands of health science students. Hand microbes were counted before and after handwashing, and the ability to produce biofilms was investigated. We found that 179 (84.8%) strains of S. epidermidis isolated from hands had the ability to form biofilm (biofilm-positive strains) in an alcohol-free culture medium. Furthermore, the presence of alcohol in the culture medium induced biofilm formation in 13 (40.6%) of the biofilm-negative strains and increased biofilm production in 111 (76.6%) strains, which were classified as low-grade biofilm-producing. Based on our findings, there is no clear evidence that the continued use of alcohol-based gels results in the selection of strains with the capacity to form biofilms. However, other disinfectant formulations that are more commonly used in clinical settings, such as alcohol-based hand-rub solutions, should be tested for their long-term effects.

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study

BACKGROUND

There is a growing body of evidence on the potential involvement of coagulase-negative Staphylococci (CoNS) in causing urinary tract infections (UTIs). The aim of this study was to delineate virulence potential, antimicrobial resistance genes, and sequence types of CoNS isolated from patients with UTI symptoms and pyuria in Tanzania.

METHODS

CoNS from patients with UTI symptoms and more than 125 leucocytes/μL were retrieved, subcultured, and whole-genome sequenced.

RESULTS

Out of 65 CoNS isolates, 8 species of CoNS were identified; Staphylococcus haemolyticus, n = 27 (41.5%), and Staphylococcus epidermidis, n = 24 (36.9%), were predominant. The majority of S. haemolyticus were sequence type (ST) 30, with 8 new ST138-145 reported, while the majority of S. epidermidis were typed as ST490 with 7 new ST1184-1190 reported. Sixty isolates (92.3%) had either one or multiple antimicrobial resistance genes. The most frequently detected resistance genes were 53 (21%) dfrG, 32 (12.9%) blaZ, and 26 (10.5%) mecA genes conferring resistance to trimethoprim, penicillin, and methicillin, respectively. Out of 65 isolates, 59 (90.8%) had virulence genes associated with UTI, with a predominance of the icaC 47 (46.5%) and icaA 14 (13.9%) genes. Conclusion:S. haemolyticus and S. epidermidis harboring icaC, dfrG, blaZ, and mecA genes were the predominant CoNS causing UTI in Tanzania. Laboratories should carefully interpret the significant bacteriuria due to CoNS in relation to UTI symptoms and pyuria before labeling them as contaminants. Follow-up studies to document the outcome of the treated patients is needed to add more evidence that CoNS are UTI pathogens.

Extensive spinal epidural abscess caused by Staphylococcus epidermidis: A case report and literature review

Background

Extensive spinal epidural abscess (SEA) is an exceptional and threatening condition that requires prompt recognition and proper management to avoid potentially disastrous complications. We aimed to find key elements of early diagnosis and rational treatments for extensive SEA.

Case presentation

A 70-year-old man complained of intense pain in the cervical-thoracic-lumbar spine that radiated to the lower extremity. Laboratory test results revealed a marked increase in all indicators of infection. The spinal magnetic resonance imaging (MRI) revealed a ventral SEA extending from C2 to L4. Owing to the patient's critical condition, laminectomy, drainage, and systemic antibiotic therapy were administered. And the multidrug-resistant Staphylococcus epidermidis was detected in the purulent material from this abscess.

Results

Postoperative MRI revealed diminished epidural abscess, and the clinical symptoms were dramatically and gradually relieved after two rounds of surgery and systemic antibiotic therapy involving the combination of ceftriaxone, linezolid, and rifampicin.

Conclusions

A comprehensive emergency assessment based on neck or back pain, neurological dysfunctions, signs of systemic infection, and MRI are important for early diagnosis of extensive SEA. Further, the combination of laminectomy, drainage, and systemic antibiotic therapy may be a rational treatment choice for patients with SEA, especially for extensive abscess or progressive neurological dysfunction.

Persistent Coagulase-Negative Staphylococcal Bacteremia in Neonates: Clinical, Microbiological Characteristics and Changes within a Decade

Atypical outbreaks of persistent coagulase-negative staphylococci (CoNS) bacteremias, defined as three or more consecutive positive blood cultures with the same CoNS species, at least 48 h apart, have been reported in neonatal intensive-care units (NICUs). Our aim was to describe the profile of these cases in our NICU over a two-year period with the objective of assessing possible changes within a decade. Demographics, clinical and microbiological data were recorded for all CoNS bacteremias in our tertiary NICU during 2016-2017 and compared with the results of the same study in 2006-2007. Fifty-six cases of CoNS sepsis were recorded. Fourteen (25%) of them were persistent. There were no significant differences in demographic and clinical characteristics between cases with persistent vs. non-persistent bacteremia. Staphylococcus epidermidis was the most common species. In logistic regression analysis, biofilm production (β = 2.464, p = 0.04) was the most significant determinant for the development of persistent CoNS bacteremia. Our isolates were less likely to produce biofilm and carry ica operon as compared to those of 2006-2007. The cases of persistent CoNS sepsis have decreased within a decade, which could be attributed to the implementation of intensive infection control practices. Biofilm production remains the most important risk factor.

The Dissemination of Fusidic Acid Resistance Among Staphylococcus epidermidis Clinical Isolates in Wenzhou, China

Purpose

Fusidic acid (FA), a potent steroidal antibiotic, is used topically to treat skin and soft tissue infections (SSTIs) caused by Staphylococci. The aim of this study is to report the prevalence of fusidic acid resistance among Staphylococcus epidermidis clinical isolates from a tertiary hospital in Wenzhou, east China.

Methods

The antibiotic susceptibility of S. epidermidis isolates was determined by disc diffusion method and agar dilution method. Then, FA-resistant S. epidermidis isolates were characterized by multi-locus sequence typing, SCCmec typing and pulsed-field gel electrophoresis.

Results

In the present study, the 55 (7.7%) FA-resistant S. epidermidis among 711 S. epidermidis clinical isolates were isolated from different parts of 53 patients. Fifty-five FA-resistant S. epidermidis isolates with FA MIC values ranged from 4 to 32 μg/mL. Among them, 50 (90.9%) were identified as methicillin-resistant Staphylococcus epidermidis (MRSE), in which mecA were positive. Meanwhile, the positive rates of fusB and fusC genes among FA-resistant S. epidermidis isolates were 85.5% (47/55) and 7.3% (4/55), respectively. All 55 isolates mentioned above were susceptible to vancomycin. More than 50% of FA-resistant isolates were resistant to non-β-lactam antimicrobials including erythromycin (80.0%, 44/55), clindamycin (65.5%, 36/55), ciprofloxacin (63.6%, 35/55) and sulfamethoxazole (63.6%, 35/55). A total of 14 sequence types (STs) were identified among the 55 FA-resistant S. epidermidis isolates, of which, ST2 (24/55, 43.6%) was the most predominant type. And the eBURST analysis showed that CC2, CC5 and CC247 accounted for 43.6% (24/55), 27.3% (15/55) and 14.5% (5/55), respectively. Meanwhile, a total of four SCCmec types (I, III, IV, V) were identified among the 55 FA-resistant S. epidermidis. Furthermore, the pulsed field gel electrophoresis divided the 55 isolates into 20 types, namely A-T. Q-type strains were most prevalent, accounting for 30.9% (17/55).

Conclusion

Taken together, the dissemination of S. epidermidis ST2 clone with FA resistance can cause trouble in controlling S. epidermidis infections.

Efflux Pump Mediated Antimicrobial Resistance by Staphylococci in Health-Related Environments: Challenges and the Quest for Inhibition

The increasing emergence of antimicrobial resistance in staphylococcal bacteria is a major health threat worldwide due to significant morbidity and mortality resulting from their associated hospital- or community-acquired infections. Dramatic decrease in the discovery of new antibiotics from the pharmaceutical industry coupled with increased use of sanitisers and disinfectants due to the ongoing COVID-19 pandemic can further aggravate the problem of antimicrobial resistance. Staphylococci utilise multiple mechanisms to circumvent the effects of antimicrobials. One of these resistance mechanisms is the export of antimicrobial agents through the activity of membrane-embedded multidrug efflux pump proteins. The use of efflux pump inhibitors in combination with currently approved antimicrobials is a promising strategy to potentiate their clinical efficacy against resistant strains of staphylococci, and simultaneously reduce the selection of resistant mutants. This review presents an overview of the current knowledge of staphylococcal efflux pumps, discusses their clinical impact, and summarises compounds found in the last decade from plant and synthetic origin that have the potential to be used as adjuvants to antibiotic therapy against multidrug resistant staphylococci. Critically, future high-resolution structures of staphylococcal efflux pumps could aid in design and development of safer, more target-specific and highly potent efflux pump inhibitors to progress into clinical use.

Evaluation of microbial contamination on cuff syringe, cuff pressure gauge, and their surroundings in the operating room

Background

Some institutions reuse cuff syringes and do not periodically sterilize cuff pressure gauges. Pathogenic bacterial contamination of such equipment may increase the probability of pathogen transmission to patients during anesthetic procedures. Therefore, microbial contamination on cuff syringes, cuff pressure gauges, and their surroundings was assessed in the operating rooms of a university-affiliated tertiary care hospital in Japan.

Methods

This study was conducted between April and May 2019 in 14 operating suites at a hospital. The following sites in each operating suite were sampled: cuff syringe (inner/outer components), outer components of cuff pressure gauge, cuff syringe and cuff pressure gauge storage drawers, and computer mice. The swabs were directly streaked onto agar plates and incubated. Then, the bacterial species were identified using mass spectrometry.

Results

The highest bacterial isolation was observed in computer mice, followed by the outside of cuff pressure gauges and the drawers of cuff pressure gauges (92.9, 78.6, and 64.3%, respectively). Most of the identified bacteria belonged to the Bacillus species, with colonization rates of 85.7, 57.1, and 57.1% on computer mice, cuff pressure gauges, and cuff pressure gauge storage drawers, respectively. Coagulase-negative Staphylococcus was found in 35.7% of the specimens and was more prevalent on computer mice (71.4%), followed by on cuff pressure gauges (64.3%).

Conclusion

Anesthesiologists should be aware of the possible pathogen contamination risk from cuff syringes, cuff pressure gauges, or associated equipment and take appropriate infection control measures to minimize the risk of pathogenic transmission.

Molecular epidemiology of methicillin resistant Staphylococcus species in healthcare workers of a blood bank in the Brazilian Amazon

BACKGROUND

Healthcare workers are susceptible to colonization by multiresistant bacteria, which can increase the risk of outbreaks.

METHODS

Samples were collected from the nasopharynx, hands, and lab coats of healthcare workers. The phenotypic identification was carried out using a VITEK®2 rapid test system. PCR tests for the mecA gene and the sequencing of the amplicons were performed. Staphylococcus epidermidis and Staphylococcus aureus phylogenies were reconstructed using the Bayesian inference.

RESULTS

A total of 225 healthcare workers participated in this study. Of these, 21.3% were male and 78.7% female. S. epidermidis and S.aureus showed high levels of resistance to penicillin, ampicillin, erythromycin, tetracycline and cefoxitin. The prevalence of methicillin resistant S. aureus was 3.16% and methicillin resistant S. epidermidis was 100%. Multilocus sequence typing identified 23 new S. epidermidis sequence types, and one new allele and sequence type for S. aureus. The frequency of methicillin-resistant S. epidermidis in nursing and hemotherapy technicians as a percentage of the total number of healthcare workers was 5.8-3.1%, while the frequency of methicillin resistant S. aureus in hemotherapy technicians and biomedics, as a percentage of the total number of healthcare workers was 4.2-8.9%%.

CONCLUSIONS

The healthcare workers at the city's blood bank, even when taking the necessary care with their hands, body and clothes, harbour methicillin-resistant S. aureus and S. epidermidis sequence types, which, as a potential source of multidrug resistant bacteria, can contribute to nosocomial infections among hematological patients.

Methicillin-Resistant Coagulase Negative Staphylococci and Their Antibiotic Susceptibility Pattern from Healthy Dogs and Their Owners from Kathmandu Valley

This cross-sectional study was designed to identify information on the frequency, antimicrobial resistance and species diversity of methicillin-resistant coagulase negative staphylococci (MRCoNS) among pet dogs and humans within households. Fifty five nasal swabs each from dogs and their owners were collected. MRCoNS were identified based on gram staining, culture on mannitol salt agar, biochemical tests, and mecA gene amplification. The antibiotic susceptibility of the isolates was assessed by a disc diffusion test. Uniplex and multiplex polymerase chain reaction (PCR) were employed for the species identification of MRCoNS and SCCmec typing, respectively. Species were further confirmed by MALDI-TOF-MS. The prevalence of MRCoNS was 29% in dog owners and 23.6% in dogs. Four different species of MRCoNS, Staphylococci saprophyticus (48.3%), S. haemolyticus (24.1%), S. warneri (17.2%), and S. epidermidis (10.3%), were detected. Two isolates each from dog owners and dogs showed a constitutive resistance to macrolide-lincosamide-streptogramin B (cMLSB) resistance, eight isolates each from dogs and their owners showed a macrolide-streptogramin B (MSB) resistance, and only two isolates from dog owners revealed an inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB) resistance. SCCmec types were SCCmec type IV (55.2%), SCCmec type V (24.1%), SCCmec III (10.3%), SCCmec II (3.4%); two isolates were non-typable. MRCoNS are prevalent and genetically diverse in companion animals and humans. Different species of MRCoNS were found in dogs and their owners.

The Keratinocyte as a Crucial Cell in the Predisposition, Onset, Progression, Therapy and Study of the Atopic Dermatitis

The keratinocyte (KC) is the main functional and structural component of the epidermis, the most external layer of the skin that is highly specialized in defense against external agents, prevention of leakage of body fluids and retention of internal water within the cells. Altered epidermal barrier and aberrant KC differentiation are involved in the pathophysiology of several skin diseases, such as atopic dermatitis (AD). AD is a chronic inflammatory disease characterized by cutaneous and systemic immune dysregulation and skin microbiota dysbiosis. Nevertheless, the pathological mechanisms of this complex disease remain largely unknown. In this review, we summarize current knowledge about the participation of the KC in different aspects of the AD. We provide an overview of the genetic predisposing and environmental factors, inflammatory molecules and signaling pathways of the KC that participate in the physiopathology of the AD. We also analyze the link among the KC, the microbiota and the inflammatory response underlying acute and chronic skin AD lesions.

Vancomycin-resistant enterococci and coagulase-negative staphylococci prevalence among patients attending at Felege Hiwot Comprehensive Specialized Hospital, Bahir Dar, Ethiopia

Background

Vancomycin resistant enterococci (VRE) and vancomycin resistance coagulase negative staphylococci (VRCoNS) are common pathogens causing difficult to treat health care associated infections (HAI). Hence, the World Health Organization listed VRE as one of the high priority pathogens for new antibiotic discovery and antimicrobial resistance surveillance. Despite this, data on the prevalence of VRE and VRCoNS in Ethiopia is scarce. Thus, the present study determined prevalence of VRE and VRCoNS among patients attending Felege-Hiwot comprehensive specialized hospital, Ethiopia.

Methods

A hospital based cross-sectional study was conducted on 384 patients selected conveniently from February to March 2020. Data on demographic and clinical variables were collected using a structured questionnaire by face-to-face interview. Simultaneously urine, venous blood and wound swab were collected and processed following standard bacteriological technique. Antimicrobial susceptibility test was performed by minimum inhibitory concentration method using E-test for vancomycin and Kirby-Bauer disc diffusion method for other classes of antibiotics. Data was entered and analyzed using SPSS version 23. Logistic regression was performed to identify factors associated with VRE infection. P. value < 0.05 was considered as statistically significant.

Results

The prevalence of enterococci and CoNS were 6.8% and 12% respectively. The prevalence of VRE was 34.61% (9/26), while all CoNS (46 isolates) were susceptible to vancomycin. The majority (66.7%) of VRE was isolated from blood samples. Furthermore all VRE (100%), 58.8% of vancomycin susceptible enterococci and 45.7% of CoNS were multidrug resistant (MDR). Having educational level of secondary school and below (AOR = 12.80, CI = 1.149–142.5), previous exposure to catheterization (AOR = 56.0, CI = 4.331–724.0) and previous antibiotic use practice (AOR = 26.25, CI = 3.041–226.2) were a significant associated explanatory factor for VRE infection.

Conclusions

The prevalence of vancomycin resistance enterococci, which is also multidrug resistant, was significantly high. Though no vancomycin resistance CoNS detected, the MDR level of CoNS was high. Thus to limit enterococci and CoNS infections and MDR development, focused infection prevention measures should be implemented.

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.

Virulence Factors in Coagulase-Negative Staphylococci

Coagulase-negative staphylococci (CoNS) have emerged as major pathogens in healthcare-associated facilities, being S. epidermidis, S. haemolyticus and, more recently, S. lugdunensis, the most clinically relevant species. Despite being less virulent than the well-studied pathogen S. aureus, the number of CoNS strains sequenced is constantly increasing and, with that, the number of virulence factors identified in those strains. In this regard, biofilm formation is considered the most important. Besides virulence factors, the presence of several antibiotic-resistance genes identified in CoNS is worrisome and makes treatment very challenging. In this review, we analyzed the different aspects involved in CoNS virulence and their impact on health and food.

Correlation of Staphylococcus Epidermidis Phenotype and Its Corneal Virulence

PURPOSE

S. epidermidis is an ocular pathogen and a leading cause of keratitis. It produces hemolysins and at least 3 proteases. The purpose of the present study is to compare the secretion of hemolysins and proteases between 28 ocular isolates and one non-ocular strain and to determine their relationship to ocular virulence in selected strains using a rabbit model of infection.

MATERIALS AND METHODS

Culture supernatants were compared for protease production and hemolysis. Selected strains were injected into rabbit corneas and their virulence and pathology recorded. The major protease activity in a virulent strain was identified and the gene was cloned and expressed as a recombinant protein. The corneal toxicity of this protease was determined. Antibodies to the native protease were generated and tested for neutralizing activity in vivo and in vitro. The corneal pathology of the S. epidermidis protease was compared to the pathology of S. aureus V8 protease.

RESULTS

Strains that exhibited the least protease activity in vitro caused significantly less ocular pathology in vivo (p ≤ 0.003). Strains that were hemolytic and secreted a major protease had numerically higher SLE scores. This protease was identified as the serine protease Esp. The recombinant Esp protease caused extensive pathology when injected into the corneal stroma (7.62 ± 0.33). Antibody generated against native Esp did not neutralize the activity of the protease in vivo or in vitro. The antibody reacted with Esp proteases secreted by other S. epidermidis strains. S. epidermidis Esp protease and its homologue in S. aureus caused similar ocular pathology when injected in the rabbit corneal stroma.

CONCLUSION

Hemolysins and proteases seem to be important in corneal pathology caused by S. epidermidis infections. The Esp protease mediates significant corneal damage. S. epidermidis Esp and S. aureus V8 protease caused similar and extensive edema in rabbit corneas.

Glycation of gut proteins initiates microbial dysbiosis and can promote establishment of diabetes in experimental animals

Diabetes and obesity is associated with change in the gut microbiota, however, the reason for such transition is still unknown. The secondary complications in diabetes mainly stem from protein glycation, oxidative stress and inflammatory response. It is intended to study the correlation between gut proteins glycation and microbial dysbiosis and thereby progression to diabetes. The study was carried out through feeding high fructose to male Wistar rats and evaluating their gut microbiota. The rate of gut flora excretion via faecal matter was found to decrease on fructose feed for 7 days. Intestinal flora was drastically reduced and pathogenic succession observed. Intestinal fluorescence studies confirmed that there is heavy glycation of gut proteins. Microbes obtained from fructose fed animals could grow on glycated BSA. There was significant increase in level of TNF-α and IFN-γ providing evidence of inflammation. Though microbial dysbiosis was observed in diabetes, the cause for this remained elusive. In the present study we prove that high fructose feed and glycation of the gut proteins probably prevent adherence/survival of the gut microflora in control animals and promotes transition to a changed microflora which is capable of adhering/utilizing glycated proteins as well as high fructose. The changed microbiota, enhanced protein glycation and inflammation help in establishing insulin resistance.

Routine scrubbing reduced central line associated bloodstream infection in NICU

BACKGROUND

The main aim of this study was to estimate the effectiveness of routine scrubbing by change of the incidence of central line-associated bloodstream infections (CLABSI).

METHODS

We surveyed cultures from the NICU environment in December 2017. We found that areas close to infants harbored more bacteria. We implemented routine scrubbing to control sites with the most bacteria starting from January 2018. We retrospectively reviewed and compared the data between the pre (2017) and post (2018) intervention periods.

RESULTS

A total of 916 infants were included; 10 CLABSI episodes were identified, 9 and 1 episodes in the pre- and postintervention periods, respectively. We found that the incidence of CLABSI decreased significantly among all admitted infants (P = .006) and also among very low birth weight infants (P = .085). The number of CLABSI cases per 1,000 central line days decreased from 1.89 in 2017 to 0.23 in 2018 (P = .018). The most common bacterial species found in the cultures established from the NICU environment were identical to the CLABSI-causing coagulase-negative Staphylococcus.

CONCLUSIONS

Routine scrubbing significantly reduced CLABSI in the NICU.

Evaluation of the genetic relatedness of Bacteroides fragilis isolates by TRs analysis

OBJECTIVES

Human gastrointestinal tract harbors a variety of bacteria with vital roles in human health. Bacteroides fragilis is considered one of the dominant constituents of gut microflora which can act as an opportunistic pathogen leading to various diseases, including colon cancer, diarrhea, uterine and intrathecal abscesses, septicemia, and pelvic inflammation. In this study, multiple locus variable number of tandem repeats analysis (MLVA) was performed to genetically differentiate 50 B. fragilis isolates.

MATERIALS AND METHODS

Eight suitable tandem repeats (TRs) were selected by bioinformatics tools and were then subjected to PCR amplification using specific primers. Finally, MLVA profiles were clustered using BioNumerics 7.6 software package.

RESULTS

All VNTR loci were detected in all isolates using the PCR method. Overall, B. fragilis isolates were differentiated into 27 distinct MLVA types. The highest diversity index was allocated to TR1, TR2, TR5, TR6, and TR8; with this taken into account, strain type 14 was the most prevalent with 12 strains belonging to this type. Clustering revealed three major clusters of A, B, and C. With regards to the pathogenicity of B. fragilis and the outcomes of infections related to this microorganism, it is imperative to study this microorganism isolated from both patients and healthy individuals.

CONCLUSION

This study aimed at evaluating the efficiency of MLVA for the genetic differentiation of B. fragilis. The results of this study indicate the promising efficiency of MLVA typing for cluster detection of this bacterium.

Food-derived coagulase-negative Staphylococcus as starter cultures for fermented foods

Food safety is of significant concern to consumers and is a major issue for the food industry. As such, the industry is aware of the importance of safety assessments of starters used in the production of fermented foods. Coagulase-negative staphylococci (CNS) are the predominant bacteria found in fermented foods worldwide. Because of this, food-derived CNS are used as starters for cheese and meat fermentation, and have been investigated for use as starters in soybean fermentation. Although food-derived CNS are generally considered non-pathogenic, their safety remains uncertain following the isolation of CNS from skin infections in humans and animals, and because they belong to the same genus as the highly pathogenic species Staphylococcus aureus. This review explores what is known about the safety of food-derived CNS, focusing on antibiotic resistance, enterotoxin genes, and biogenic amine production, to aid in the selection of starter candidates.

Isolation, identification and characterization of Staphylococcus sp. from Indian ethnic fermented fish product

Staphylococci from Sheedal of Northeast India was isolated, identified and characterized. All the isolated staphylococci were found to be coagulase negative. Based on the rpoB gene sequences followed by analysis using NCBI-BLAST software, seven species of Staphylococcus namely, S. piscifermentans, S. condimenti, S. arlettae, S. sciuri, S. warneri, S. nepalensis and S. hominis were recognized. Phylogenetic analyses revealed three major cluster groups. All the seven Staphylococcus showed their NaCl tolerance from 2 to 8%. No species was able to grow at 55°C. Except S. arlettae and S. sciuri, all the isolated staphylococcal species exhibited growth at pH 4-8. No isolated species was able to ferment mannitol, sucrose and arabinose. All the species exhibited moderate to maximum proteolytic and lipolytic activities. All the seven species were found to be sensitive to the antibiotics, namely, erythromycin, norfloxacin, ampicillin, streptomycin and vancomycin, whereas all were resistant to co-trimoxazole. Only S. piscifermentans was found antagonist to Salmonella enterica, Escherichia coli and Bacillus subtilis, although the clear zone was minimal. All the staphylococcal species except S. arlettae and S. sciuri exhibited hydrophobicity ranging from 25 to 66%. The observed characteristics of isolated Staphylococci from Sheedal revealed their role in fish fermentation.

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica

Long-standing evidence supports the importance of maintaining healthy populations of microbiota for the survival, homeostasis, and complete development of marine mollusks. However, the long-term ecological effects of agricultural runoff on these populations remains largely unknown. Atrazine (6-Chloro-n-ethyl-n'-(1-methylethyl)-triazine-2,4-diamine), a prevalent herbicide in the United States, is often used along tributaries of the Chesapeake Bay where oyster breeding programs are concentrated. To investigate any potential effects atrazine maybe having on mollusk-prokaryote interactions, we used 16S rRNA gene amplicons to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine previously found within the Chesapeake Bay. The dominant bacterial genera found within all groups included those belonging to Pseudoalteromonas, Burkholderia, Bacteroides, Lactobacillis, Acetobacter, Allobaculum, Ruminococcus, and Nocardia. Our results support previously published findings of a possible core microbial community in Crassostrea virginica. We also report a novel finding: oysters exposed to atrazine concentrations as low as 3 µg/L saw a significant loss of a key mutualistic microbial species and a subsequent colonization of a pathogenic bacteria Nocardia. We conclude that exposure to atrazine in the Chesapeake Bay may be contributing to a significant shift in the microbiomes of juvenile oysters that reduces fitness and impedes natural and artificial repopulation of the oyster species within the Bay.

In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus

Staphylococcus saprophyticus is a uropathogenic bacteria responsible for acute urinary tract infections (UTIs) mainly in young female patients. Patients suffering from urinary catheterization, pregnant patients, the elderly as well as those with nosocomial UTIs are at greater risk of the colonizing S. saprophyticus infection. The causative factors include benign prostatic hyperplasia, indwelling catheter, neurogenic bladder, pregnancy, and history of frequent UTIs. Recent findings have exhibited that S. saprophyticus is resistant to several antimicrobial agents. Moreover, there is a global concern regarding the increasing level of antimicrobial resistance, which leads to treatment failure and reduced effectiveness of broad-spectrum antimicrobials. Therefore, a novel approach is being utilized to combat resistant microbes since the past few years. Subtractive proteome analysis has been performed with the entire proteome of S. saprophyticus strain American Type Culture Collection (ATCC) 15305 using several bioinformatics servers and software. The proteins that were non-homologous to humans and bacteria were identified for metabolic pathway analysis. Only four cytoplasmic proteins were found possessing the potential of novel drug target candidates. The development of innovative therapeutic agents by targeting the inhibition of any essential proteins may disrupt the metabolic pathways specific to the pathogen, thus causing destruction as well as eradication of the pathogen from a particular host. The identified targets can facilitate in designing novel and potent drugs against S. saprophyticus strain ATCC 15305.

Coagulase-negative staphylococci in outpatient routines: the implications of switching from CLSI to BrCAST/EUCAST guidelines

Coagulase-negative staphylococci (CoNS) are frequently isolated in clinical specimens and are important reservoirs of resistance genes. In 2019, the Brazilian government set the BrCAST/EUCAST (Brazilian Committee on Antimicrobial Susceptibility Testing) guidelines as the national standard, resulting in changes in the interpretation of CoNS susceptibility tests. From outpatients, disk-diffusion susceptibility of 65 CoNS cultures were evaluated and compared using classification criteria from both CLSI and BrCAST/EUCAST. The isolates were identified using matrix assisted laser desorption ionization-time of flight (MALDI-TOF), and the presence of the mecA gene was determined. The most prevalent species were Staphylococcus saprophyticus (32.3%), S. haemolyticus (18.5%), and S. epidermidis (9.2%). Almost perfect agreement was seen between the guidelines, except concerning oxacillin and gentamicin, and the prevalence of multidrug resistant isolates increased with the use of BrCAST/EUCAST. Of all, 15 (23.1%) isolates, mainly S. epidermidis and S. haemolyticus, were positive for the mecA gene, and only three were detected when using CLSI or BrCAST/EUCAST disk-diffusion screening. This, using either guideline, could reveal the difficulty of determining oxacillin resistance. Using warning zones or molecular methods might well be indicated for CoNS. In conclusion, adoption of the BrCAST/EUCAST guidelines will result in certain artificial changes in epidemiological susceptibility profiles, and clinicians and institutions should be aware of the possible implications.

Detection of sasX Gene and Distribution of SCCmec Types in Invasive and Non-invasive Coagulase-negative Staphylococci

Background

Coagulase-negative staphylococci, which belong to the normal microbiota of the skin and mucous membranes, are opportunistic pathogens. sasX, a newly described protein, is thought to play an important role in nasal colonization and methicillin-resistant Staphylococcus aureus virulence, and it may be acquired from coagulase-negative staphylococci by horizontal gene transfer. It has been considered that understanding the function of sasX gene may help clarify the relevance of the different adhesion mechanisms in the pathogenesis of infections associated with biofilm.

Aims

To investigate the sasX gene presence, staphylococcal cassette chromosome mec types, and antimicrobial resistance patterns of invasive and noninvasive coagulase-negative staphylococci isolates.

Study Design

Cross-sectional study.

Methods

The study included a total of 180 coagulase-negative staphylococci strains. Non-invasive isolates (n=91) were obtained from the hands of healthy volunteers who do not work at the hospital (n=30), the nasal vestibule of healthy volunteer hospital workers (n=26), and central venous catheter (n=35). Invasive isolates (n=89) were isolated from peripheral blood cultures of inpatients who do not have catheters. All isolates were identified by conventional microbiological methods, automated systems, and, if needed, with matrix-assisted laser desorption/ionization-time of flight. Staphylococcal cassette chromosome mec typing, sasX and mec gene detection, antibiotic susceptibility, and sasX gene sequence analysis were performed.

Results

Peripheral blood, central venous catheter colonization, and nasal vestibule isolates were positive for the sasX gene, whereas hand isolates were negative. sasX gene was present in 17 isolates, and no statistical significance was found between invasive and noninvasive isolates (p=0.173). Sequence analysis of the sasX genes showed high homology to related proteins of Staphylococcus phage SPbeta-like and Staphylococcus epidermidis RP62A. staphylococcal cassette chromosome mec type V was the most prevalent regardless of species. staphylococcal cassette chromosome mec type II was more frequent in invasive isolates and found to be statistically important for invasive and noninvasive S. epidermidis isolates (p=0.029). Staphylococcus haemolyticus isolates had the overall highest resistance rates. Resistance to ciprofloxacin, trimethoprim-sulfamethoxazole, and erythromycin was found to be higher in isolates from catheter and blood culture. Staphylococcus hominis isolates had the highest rate for inducible clindamycin resistance. None of the isolates were resistant to vancomycin, teicoplanin, and linezolid.

Conclusion

The sasX gene is detected in 9.44% of the isolates. There is no statistical difference between the sasX-positive and -negative isolates in terms of antibacterial resistance and the presence of sasX and SCCmec types. Further studies about the role of sasX at virulence in coagulase-negative staphylococci, especially from clinical samples such as tracheal aspirate and abscess isolates, and distribution of staphylococcal cassette chromosome mec types are needed.

Pentadecanal and pentadecanoic acid coatings reduce biofilm formation of Staphylococcus epidermidis on PDMS

Staphylococcus epidermidis is well known to be one of the major causes of infections related to medical devices, mostly due to its strong capacity to form device-associated biofilms. Nowadays, these infections represent a severe burden to the public health system and the necessity of novel antibacterial strategies for the treatment of these difficult-to-eradicate infections is urgent. The Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 was found to be able to produce an anti-biofilm molecule, the pentadecanal, active against S. epidermidis. In this work, we modified one of the most widely used silicone-based polymers, polydimethylsiloxane (PDMS), by adsorption of pentadecanal and its most promising derivative, pentadecanoic acid, on the PDMS surface. The biofilm formation of S. epidermidis RP62A on both untreated and modified PDMS was performed in a parallel plate flow chamber system, demonstrating the capability of the proposed anti-biofilm coatings to strongly reduce the biofilm formation. Furthermore, drug-release capacity and long-term efficacy (21 days) were also proven for the pentadecanoic acid coating.

Comparative Genomic Analysis of Food-Originated Coagulase-Negative Staphylococcus: Analysis of Conserved Core Genes and Diversity of the Pan-Genome

To shed light on the genetic differences among food-originated coagulase-negative Staphylococcus (CNS), we performed pan-genome analysis of five species: Staphylococcus carnosus (two strains), Staphylococcus equorum (two strains), Staphylococcus succinus (three strains), Staphylococcus xylosus (two strains), and Staphylococcus saprophyticus (one strain). The pan-genome size increases with each new strain and currently holds about 4,500 genes from 10 genomes. Specific genes were shown to be strain dependent but not species dependent. Most specific genes were of unknown function or encoded restriction-modification enzymes, transposases, or prophages. Our results indicate that unique genes have been acquired or lost by convergent evolution within individual strains.

High concentration of coagulase-negative staphylococci carriage among bioaerosols of henhouses in Central China

Background

Coagulase-negative staphylococci (CoNS) are a group of opportunistic pathogens, which are widely spread in the environment. Animal breeding is an important source of pathogen spreading. However, the concentration and characteristics of CoNS in the bioaerosols of henhouses are unclear.

Results

In this study, we showed that CoNS were significantly increased in bioaerosols of henhouses during the first 60 days, and reached 2.0 × 10⁶ CFU/m³, which account for 75.4% of total bacteria. One hundred and two CoNS isolates from bioaerosols and nasal swabs of farmers were further identified, covering seven species. Among these, 41.2% isolates were Staphylococcus sciuri, which was the predominant species, followed by S. equorum, S. saprophyticus, S. haemolyticus, S. xylosus, S. arlettae and S. gallinarum. There were high rates of resistance to oxacillin in CoNS (49.0%), which were defined as Methicillin-Resistant CoNS (MRCoNS), and 36.3% isolates contained resistance gene mecA. Bioaerosol infection models showed that, chickens exposed to aerosolized S. sciuri had significant induction of inflammatory cytokines interleukin (IL)-1β, IL-6, IL-8 and IL-10 at 5 days post-infection (dpi) in lungs and at 7 dpi in spleens.

Conclusions

We reported a high concentration of CoNS in henhouses, and S. sciuri was the preponderant CoNS species. Antibiotic resistance analysis and bioaerosols infection of CoNS further highlighted its hazards on resistance and immunological challenge. These results suggested that, CoNS in bioaerosols could be one serious factor in the henhouses for not only poultry industry but also public health.

Incidence of coagulase-negative staphylococcal bacteremia among ICU patients: decontamination studies as a natural experiment

The epidemiology of coagulase-negative staphylococcal (CNS) bacteremia among adult ICU patients remains unclear. Decontamination studies among ICU patients provide a unique opportunity to study the impacts of different diagnostic criteria, exposure to various decontamination interventions, and various other factors, on its incidence over three decades. Decontamination studies among ICU patients reporting CNS bacteremia incidence data were obtained mostly from recent systematic reviews. The CNS bacteremia incidence within component (control and intervention) groups of decontamination studies was benchmarked versus studies without intervention (observational groups). The impacts of antibiotic versus chlorhexidine decontamination interventions, control group concurrency, publication year, and diagnostic criteria were examined in meta-regression models. Among non-intervention (observational) studies which did versus did not specify stringent (≥ 2 positive blood cultures) diagnostic criteria, the mean CNS bacteremia incidence per 100 patients (and 95% CI; n) is 1.3 (0.9–2.0; n = 23) versus 3.6 (1.8–6.9; n = 8), respectively, giving an overall benchmark of 1.8 (1.2–2.4; n = 31). Versus the benchmark incidence, the mean incidence is high among concurrent control (5.7; 3.6–9.1%) and intervention (5.2; 3.6–6.9%), but not non-concurrent control (1.0; 0.4–3.9%) groups of 21 antibiotic studies, nor among eleven component groups of chlorhexidine studies. This high incidence remained apparent (p < 0.01) in meta-regression models adjusting for group wide factors such as diagnostic criteria and publication year. The incidence of CNS bacteremia within both intervention and concurrent (but not non-concurrent) control groups of antibiotic-based decontamination studies are unusually high even accounting for variable diagnostic criteria and other factors.

The emergence of Staphylococcus epidermidis simultaneously nonsusceptible to linezolid and teicoplanin in China

Two linezolid-resistant and teicoplanin-intermediate Staphylococcus epidermidis strains were isolated from blood cultures in China. The 2 S. epidermidis strains were methicillin-resistant and showed multidrug-resistance patterns; in addition, population analysis profiling/area under the curve (PAP/AUC) result showed heterogeneous resistant to vancomycin. Comparing to teicoplanin susceptible strains, the 2 isolates showed reduced autolytic activity. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) indicated that the 2 S. epidermidis isolates belonged to the same clone. Furthermore, the cfr gene, a G2576T mutation, and a novel C2146T mutation were detected in the 2 isolates. This was the first report of S. epidermidis simultaneously nonsusceptible to linezolid and teicoplanin in China.

Evaluation of Oxacillin and Cefoxitin Disk Diffusion and Microbroth Dilution Methods for Detecting mecA-Mediated β-Lactam Resistance in Contemporary Staphylococcus epidermidis Isolates

Methicillin (β-lactam) resistance in Staphylococcus epidermidis is mediated by the mecA gene, with resistance reported to be as high as 90%. The goal of this study was to evaluate oxacillin and cefoxitin disk diffusion (DD) and broth microdilution (BMD) methods for the detection of mecA-mediated β-lactam resistance in 100 human isolates of S. epidermidis (48 mecA-positive isolates and 52 mecA negative isolates). Oxacillin DD tests using the Clinical and Laboratory Standards Institute (CLSI) M100-S28 breakpoints for S. pseudintermedius/S. schleiferi accurately differentiated mecA-positive and -negative S. epidermidis isolates, with categorical agreement (CA) of 100% and no very major errors (VMEs) or major errors (MEs) identified. Likewise, oxacillin BMD and cefoxitin DD tests using the coagulase-negative Staphylococcus species (CoNS) breakpoints were highly reliable for detecting mecA-mediated β-lactam resistance in S. epidermidis isolates. For cefoxitin DD and BMD results interpreted using S. aureus/S. lugdunensis breakpoints, the CA was 97.6% and 96.2%, respectively. There were 4.9% VMEs for cefoxitin DD with 0% MEs, and 3.6% VMEs and 3.9% MEs for cefoxitin BMD. Oxacillin BMD using S. aureus/S. lugdunensis breakpoints yielded the highest VMEs at 17.4% and 90% CA. Our findings demonstrate that oxacillin DD tests using the CLSI M100-S28 breakpoints for S. pseudintermedius/S. schleiferi and oxacillin BMD and cefoxitin DD tests using the CoNS breakpoints reliably identified mecA-mediated β-lactam resistance in S. epidermidis Using mecA PCR as the gold standard, the PBP2a SA culture colony test (Abbott Diagnostics) exhibited 100% sensitivity and specificity whereas 2 false negatives were identified using the PBP2' latex agglutination test kit (Thermo Fisher Scientific) with sensitivity and specificity of 95.8% and 100%, respectively.

The Natural History and Composition of Urinary Catheter Biofilms: Early Uropathogen Colonization with Intraluminal and Distal Predominance

PURPOSE

We sought to determine the composition and initiation site of bacterial biofilm on indwelling urinary catheters and to track biofilm progression with time.

MATERIALS AND METHODS

Indwelling urinary catheters were collected from 2 tertiary care centers following removal from patients. Indwelling time was noted and catheters were de-identified. Catheters were sectioned, stained for biofilms and analyzed by spectrophotometry and visualization. Biofilm colonization patterns were analyzed using descriptive statistical analysis and bacterial composition was determined using next generation sequencing.

RESULTS

We collected and analyzed a total of 33 catheters from 26 males and 7 females with indwelling time ranging from 15 minutes to 43 days. Biofilm colonization was consistently high on the region of the balloon for all indwelling times. After week 1 the distal third of the catheter had higher biofilm colonization than the proximal third (week 2 p=0.034). At all indwelling times the intraluminal surface of the catheter had greater biofilm colonization than the outer surface. Next generation sequencing detected potential uropathogenic bacteria in all 10 analyzed samples.

CONCLUSIONS

The catheter balloon, its distal aspect and its lumen were the predominant locations of biofilm comprising uropathogenic bacteria. Strategies to prevent or treat biofilm should be targeted to these areas.

Antimicrobial susceptibility, virulence determinants profiles and molecular characteristics of Staphylococcus epidermidis isolates in Wenzhou, eastern China

BACKGROUND

Staphylococcus epidermidis has emerged as an often encountered pathogen responsible for hospital-acquired infections. The aim of present study is to investigate the microbiological characteristic of S. epidermidis isolates isolated from sterile specimens and skin in a Chinese tertiary hospital.

METHODS

A total of 223 non-duplicate S. epidermidis were collected from various sterile specimens of inpatients among 10 years in Wenzhou, China. 106 S. epidermidis obtained from the skin (urethral orifices) of healthy volunteers. All isolates were tested for antimicrobial susceptibility. PCR was used to detect the virulence- and resistance-associated genes and 7 housekeeping genes to determine the sequence types (STs) of selected isolates.

RESULTS

The resistance rates to antimicrobials tested except linezolid and vancomycin and the prevalence of methicillin-resistant S. epidermidis (MRSE) of S. epidermidis clinical isolates were significantly higher than those among colonized isolates (P < 0.05). The positive rates of virulence-associated genes including aap, sesI, ACME-arcA, IS256, bhp, altE, aae and gehD for S. epidermidis clinical isolates were significantly higher than those for colonized isolate (P < 0.05). A total of 60 STs including 28 from clinical isolates and 32 from colonized isolates were identified by MLST. A novel, rarely encountered clone, ST466, was found to be the second prevalent clone among clinical isolates. The great majority of the S. epidermidis isolates tested (73.86%) belonged to clone complex 2 (CC2). Compared with ST2, ST130, ST20 and ST59 clones, ST466 clone had the highest resistance rate to tetracycline (50.00%), the second highest prevalence of ACME-arcA (65.00%), bhp (30.00%) and qacA/B (65.00%), very low prevalence of carriage of icaA (0.00%) and biofilm formation (0.00%), the lack of sesI and high prevalence of aap, altE and aae (> 90%), which was similar to the characteristics of ST59 clone with one locus difference from ST466. ST466 clone competence with Staphylococcus aureus was relatively stronger, relative to ST2, ST20, ST130 and ST59 clones.

CONCLUSION

Taken together, a high-level of genetic diversity was found between clinical and colonized S. epidermidis isolates. A novel ST466 clone with distinct and similar characteristics relative to other prevalent clones, emerging as a prevalent clone in China, should be of major concern.

Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains. We provide sequence data for type strains of 64 taxa in the genus that at the time of this writing have standing in the nomenclature.

A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation

Polysaccharide intercellular adhesin (PIA)-associated biofilm formation is mediated by the intercellular adhesin (ica) locus and represents a major pathomechanism of Staphylococcus epidermidis. Here, we report on a novel long non-coding (nc)RNA, named IcaZ, which is approximately 400 nucleotides in size. icaZ is located downstream of the ica repressor gene icaR and partially overlaps with the icaR 3' UTR. icaZ exclusively exists in ica-positive S. epidermidis, but not in S. aureus or other staphylococci. Inactivation of the gene completely abolishes PIA production. IcaZ is transcribed as a primary transcript from its own promoter during early- and mid-exponential growth and its transcription is induced by low temperature, ethanol and salt stress. IcaZ targets the icaR 5' UTR and hampers icaR mRNA translation, which alleviates repression of icaADBC operon transcription and results in PIA production. Interestingly, other than in S. aureus, posttranscriptional control of icaR mRNA in S. epidermidis does not involve icaR mRNA 5'/3' UTR base pairing. This suggests major structural and functional differences in icaADBC operon regulation between the two species that also involve the recruitment of ncRNAs. Together, the IcaZ ncRNA represents an unprecedented novel species-specific player involved in the control of PIA production in NBSP S. epidermidis.

Biofilm formation by staphylococci in health-related environments and recent reports on their control using natural compounds

Staphylococci are Gram-positive bacteria that are ubiquitous in the environment and able to form biofilms on a range of surfaces. They have been associated with a range of human health issues such as medical device-related infection, localized skin infection, or direct infection caused by toxin production. The extracellular material produced by these bacteria resists antibiotics and host defence mechanism which complicates the treatment process. The commonly reported Staphylococcus species are Staphylococcus aureus and S. epidermidis as they inhabit human bodies. However, the emergence of other staphylococci, such as S. haemolyticus, S. lugdunensis, S. saprophyticus, S. capitis, S. saccharolyticus, S. warneri, S. cohnii, and S. hominis, is also of concern and they have been associated with biofilm formation. This review critically assesses recent cases on the biofilm formation by S. aureus, S. epidermidis, and other staphylococci reported in health-related environments. The control of biofilm formation by staphylococci using natural compounds is specifically discussed as they represent potential anti-biofilm agents which may reduce the burden of antibiotic resistance.

Variation in Mutant Prevention Concentrations

Objectives:Understanding how phenotypic traits vary has been a longstanding goal of evolutionary biologists. When examining antibiotic-resistance in bacteria, it is generally understood that the minimum inhibitory concentration (MIC) has minimal variation specific to each bacterial strain-antibiotic combination. However, there is a less studied resistance trait, the mutant prevention concentration (MPC), which measures the MIC of the most resistant sub-population. Whether and how MPC varies has been poorly understood. Here, we ask a simple, yet important question: How much does the MPC vary, within a single strain-antibiotic association? Using a Staphylococcus species and five antibiotics from five different antibiotic classes—ciprofloxacin, doxycycline, gentamicin, nitrofurantoin, and oxacillin—we examined the frequency of resistance for a wide range of concentrations per antibiotic, and measured the repeatability of the MPC, the lowest amount of antibiotic that would ensure no surviving cells in a 10¹⁰ population of bacteria.

Results: We found a wide variation within the MPC and distributions that were rarely normal. When antibiotic resistance evolved, the distribution of the MPC changed, with all distributions becoming wider and some multi-modal.

Conclusion: Unlike the MIC, there is high variability in the MPC for a given bacterial strain-antibiotic combination.

Tetrasodium EDTA Is Effective at Eradicating Biofilms Formed by Clinically Relevant Microorganisms from Patients' Central Venous Catheters

The colonization of catheters by microorganisms often precludes their long-term use, which can be a problem for human patients that have few body sites available for new catheters. The colonizing organisms often form biofilms, and increasingly these organisms are resistant to multiple antibiotics, making them difficult to treat. In this article, we have taken microorganisms that are associated with biofilm formation in catheters from two Canadian hospitals and tested them with tetrasodium EDTA, a new antimicrobial catheter lock solution. Tetrasodium EDTA was effective at eliminating Gram-positive, Gram-negative, and fungal species and represents a promising alternative to antibiotic treatment with less chance of the organisms developing resistance. We expect that our results will be of interest to researchers and clinicians and will lead to improved patient care.

Central venous access devices (CVADs) are an essential component of modern health care. However, their prolonged use commonly results in microbial colonization, which carries the potential risk of hospital-acquired bloodstream infections. These infections complicate the treatment of already sick individuals and cost the existing health care systems around the world millions of dollars. The microbes that colonize CVADs typically form multicellular biofilms that are difficult to dislodge and are resistant to antimicrobial treatments. Clinicians are searching for better ways to extend the working life span of implanted CVADs, by preventing colonization and reducing the risk of bloodstream infections. In this study, we analyzed 210 bacterial and fungal isolates from colonized CVADs or human bloodstream infections from two hospitals geographically separated in the east and west of Canada and screened the isolates for biofilm formation in vitro. Twenty isolates, representing 12 common, biofilm-forming species, were exposed to 4% tetrasodium EDTA, an antimicrobial lock solution that was recently approved in Canada for use as a medical device. The EDTA solution was effective at eradicating surface-attached biofilms from each microbial species, indicating that it could likely be used to prevent biofilm growth within CVADs and to eliminate established biofilms. This new lock solution fits with antibiotic stewardship programs worldwide by sparing the use of important antibiotic agents, targeting prevention rather than the expensive treatment of hospital-acquired infections.

IMPORTANCE The colonization of catheters by microorganisms often precludes their long-term use, which can be a problem for human patients that have few body sites available for new catheters. The colonizing organisms often form biofilms, and increasingly these organisms are resistant to multiple antibiotics, making them difficult to treat. In this article, we have taken microorganisms that are associated with biofilm formation in catheters from two Canadian hospitals and tested them with tetrasodium EDTA, a new antimicrobial catheter lock solution. Tetrasodium EDTA was effective at eliminating Gram-positive, Gram-negative, and fungal species and represents a promising alternative to antibiotic treatment with less chance of the organisms developing resistance. We expect that our results will be of interest to researchers and clinicians and will lead to improved patient care.

Evaluation of methods to detect in vitro biofilm formation by staphylococcal clinical isolates

Objective

Staphylococcus genus comprising both Staphylococcus aureus and coagulase negative staphylococci (CoNS) are widely distributed in nature and can infect diversity of hosts. Indeed, staphylococci are the major pathogens causing biofilm associated infections caused by contaminated hospital indwelling devices. These infections are persistent in nature being highly refractory to various stresses including antibiotics. Implementation of efficient diagnostic techniques for the biofilm production would help minimize the disease burden. Thus, early detection of pathogenic strains producing biofilms warrant the utmost importance in diagnostic laboratories especially in resource limited settings.

Result

Among 375 isolates collected from different clinical specimens, 214 (57%) were identified as coagulase negative staphylococci and 161 (43%) S. aureus. Detection of In-vitro biofilm formation in these isolates were carried out by three commonly used phenotypic assays and a genotypic assay. While evaluating the results, tissue-culture method with supplemented glucose and sucrose showed the best correlation with the results of genotypic assay.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3820-9) contains supplementary material, which is available to authorized users.

Application of tuf gene sequence analysis for the identification of species of coagulase-negative staphylococci in clinical samples and evaluation of their antimicrobial resistance pattern

Introduction

Coagulase-negative staphylococci (CoNS) are normal inhabitants of human skin and mucous membranes. However, CoNS represent one of the major nosocomial pathogens, especially in immunocompromised patients. The increasing incidence of CoNS and mainly methicillin-resistant strains underlines the need for an accurate identification of Staphylococcus isolates at the species level. Analysis of the tuf gene proved to be an accurate tool for the species identification of CoNS. The aims of this study were to identify the CoNS species by tuf gene-based polymerase chain reaction method and sequencing, and to determine the frequency of CoNS clinical isolates resistant to methicillin (MRCoNS) and other antibiotics.

Methods

A total of 200 staphylococci isolates were collected from various clinical samples. Phenotyping methods were used for initial identification followed by polymerase chain reaction amplification of tuf gene with subsequent sequencing. The phylogenetic relationships among species were analyzed using the neighbor-joining method based on the partial gene sequence of tuf. Microbroth dilution test was used for screening methicillin resistance, and disk diffusion susceptibility testing was performed for evaluation of antibiotic resistance among the isolates.

Results

In the present study, 125 isolates were identified as CoNS; among them, Staphylococcus epidermidis 54(43.2%) and Staphylococcus haemolyticus 50 (40.0%) were demonstrated as the most prevalent species. Resistance to methicillin was detected in 54.4% of the CoNS based on microbroth dilution method. In disk diffusion susceptibility testing, the greatest resistance of CoNS was demonstrated for cefoxitin (65.4%), cotrimethoxazole (54.4%), and clindamycin (49.6%), while daptomycin (87.2%) and linezolid (83.2%) showed the greatest effectiveness for CoNS isolates.

Conclusion

Our results confirmed the predominance of S. epidermidis and S. haemolyticus among CoNS isolates. The high prevalence of MRCoNS strains is a serious concern and strongly suggests the need for control program measures in our hospitals in order to reduce MRCoNS infections, especially in immunocompromised patients.

Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis

Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.

Unusual Manifestation of Live Staphylococcus saprophyticus, Corynebacterium urinapleomorphum, and Helicobacter pylori in the Gallbladder with Cholecystitis

Culture-independent studies have identified DNA of bacterial pathogens in the gallbladder under pathological conditions, yet reports on the isolation of corresponding live bacteria are rare. Thus, it is unclear which pathogens, or pathogen communities, can colonize the gallbladder and cause disease. Using light microscopy, scanning electron microscopy, culture techniques, phylogenetic analysis, urease assays and Western blotting, we investigated the presence of live bacterial communities in the gallbladder of a cholecystitis patient after cholecystectomy. 16S rRNA gene sequencing of isolated bacterial colonies revealed the presence of pathogens most closely resembling Corynebacterium urinapleomorphum nov. sp., Staphylococcus saprophyticus and Helicobacter pylori. The latter colonies were confirmed as H. pylori by immunohistochemistry and biochemical methods. H. pylori cultured from the gallbladder exhibited both the same DNA fingerprinting and Western cagA gene sequence with ABC-type EPIYA (Glu-Pro-Ile-Tyr-Ala) phosphorylation motifs as isolates recovered from the gastric mucus of the same patient, suggesting that gastric H. pylori can also colonize other organs in the human body. Taken together, here we report, for the first time, the identification and characterization of a community consisting of live S. saprophyticus; C. urinapleomorphum, and H. pylori in the gallbladder of a patient with acute cholecystitis. Their potential infection routes and roles in pathogenesis are discussed.

FDA 2014 survey of eye area cosmetics for microbiological safety

In an attempt to assess cosmetics containing 'nontraditional' preservatives, 93 eye area cosmetic products were selected based on labelled or marketed claims that these products were 'green', 'natural', 'paraben-free', 'preservative-free' or contained nontraditional preservatives (e.g. botanical extracts). Products were analysed for water activity, pH and microbiological content, which included enumeration of aerobic micro-organisms, detection of microbial growth after a 7-day enrichment and identification of microbial isolates. The survey found that 60% (56/93) of the eye area cosmetics were free of microbiological growth under test conditions, 32% (30/93) showed the presence of micro-organisms at low levels (<100 CFU per ml or g) and 8% (7/93) showed microbiological growth at higher levels (> 100 CFU per ml or g). Gram-positive bacteria such as Bacillus and Staphylococcus were the dominant genera identified in these cosmetic products, whereas Gram-negative species were relatively uncommon. The survey found a positive association between lower water activity cosmetics and the presence of micro-organisms in these products. Similarly, colour cosmetics were more likely to contain micro-organisms than noncolour cosmetics. The most represented micro-organisms in the survey were from genus Bacillus, suggesting that the natural raw materials are the likely source of observed microbial loads.

SIGNIFICANCE AND IMPACT OF THE STUDY

In the United States, cosmetic products are regulated postmarket; therefore, surveillance programmes are one of FDA's most important tools for monitoring microbiological safety of cosmetics. 'Traditional' preservatives, such as parabens and formaldehyde releasers, are perceived unfavourably by some consumers, resulting in cosmetic manufacturers increasingly using 'nontraditional' preservatives. FDA conducted an analytical survey of eye area cosmetics that claimed to be free of traditional preservatives and determined microbiological loads in tested products. This study explores the association of microbial loads with the physical and chemical characteristics of the cosmetic products, and points to the limits of preservative activity in cosmetics.

Changes in mouse gut bacterial community in response to different types of drinking water

Gut microbiota exerts a fundamental role on host physiology, and how extrinsic perturbations influence its composition has been increasingly examined. However, the effect of drinking water on gut microbiota is still poorly understood. In this study, we explored the response of mouse gut bacterial community (fecal and mucosa-adhered) to the ingestion of different types of drinking water. The experimental cohort was divided according to different water sources into four groups of mice that consumed autoclaved tap water (control group), water collected directly from a drinking water treatment plant, tap water, and commercial bottled mineral water. Differences among groups were observed, especially related to control group, which exhibited the smallest intra-group variation, and the largest distance from test groups on the last experimental day. Clinically important taxa, such as Acinetobacter and Staphylococcus, increased in feces of mice that drank tap water and in mucosa-adhered samples of animals from disinfected and tap water groups. Furthermore, statistical analyses showed that both time elapsed between samplings and water type significantly influenced the variation observed in the samples. Our results reveal that drinking water potentially affects gut microbiota composition. Additionally, the increase of typical drinking water clinically relevant and antibiotic resistance-associated bacteria in gut microbiota is a cause of concern.

Occurrence of virulence-associated genes among Staphylococcus saprophyticus isolated from different sources

Staphylococcus saprophyticus is an important pathogen responsible for community urinary tract infections (UTI). Besides composing the human microbiota, this species is widely distributed in the environment and the origins of this organism for human infection is not fully characterized. Although some virulence determinants are known, such as d-serine deaminase (DsdA), urease and cell-wall associated proteins, few studies investigated the distribution of virulence-associated genes and analyzed the pathogenic potential of S. saprophyticus strains from different sources. The aim of the present study was to detect the presence of S. saprophyticus genes encoding surface proteins UafA, Aas, Ssp, SdrI, SssF as well as the DsdA and urease enzymes. A total of 142 S. saprophyticus strains were obtained from four sources: UTI, colonization, water and food. It was found, in every tested strain, the presence of genes encoding the surface proteins UafA, Aas, Ssp and SssF and the DsdA and urease enzymes. In contrast, the gene encoding SdrI surface protein was not detected in any of the strains of S. saprophyticus. These results provide a better understanding of the characteristics of S. saprophyticus strains and suggest that isolates from non-human sources have a potential to colonize the urinary tract.

Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates

Staphylococcus epidermidis is a prominent commensal member of human skin microbiome and an emerging nosocomial pathogen, making it a good model organism to provide genomic insights, correlating its transition between commensalism and pathogenicity. While there are numerous studies to understand differences in commensal and pathogenic isolates, systematic efforts to understand variation and evolutionary pattern in multiple strains isolated from healthy individuals are lacking. In the present study, using whole genome sequencing and analysis, we report presence of diverse lineages of S. epidermidis isolates in healthy individuals from two geographically diverse locations of India and North America. Further, there is distinct pattern in the distribution of candidate gene(s) for pathogenicity and commensalism. The pattern is not only reflected in lineages but is also based on geographic origin of the isolates. This is evident by the fact that North American isolates under this study are more genomically dynamic and harbor pathogenicity markers in higher frequency. On the other hand, isolates of Indian origin are less genomically dynamic, harbor less pathogenicity marker genes and possess two unique antimicrobial peptide gene clusters. This study provides a basis to understand the nature of selection pressure in a key human skin commensal bacterium with implications in its management as an opportunistic pathogen.