Prevalence of biofilm-producing Staphylococcus epidermidis in the healthy skin of individuals in Tamil Nadu, India

Biofilm-producing antibiotic-resistant bacteria in Indian patients: a comprehensive review

For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable impact in the field of infectious diseases, in particular healthcare-associated infections related to indwelling devices such as catheters, implants, artificial heart valves, and prosthetic joints. Bacterial biofilm potentially adheres to any biotic or abiotic surfaces that give specific shelter to the microbial community, making them less susceptible to many antimicrobial agents and even resistant to the immune cells of animal hosts. Around thirty clinical research reports available in PUBMED have been considered to establish the occurrence of biofilm-forming bacteria showing resistance against several regular antibiotics prescribed against infection by clinicians among Indian patients. After the extensive literature review, our observation exhibits a high predominance of biofilm formation among bacteria such as Escherichia sp., Streptococcus sp., Staphylococcus sp., and Pseudomonas sp., those are the most common biofilm-producing antibiotic-resistant bacteria among Indian patients with urinary tract infections and/or catheter-related infections, respiratory tract infections, dental infections, skin infections, and implant-associated infections. This review demonstrates that biofilm-associated bacterial infections constantly elevate in several pathological conditions along with the enhancement of the multi-drug resistance phenomenon.

Characteristics of Biofilm-Forming Ability and Antibiotic Resistance of Cutibacterium acnes and Staphylococcus epidermidis from Acne Vulgaris Patients

Introduction

Acne vulgaris (AV) is a common and chronic disorder of the pilosebaceous unit and has a multifactorial pathology, including activities of Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis). Antibiotic resistance has become a major concern in dermatology daily practice, and the ability of biofilm formation by both bacteria is suggested to increase antibiotic resistance in acne.

Purpose

Our aim was to analyze the comparison of antibiotic resistance between biofilm-forming (BF) and non-biofilm-forming (NBF) strains of C. acnes and S. epidermidis towards seven antibiotics commonly used for acne.

Methods

This is a cross-sectional analytical study involving 60 patients with AV. Samples were obtained from closed comedones on the forehead using the standardized skin surface biopsy (SSSB) method at the Cosmetic Dermatology Clinic Dr. Hasan Sadikin in Bandung, Indonesia. Isolates were cultured and identified before undergoing the biofilm-forming test using the tissue culture plate method. Antibiotic susceptibility testing for each antibiotic was then performed using the disc diffusion method.

Results

The incidence of antibiotic resistance to clindamycin in BF and NBF C. acnes isolates was 54.5% (p=1.00), while in BF and NBF S. epidermidis isolates, it was 54.5% and 45.5% respectively (p=0.67). The incidence of antibiotic resistance to erythromycin and azithromycin in BF and NBF C. acnes isolates was 54.5% and 63.6% respectively (p=1.00), whereas for S. epidermidis BF and NBF isolates, it was 54.5% (p=1.00). There was no resistance observed to tetracycline, doxycycline, levofloxacin, and cotrimoxazole in all groups.

Conclusion

There were no significant differences in resistance against seven antibiotics between the C. acnes and S. epidermidis in BF and NBF groups. Furthermore, although statistically not significant, some resistances were observed against clindamycin, erythromycin, and azithromycin. Consequently, the use of these three antibiotics should be judiciously regulated.

No Correlation between Biofilm-Forming Capacity and Antibiotic Resistance in Environmental Staphylococcus spp.: In Vitro Results

The production of biofilms is a critical factor in facilitating the survival of Staphylococcus spp. in vivo and in protecting against various environmental noxa. The possible relationship between the antibiotic-resistant phenotype and biofilm-forming capacity has raised considerable interest. The purpose of the study was to assess the interdependence between biofilm-forming capacity and the antibiotic-resistant phenotype in 299 Staphylococcus spp. (S. aureus n = 143, non-aureus staphylococci [NAS] n = 156) of environmental origin. Antimicrobial susceptibility testing and detection of methicillin resistance (MR) was performed. The capacity of isolates to produce biofilms was assessed using Congo red agar (CRA) plates and a crystal violet microtiter-plate-based (CV-MTP) method. MR was identified in 46.9% of S. aureus and 53.8% of NAS isolates (p > 0.05), with resistance to most commonly used drugs being significantly higher in MR isolates compared to methicillin-susceptible isolates. Resistance rates were highest for clindamycin (57.9%), erythromycin (52.2%) and trimethoprim-sulfamethoxazole (51.1%), while susceptibility was retained for most last-resort drugs. Based on the CRA plates, biofilm was produced by 30.8% of S. aureus and 44.9% of NAS (p = 0.014), while based on the CV-MTP method, 51.7% of S. aureus and 62.8% of NAS were identified as strong biofilm producers, respectively (mean OD570 values: S. aureus: 0.779±0.471 vs. NAS: 1.053±0.551; p < 0.001). No significant differences in biofilm formation were observed based on MR (susceptible: 0.824 ± 0.325 vs. resistant: 0.896 ± 0.367; p = 0.101). However, pronounced differences in biofilm formation were identified based on rifampicin susceptibility (S: 0.784 ± 0.281 vs. R: 1.239 ± 0.286; p = 0.011). The mechanistic understanding of the mechanisms Staphylococcus spp. use to withstand harsh environmental and in vivo conditions is crucial to appropriately address the therapy and eradication of these pathogens.

Evaluation of antibacterial and acute oral toxicity of Impatiens tinctoria A. Rich root extracts

The high prevalence of morbidity and mortality from bacterial infections, together with the growing threat of antibacterial resistance, necessitated the development of alternative new drugs from traditional medicine. In Ethiopia, Impatiens tinctoria A. Rich has been traditionally used for the treatment of fungal infections such as ringworms that cause tinea pedis and it have also different medical values. Scientific information on its biological activity against a broad range of bacteria and safety data is scant, compared to its folklore data. In this study, we evaluated antibacterial activities and acute oral toxicity of aqueous, ethanol and ethyl acetate root extracts of Impatiens tinctoria A. Rich. Aqueous, ethanol and ethyl acetate extracts of the plant were evaluated using agar hole diffusion and agar dilution methods. Biological activities of the plant extracts were expressed as a zone of inhibition diameter, minimum inhibitory concentration (mg/ml), and minimum bactericidal concentration (mg/ml). The safety studies were performed by oral acute toxicity study according to the organization of economic cooperation and development test Guidelines 420.Gram-positive bacteria were more susceptible to the extracts compared to gram-negative bacteria, especially against S. aureus and S. epidermidis, which are commonly found in the skin. Ethyl acetate extract was more potent than ethanol and aqueous extracts. The 50% lethal dose (LD50) of tested mice was above 9600 mg/kg. This study provides a scientific basis for the antibacterial activity of the root extracts of I. tinctoria A. Rich, where, the ethyl acetate extract showed the most promising activity. Therefore, the antibacterial potential and practical non-toxicity of the study plant extracts suggested the possibility of using it for the development of antimicrobial drugs by further studying the plant in different directions.

Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.

Distribution of antibiotic resistance and virulence factors among the bacteria isolated from diseased Etroplus suratensis

Considering the emerging concern with the antimicrobial resistance (AMR) evolution, the study has been designed to identify the antibiotic resistance and virulence properties of culturable bacteria isolated from the diseased fish Etroplus suratensis. This has resulted in the purification of 18 morphologically distinct bacterial isolates which were identified by both biochemical and molecular methods. Antibiotic resistance analysis showed the resistance of these isolates to multiple antibiotics and remarkable evolution of AMR. Further screening for virulence factors confirmed five isolates to be positive for haemolytic activity, eight with caseinase, four with DNase, one with gelatinase and three with biofilm-forming properties. In addition to these, the isolates were subjected to PCR-based screening to detect the presence of genes coding for aerolysin and haemolysin. Results showed the presence aerolysin gene in the isolates ESS3.2, ESS3.8, ESI3.3 and ESS3.6, while haemolysin gene was observed to be present in ESG3.1 and ESI3.2. The observed results hence indicate the need for frequent monitoring of these properties among bacterial isolates from diverse environment especially those associated with edible fish.

Use of MALDI-TOF MS to Discriminate between Biofilm-Producer and Non-Producer Strains of Staphylococcus epidermidis

For the management of Staphylococci coagulase-negative infection, often related to biofilm formation, rapid and accurate identification is necessary in choosing a correct antibiotic therapy. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is becoming increasingly important for bacterial identification over traditional methods. Our aim was to validate the use of MALDI to discriminate Staphylococcus epidermidis biofilm-producing strains. Clinical strains coming from suture wires were identified and their protein profiles were compared to that obtained from two ATCC reference strains (biofilm producer and non-producer). MALDI identified the eighteen isolates as S. epidermidis, combining sixteen profiles with the biofilm producer and two with the non-producer, confirming the results of crystal violet assay. Our data highlight that MALDI can be considered a good tool to discriminate between biofilm-producer and non-producer strains of S. epidermidis, thus helping to establish an effective antibiotic therapy.

Role of insertion sequence element is256 as a virulence marker and its association with biofilm formation among methicillin-resistant Staphylococcus epidermidis from hospital and community settings in Chennai, South India

The objective of this study was to detect the association of biofilm formation with IS256 among clinical and carrier isolates of methicillin-resistant Staphylococcus epidermidis (MRSE). A total of 71 MRSE isolates were included in this study. Phenotypic detection of biofilm formation was done by Congo red agar method. Detection of genes associated with biofilm formation (icaAD, aap and atlE) and insertion sequence IS256 was done by polymerase chain reaction. Of the 71 MRSE isolates,19/40 (47.5%) clinical isolates from hospital settings and 11/31 (35.5%) carrier isolates from community settings respectively were found to be positive for all the three genes tested, namely, icaAD⁺, aap⁺ and atlE⁺ genes. Nearly 80% of clinical isolates were found to harbour IS256, whereas only 13% of community isolates harboured IS256.

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.

Virulence factors associated with Coagulase Negative Staphylococci isolated from human infections

Infections caused by commensal organisms by changing to infectious life style generate much challenge to the current treatment strategies. Coagulase Negative Staphylococci (CoNS) are one of them, with their coexisting biofilm forming and multiple antibiotic resistance properties form important agents of nosocomial infection. To evaluate species distribution, biofilm formation, and antibiogram, CoNS isolates from various clinical samples were isolated. The presence of biofilm and associated genes icaAB, aap, atlE, embp, bhp, and fbe in CoNS was screened by PCR. The biofilm chemical composition and its correlation with the genotypes were also analysed. Staphylococcus epidermidis (59%) was found to be the most prevalent CoNS species. Most of the CoNS isolates harboring biofilm gene showed carbohydrate-protein-eDNA biofilm, whereas carbohydrate-protein biofilms were also observed. High percentage of multiple drug resistance, and biofilm gene frequency among these CoNS isolates point towards the need of periodic surveillance as CoNS are recently identified to cause difficult to treat infections.

Studies on prevalence of biofilm associated genes and primary observation on sasX gene in clinical isolates of coagulase negative staphylococci (CoNS)

Coagulase negative staphylococci (CoNS) are nosocomial pathogens that cause indwelling medical device associated infections due to its biofilm forming potential and multiple antibiotic resistance. The current study focused on species identification, antibiotic resistance profile and molecular basis of biofilm formation and attachment of CoNS isolated from clinical samples. Along with this, molecular screening for mecA and newly identified surface colonization protein encoded by sasX gene was also conducted. S. epidermidis (n = 19, 47%) was identified as the most prevalent CoNS species and very interestingly two biofilm forming, mecA positive S. epidermidis isolates were found to carry all the biofilm associated genes screened in this study, which indicates its potential to form the strong biofilm. Another novel observation of the study is the detection of sasX gene in one biofilm positive S. epidermidis isolate. The study also identified one doxycycline resistant mecA positive, multidrug resistant S. haemolyticus isolate. In conclusion, the study signifies the existence of multiple biofilm related genes, multidrug resistance and the presence of sasX gene among clinical isolates of CoNS.

Comparative genomic and transcriptomic analyses of NaCl-tolerant Staphylococcus sp. OJ82 isolated from fermented seafood

Bacteria belonging to the Staphylococcus genus reside in various natural environments; however, only disease-associated Staphylococcus strains have received attention while ecological function and physiologies of non-pathogenic strains were often neglected. Because high level of tolerance against NaCl is a common trait of Staphylococcus, we investigated the characteristics of halotolerance in Staphylococcus sp. OJ82 isolated from fermented seafood containing a high concentration of NaCl. Among the 292 isolates screened, OJ82 showed the highest β-galactosidase and extracellular protease activities under high-salt conditions. Comparative genomic analysis with other Staphylococcus strains showed that (a) replication origins are highly conserved, (b) the OJ82 strain has a high number of amino acid transport- and metabolism-related genes, and (c) OJ82 has many unique proteins (15 %) and 12 prophage-related genomic islands. RNA-seq analysis under high-salt conditions showed that genes involved in cell membranes, transport, osmotic stress, ATP synthesis, and translation are highly expressed. OJ82 may use the ribulose monophosphate pathway to detoxify some toxic intermediates under high-salt conditions. Six new and three known non-coding small RNAs of the OJ82 strain were also found in the RNA-seq analysis. Genomic and transcriptomic analyses identified target β-galactosidase and extracellular protease. Interestingly, the OJ82 strain became resistant to bacteriocin produced by the Bacillus strain only under high-salt conditions. Our data showed that the OJ82 strain adapted to high-salt conditions by expressing core cellular processes (translation, ATP production) and defense genes (membrane synthesis, compatible solute transports, ribulose monophosphate pathway) could survive bacteriocin exposure under high-salt conditions.