Frequency of small-colony variants and antimicrobial susceptibility of methicillin-resistant Staphylococcus aureus in cystic fibrosis patients

Phenotypic and genomic characterization of a small colony variant of Klebsiella pneumoniae isolated from urine of a prostate cancer case

Small colony variants (SCVs) in Klebsiella pneumoniae are rare and understudied. We report an SCV of Klebsiella pneumoniae isolated from the urine of a prostate cancer patient undergoing prolonged radiotherapy. The strain was non-lactose fermenting, non-mucoid, slow-growing, multi-drug resistant, and showed atypical biochemical reactions and biofilm formation. On whole genome sequencing, it showed low-level virulence, sequence type 231 and gene CTX-M-15. Three major porins OmpK35, OmpK36 and OmpK37 were found. SCVs pose challenges like difficulties in identification, altered metabolism, and increased biofilm formation, which contribute to persistent infections. Radiotherapy and chemotherapy may have led to the formation of the SCV phenotype.

The role of Staphylococcus aureus in cystic fibrosis pathogenesis and clinico-microbiological interactions

Cystic fibrosis (CF) is a progressive and inherited disease that affects approximately 70000 individuals all over the world annually. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene serves as its defining feature. Bacterial infections have a significant impact on the occurrence and development of CF. In this manuscript, we discuss the role and virulence factors of Staphylococcus aureus as an important human pathogen with the ability to induce respiratory tract infections. Recent studies have reported S. aureus as the first isolated bacteria in CF patients. Methicillin-resistant Staphylococcus aureus (MRSA) pathogens are approximately resistant to all β-lactams. CF patients are colonized by MRSA expressing various virulence factors including toxins, and Staphylococcal Cassette Chromosome mec (SCCmec) types, and have the potential for biofilm formation. Therefore, variations in clinical outcomes will be manifested. SCCmec type II has been reported in CF patients more than in other SCCmec types from different countries. The small-colony variants (SCVs) as specific morphologic subtypes of S. aureus with slow growth and unusual properties can also contribute to persistent and difficult-to-treat infections in CF patients. The pathophysiology of SCVs is complicated and not fully understood. Patients with cystic fibrosis should be aware of the intrinsic risk factors for complex S. aureus infections, including recurring infections, physiological issues, or coinfection with P. aeruginosa.

Prevalence of antibiotic resistance of Staphylococcus aureus in cystic fibrosis infection: a systematic review and meta-analysis

OBJECTIVES

Cystic fibrosis (CF) is a hereditary recessive disease that affects the mucous clearance of the lungs and allows bacteria such as Staphylococcus aureus to settle in the lung and cause infection. This study examined the prevalence of antibiotic resistance of S. aureus in cystic fibrosis infection using a systematic review and meta-analysis.

METHODS

A comprehensive and systematic search of related articles was conducted through the PubMed, Scopus, and Web of Science databases until March 2022. The weighted pooled resistance rate of antibiotics was analysed with Freeman-Tukey double arcsine transformation in the Stata software version 17.1 using the Metaprop command.

RESULTS

In this meta-analysis, 25 studies were used based on criteria to evaluate the pattern of S. aureus resistance in CF. Vancomycin and teicoplanin were the most effective options for treatment of CF patients; the highest level of antibiotic resistance observed was to erythromycin and clindamycin.

CONCLUSION

High levels of resistance to most of the antibiotics studied was observed. The high levels of antibiotic resistance observed are worrisome and indicate the need to monitor antibiotic use.

A systematic review of the clinical impact of small colony variants in patients with cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) is a life-limiting disorder that is characterised by respiratory tract inflammation that is mediated by a range of microbial pathogens. Small colony variants (SCVs) of common respiratory pathogens are being increasingly recognised in CF. The aim of this systematic review is to investigate the prevalence of SCVs, clinical characteristics and health outcomes for patients with CF, and laboratory diagnostic features of SCVs compared to non-small colony variants (NCVs) for a range of Gram-positive and Gram-negative respiratory pathogens.

METHODS

A literature search was conducted (PubMed, Web of Science, Embase and Scopus) in April 2020 to identify articles of interest. Data pertaining to demographic characteristics of participants, diagnostic criteria of SCVs, SCV prevalence and impact on lung function were extracted from included studies for analysis.

RESULTS

Twenty-five of 673 studies were included in the systematic review. Individuals infected with SCVs of Staphylococcus aureus (S. aureus) were more likely to have had prior use of the broad-spectrum antibiotic trimethoprim sulfamethoxazole (p < 0.001), and the prevalence of SCVs in patients infected with S. aureus was estimated to be 19.3% (95% CI: 13.5% to 25.9%). Additionally, patients infected with SCVs of Gram-negative and Gram-positive pathogens were identified to have a lower forced expiratory volume in one second percentage predicted (-16.8, 95% CI: -23.2 to -10.4) than those infected by NCVs. Gram-positive SCVs were commonly described as small and non-haemolytic, grown on Mannitol salt or blood agar for 24 h at 35°C and confirmed using tube coagulase testing.

CONCLUSION

The findings of this systematic review demonstrate that SCVs of S. aureus have a high prevalence in the CF community, and that the occurrence of SCVs in Gram-positive and Gram-negative pathogens is linked to poorer respiratory function. Further investigation is necessary to determine the effect of infection by SCVs on the CF population.

The Clinical Significance of Staphylococcus aureus Small Colony Variants

A burdensome, atypical phenotype of Staphylococcus aureus (SA) called S aureus small colony variant (SA-SCV) has been identified, which is induced as a result of a combination of environmental stressors, including polymicrobial interactions. The SA-SCVs exhibit altered phenotypes as a result of metabolic dormancy caused by electron transport deficiency, leading to increased biofilm production and alterations to antimicrobial susceptibility. The SA-SCVs typically exhibit altered colony morphology and biochemical reactions compared with wild-type SA, making them difficult to detect via routine diagnostics. The SA-SCVs have been found to contribute to chronic or recurrent infections, including skin and soft-tissue infections, foreign-body associated infection, cystic fibrosis, and sepsis. There is evidence that SA-SCVs contribute to patient morbidity and mortality as a result of diagnostic difficulties and limited treatment options. New detection methods may need to be developed that can be incorporated into routine diagnostics, which would allow for better assessment of specimens and introduce new considerations for treatment.

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei

Burkholderia pseudomallei (B. pseudomallei) is an intracellular pathogen that causes melioidosis, a life-threatening infection in humans. The bacterium is able to form small colony variants (SCVs) as part of the adaptive features in response to environmental stress. In this study, we characterize the genomic characteristics, antimicrobial resistance (AMR), and metabolic phenotypes of B. pseudomallei SCV and wild type (WT) strains. Whole-genome sequence analysis was performed to characterize the genomic features of two SCVs (CS and OS) and their respective parental WT strains (CB and OB). Phylogenetic relationship between the four draft genomes in this study and 19 publicly available genomes from various countries was determined. The four draft genomes showed a close phylogenetic relationship with other genomes from Southeast Asia. Broth microdilution and phenotype microarray were conducted to determine the AMR profiles and metabolic features (carbon utilization, osmolytes sensitivity, and pH conditions) of all strains. The SCV strains exhibited identical AMR phenotype with their parental WT strains. A limited number of AMR-conferring genes were identified in the B. pseudomallei genomes. The SCVs and their respective parental WT strains generally shared similar carbon-utilization profiles, except for D,L-carnitine (CS), g-hydroxybutyric acid (OS), and succinamic acid (OS) which were utilized by the SCVs only. No difference was observed in the osmolytes sensitivity of all strains. In comparison, WT strains were more resistant to alkaline condition, while SCVs showed variable growth responses at higher acidity. Overall, the genomes of the colony morphology variants of B. pseudomallei were largely identical, and the phenotypic variations observed among the different morphotypes were strain-specific.

Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA

Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015-2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2, targets of carbapenems; no effects were achieved by other β-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

Thymidine-auxotrophic Staphylococcus aureus small-colony variant bacteremia in a patient with cystic fibrosis

BACKGROUND

Small-colony variants (SCVs) are a morphologic subtype of Staphylococcus aureus that may occur through several mechanisms including auxotrophism for thymidine, hemin, or menadione. Auxotrophic SCV for thymidine fail to synthesize DNA specifically because of mutations in the thymidylate synthase gene. We isolated S. aureus thymidine-dependent SCVs (TD-SCV) from blood and respiratory samples of a pediatric patient with cystic fibrosis and pulmonary exacerbation.

METHODS

Nutritional dependence of SCVs on hemin, menadione, and thymidine was evaluated. Antimicrobial susceptibility testing was performed through broth microdilution. Polymerase chain reaction was carried out for mecA, ermA, ermB, ermC, msrA, and msrB resistance genes. DNA sequencing was used to determine mutations in thyA and the multilocus sequence typing to identify genetic relatedness.

RESULTS

Methicillin-sensitive S. aureus with normal and TD-SCV phenotypes were isolated from respiratory samples and a TD-SCV phenotype was isolated from blood culture. Macrolides resistance was attributed to ermC and msrB genes. All isolates belonged to ST398. The thyA gene in S. aureus is 957 nucleotides in length and encodes a protein of 318 amino acids. The TD-SCV isolates carried a -2 nt frameshift mutation (delta 667GC668) in thyA, creating a stop codon at residue 222 close to the predicted binding site for deoxyuridine monophosphate.

CONCLUSIONS

The pathogenesis of SCVs is complex and not fully elucidated. Factors inherent to the patient such as physiological conditions, recurrent infections, or coinfection should be considered. Although SCVs are considered less virulent, they showed the ability to invade and cause bacteremia in the patient.

Bactericidal Activity of the Bacterial ATP Synthase Inhibitor Tomatidine and the Combination of Tomatidine and Aminoglycoside Against Persistent and Virulent Forms of Staphylococcus aureus

Tomatidine (TO), a steroid alkaloid, exerts a strong bactericidal activity on the infection-persistent phenotype of Staphylococcus aureus, the small-colony variant (SCV), with a minimal inhibitory concentration (MIC) of 0.06 μg/ml. Also, the combination of TO to an aminoglycoside (AMG) shows a strong synergistic effect against prototypical (WT) S. aureus (MIC 0.06 μg/ml), which is otherwise unaffected by TO alone (MIC > 128 μg/ml). We have recently established that the ATP synthase (subunit AtpE) was the molecular target of TO and that TO reduces the production of ATP in S. aureus. The purpose of this study was to understand how TO and the TO-AMG combination exert bactericidal activities against S. aureus SCV and WT strains, respectively. The impact of TO and of the TO-gentamicin (GEN) combination on the membrane potential and generation of reactive oxygen species (ROS) were determined using florescent probes. GEN uptake in WT was assessed in the presence of TO. Virulence of SCV and WT strains as well as of in vitro-selected mutants showing resistance to TO or the TO-GEN combination was evaluated in a murine thigh infection model. TO causes a reduction in membrane potential in both WT and SCV, but significant amounts of ROS are only produced in SCVs. Besides, the presence of TO improves the uptake of GEN by the WT strain and the combination TO-GEN generated 2.5-folds more ROS in WT, compared to that induced by GEN alone. Under anaerobic conditions, WT adopts a fermentative slow-growth phenotype and becomes susceptible to TO even if used alone. In vivo, TO- or TO-GEN-resistant strains were significantly altered in their ability to colonize tissues. These results shed light on the mechanism of action of TO and its synergy with AMGs against S. aureus WT. TO bactericidal activity against SCVs is attributable to both a critical drop in the membrane potential accompanied by a substantial ROS production. In the WT, TO helps GEN uptake and ROS is also important for the synergy. Acquiring resistance to TO significantly impairs virulence. The residual ATP synthase activity of SCVs might represent the Achilles’ heel of persistent S. aureus.

A Mutant RNA Polymerase Activates the General Stress Response, Enabling Escherichia coli Adaptation to Late Prolonged Stationary Phase

An important general mechanism of a bacterium’s adaptation to its environment involves adjusting the balance between growing fast and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favor of the general stress response about 2 weeks later. This can be established by direct mutations in the master regulator of the general stress response or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance although the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.

Escherichia coli populations undergo repeated replacement of parental genotypes with fitter variants deep in stationary phase. We isolated one such variant, which emerged after 3 weeks of maintaining an E. coli K-12 population in stationary phase. This variant displayed a small colony phenotype and slow growth and was able to outcompete its ancestor over a narrow time window in stationary phase. The variant also shows tolerance to beta-lactam antibiotics, though not previously exposed to the antibiotic. We show that an RpoC(A494V) mutation confers the slow growth and small colony phenotype on this variant. The ability of this mutation to confer a growth advantage in stationary phase depends on the availability of the stationary-phase sigma factor σ^S. The RpoC(A494V) mutation upregulates the σ^S regulon. As shown over 20 years ago, early in prolonged stationary phase, σ^S attenuation, but not complete loss of activity, confers a fitness advantage. Our study shows that later mutations enhance σ^S activity, either by mutating the gene for σ^S directly or via mutations such as RpoC(A494V). The balance between the activities of the housekeeping major sigma factor and σ^S sets up a trade-off between growth and stress tolerance, which is tuned repeatedly during prolonged stationary phase.

IMPORTANCE An important general mechanism of a bacterium’s adaptation to its environment involves adjusting the balance between growing fast and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favor of the general stress response about 2 weeks later. This can be established by direct mutations in the master regulator of the general stress response or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance although the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.

Methicillin-Resistant Staphylococcus aureus Infection and Treatment Options

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of infection worldwide, including a wide array of both hospital- and community-acquired infections-most commonly bacteremia, upper and lower respiratory tract infection, skin and soft-tissue infection, osteomyelitis, and septic arthritis. This chapter describes the epidemiology of MRSA infection, its ability to confer antibiotic resistance and produce a wide array of virulence factors, and its pivotal role in human infection, especially cystic fibrosis. It also provides an introduction to the strategies for treatment of both chronic and acute MRSA infections.

Antimicrobial Treatment of Staphylococcus aureus in Patients With Cystic Fibrosis

Staphylococcus aureus is a ubiquitous human commensal pathogen. It is commonly isolated in cystic fibrosis (CF) patients and is considered one of the main causes of the recurrent acute pulmonary infections and progressive decline in lung function that characterize this inherited life-threatening multisystem disorder. However, the true role of S. aureus in CF patients is not completely understood. The main aim of this narrative review is to discuss the present knowledge of the role of S. aureus in CF patients. Literature review showed that despite the fact that the availability and use of drugs effective against S. aureus have coincided with a significant improvement in the prognosis of lung disease in CF patients, clearly evidencing the importance of S. aureus therapy, how to use old and new drugs to obtain the maximal effectiveness has not been precisely defined. The most important problem remains that the high frequency with which S. aureus is carried in healthy subjects prevents the differentiation of simple colonization from infection. Moreover, although experts recommend antibiotic administration in CF patients with symptoms and in those with persistent detection of S. aureus, the best antibiotic approach has not been defined. All these problems are complicated by the evidence that the most effective antibiotic against methicillin-resistant S. aureus (MRSA) cannot be used in patients with CF with the same schedules used in patients without CF. Further studies are needed to solve these problems and to assure CF patients the highest level of care.

Cystic fibrosis year in review 2018, part 1

Cystic fibrosis research and case reports were robust in the year 2018. This report summarizes research and cases related to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) modulator therapies, inflammation and infection, epidemiology and the physiologic, and imaging assessment of disease.

Salmonella enterica persister cells form unstable small colony variants after in vitro exposure to ciprofloxacin

Persistence phenotype and small colony variants (SCVs) can be part of a bacterial bet-hedging strategy for survival under environmental stresses, such as antimicrobial exposure. These phenotypes are of particular concern in persistent and relapsing infections, since cells resume to normal growth after cessation of the stressful condition. In this context, we found persisters and unstable SCVs as phenotypic variants of Salmonella enterica that were able to survive ciprofloxacin exposure. A high heterogeneity in persister levels was observed among S. enterica isolates grown under planktonic and biofilm conditions and exposed to ciprofloxacin or ceftazidime, which may indicate persistence as a non-multidrug-tolerant phenotype. Nevertheless, a comparable variability was not found in the formation of SCVs among the isolates. Indeed, similar proportions of SCV in relation to normal colony phenotype (NCP) were maintained even after three successive cycles of ciprofloxacin exposure testing colonies from both origins (SCV or NCP). Additionally, we found filamentous and dividing cells in the same scanning electron microscopy images from both SCV and NCP. These findings lead us to hypothesize that besides variability among isolates, a single isolate may generate distinct populations of persisters, where cells growing under distinct conditions may adopt different and perhaps complementary survival strategies.