An unusual case of Staphylococcus pasteuri osteomyelitis

Genomic analysis of multi-drug resistant coagulase-negative staphylococci from healthy humans and animals revealed unusual mechanisms of resistance and CRISPR-Cas system

BACKGROUND

Coagulase-negative staphylococci (CoNS) are evolving as major reservoirs and vectors of unusual and critical antimicrobial resistance (AMR) mechanisms.

MATERIALS AND METHODS

In this study, the genomic characterization of 26 multidrug-resistant (MDR)-CoNS (S. borealis, S. saprophyticus, S. sciuri, S. hominis, S. epidermidis, S. pasteuri, S. hyicus, S. simulans, S. haemolyticus, and S. arlettae) previously obtained from the nasal cavity of healthy nestling storks, humans who had no contact with animals, pigs, and pig farmers, as well as dogs and dog owners from Spain was performed. High-quality draft genomes obtained by Illumina sequencing technology were used to determine their resistome, virulome, mobile genetic elements, and CRISPR-Cas types. The relatedness of three CoNS species with publicly available genomes was assessed by core-genome single nucleotide polymorphisms (SNPs).

RESULTS

AMR genes to all classes of antibiotics in staphylococci were detected including unusual ones (mecC, ermT, and cfr), of which their corresponding genetic organizations were analyzed. About 96.1% of the MDR-CoNS strains harbored diverse adherence or immune evasion genes. Remarkably, one enterotoxin-C and -L-carrying S. epidermidis-ST595 strain from a nestling stork was detected. Moreover, various plasmid bound-biocide resistance genes (qacACGJ) were identified in 34.6% of the MDR-CoNS. Two genes that encode for cadmium and zinc resistance (cadD, czrC) were found, of which czrC predominated (42.3%). Complete CRISPR-Cas system was detected in 19.2% of the CoNS strains, of which cas-1, -2, and -9 predominated, especially in 75% of the S. borealis strains. The phylogenetic analysis identified clusters of related S. epidermidis lineages with those of other countries (SNP < 100). Also, highly related S. borealis isolates (SNP < 10) from pigs was confirmed for the first time in Spain.

CONCLUSION

These findings showed that various ecological niches harbor CoNS that presented MDR phenotypes mediated by multiple AMR genes carried by mobile genetic elements with relatively low frequency of intact CRISPR-Cas systems. Furthermore, the transmission of some CoNS species in humans and animals is strongly suggested.

Co-resistance to methicillin and clindamycin among coagulase-negative staphylococci isolates recovered from pet food in Brazil

Pet food have been considered as possible vehicles of bacterial pathogens. The sudden boom of the pet food industry due to the worldwide increase in companion animal ownership calls for pet food investigations. Herein, this study aimed to determine the frequency, antimicrobial susceptibility profile, and molecular characteristics of coagulase-negative staphylococci (CoNS) in different pet food brands in Brazil. Eighty-six pet food packages were screened for CoNS. All isolates were identified at species level by MALDI-TOF MS and species-specific PCR. Antimicrobial susceptibility testing was performed by disc diffusion and broth microdilution (vancomycin and teicoplanin only) methods. The D-test was used to screen for inducible clindamycin phenotype (MLS-B). SCCmec typing and detection of mecA, vanA, vanB, and virulence-encoding genes were done by PCR. A total of 16 (18.6 %) CoNS isolates were recovered from pet food samples. Isolates were generally multidrug-resistant (MDR). All isolates were completely resistant (100 %) to penicillin. Resistances (12.5 % - 75 %) were also observed for fluoroquinolones, sulfamethoxazole-trimethoprim, tetracycline, rifampicin, erythromycin, and tobramycin. Isolates were susceptible to vancomycin (MICs <0.25-1 μg/mL) and teicoplanin (MICs <0.25-4 μg/mL). Intriguingly, 3/8 (37.5 %) CoNS isolates with the ERYRCLIS antibiotype expressed MLS-B phenotype. All isolates harboured blaZ gene. Seven (43.8 %) isolates carried mecA; and among them, the SCCmec Type III was the most frequent (n = 5/7; 71.4 %). Isolates also harboured seb, see, seg, sej, sem, etb, tsst, pvl, and hla toxin virulence-encoding genes (6.3 % - 25 %). A total of 12/16 (75 %) isolates were biofilm producers, while the icaAB gene was detected in an S. pasteuri isolate. Herein, it is shown that pet food is a potential source of clinically important Gram-positive bacterial pathogens. To the best of our knowledge, this is the first report of MLS-B phenotype and MR-CoNS in pet food in Latin America.

Biochar pH reduction using elemental sulfur and biological activation using compost or vermicompost

This study aimed to improve biochar's quality for arid land applications by using elemental sulfur as a pH reducer agent co-applied with compost or vermicompost as biological activators. Biochar pH was decreased by the addition of elemental sulfur, with the highest reduction from 8.1 to 7.2 occurring when co-amended with vermicompost. Elemental sulfur increased the water-soluble concentrations of calcium, magnesium, and many other elements, and stimulated substrate-induced respiration, especially when co-amended with vermicompost. The bacterial diversity community structure were significantly affected by all treatments. The Shannon index significantly increased in response to compost and sulfur treatments, while the vermicompost treatments showed higher microbial evenness and equitability diversity indices. Multivariate analyses indicated that elemental sulfur oxidation was associated with specific sulfur-oxidizing bacterial clusters. Integrating biochar with sulfur and (vermi)compost was found to be a promising sustainable technology for managing excessive biochar alkalinity, increasing its fertility and potential for application in aridlands.

Antibiotic Resistance Genes, Virulence Factors, and Biofilm Formation in Coagulase-Negative Staphylococcus spp. Isolates from European Hakes (Merluccius merluccius, L.) Caught in the Northeast Atlantic Ocean

The indiscriminate use of antibiotics has contributed to the dissemination of multiresistant bacteria, which represents a public health concern. The aim of this work was to characterize 27 coagulase-negative staphylococci (CoNS) isolated from eight wild Northeast Atlantic hakes (Merluccius merluccius, L.) and taxonomically identified as Staphylococcus epidermidis (n = 16), Staphylococcus saprophyticus (n = 4), Staphylococcus hominis (n = 3), Staphylococcus pasteuri (n = 2), Staphylococcus edaphicus (n = 1), and Staphylococcus capitis (n = 1). Biofilm formation was evaluated with a microtiter assay, antibiotic susceptibility testing was performed using the disk diffusion method, and antibiotic resistance and virulence determinants were detected by PCR. Our results showed that all staphylococci produced biofilms and that 92.6% of the isolates were resistant to at least one antibiotic, mainly penicillin (88.8%), fusidic acid (40.7%), and erythromycin (37%). The penicillin resistance gene (blaZ) was detected in 66.6% (18) of the isolates, of which 10 also carried resistance genes to macrolides and lincosamides (mphC, msr(A/B), lnuA, or vgaA), 4 to fusidic acid (fusB), and 3 to trimethoprim-sulfamethoxazole (dfrA). At least one virulence gene (scn, hla, SCCmecIII, and/or SCCmecV) was detected in 48% of the isolates. This study suggests that wild European hake destined for human consumption could act as a vector of CoNS carrying antibiotic resistance genes and/or virulence factors.

Case Report: Rare Case of Staphylococcus pasteuri Endocarditis

A 45-year-old woman was admitted with severe pain in the right leg and dyspnea. Her medical history included previous Staphylococcus aureus endocarditis, biological aortic valve replacement, and intravenous drug abuse. She was febrile but did not have any focal signs of infection. Blood tests showed raised infectious markers and troponin levels. Electrocardiogram showed sinus rhythm without signs of ischemia. Ultrasound revealed thrombosis of the right popliteal artery. The leg was not critically ischemic, and therefore, treatment with dalteparin was chosen. Transesophageal echocardiography showed an excrescence on the biological aortic valve. Empiric treatment for endocarditis was started with intravenous vancomycin, gentamicin, and oral rifampicin. Blood cultures subsequently grew Staphylococcus pasteuri. On day 2, treatment was changed to intravenous cloxacillin. Due to the comorbidity, the patient was not a candidate for the surgical treatment. On day 10, the patient developed moderate expressive aphasia and weakness in the right upper limb. Magnetic resonance imaging showed micro-embolic lesions scattered across both hemispheres of the brain. Treatment was changed from cloxacillin to cefuroxime. On day 42, infectious markers were normal, and echocardiography showed regression of the excrescence. Antibiotic treatment was stopped. Follow-up on day 52 did not show any signs of active infection. However, on day 143, the patient was readmitted with cardiogenic shock due to aortic root fistulation to the left atrium. She quickly deteriorated and died.

Microbiological Evaluation of Water Used in Dental Units

In modern dentistry, dental units are used for the treatment of patients’ teeth, and they need water to operate. Water circulates in a closed vessel system and finally reaches the mucous membranes of the patient as well as the dentist themselves. Therefore, the microbiological safety of this water should be a priority for physicians. This study aims to identify and determine the microbial count, expressed in CFU/mL, in water samples from various parts of the dental unit that are in direct contact with the patient. Thirty-four dental units located in dentistry rooms were analysed. The dentistry rooms were divided into three categories: surgical, conservative, and periodontal. It was found that in surgical rooms, the bacterial count was 1464.76 CFU/mL, and the most common bacterium was Staphylococcus pasteuri—23.88% of the total bacteria identified. In dentistry rooms where conservative treatments were applied, the average bacterial concentration was 8208.35 CFU/mL, and the most common bacterium was Ralsonia pickettii (26.31%). The periodontal rooms were also dominated by R. pickettii (45.13%), and the average bacterial concentration was 8743.08 CFU/mL. Fungi were also detected. Rhodotorula spp., Alternaria spp., and Candida parapsilosis were found to be the most common bacteria which are potentially harmful. This study indicates the need for effective decontamination of the water that is used in dental units and for constant monitoring of the level of contaminants present in the closed vessel system.

Bacterial microbiota of the contact lens surface and associated care behaviours

Introduction

Contact lens (CL) wear has been reported to cause changes to the microbiome of the ocular surface. More insight into the alteration of this microenvironment can help to understand the pathogenesis of CL-related eye infections. Knowledge of the relationship between the CL wearer's behaviours and pathogens would help health care providers focus on each step of proper CL care. This study aims to determine the behaviours that might be associated with the community of bacteria on CL.

Methods

A cross-sectional design was performed using anonymous questionnaires to obtain demographic data and assess hygiene practices among volunteering wearers. The CLs used were collected to evaluate the prevalence of pathogenic bacteria associated with ocular infections by PCR and microbiota analysis.

Results

The bacterial microbiota study revealed a total of 19 genera and 26 isolated strains from 20 eligible CLs. Enterobacter, Staphylococcus, and Achromobacter were the main genus in this subject population. Staphylococcus pasteuri and Achromobacter agilis were the most common pathogens at 65% and 35%, respectively. Enterobacter mori, a nonpathogenic organism, was found to be the most predominant strain, accounting for 27.51% of the total bacterial constituents. The risk behaviour of CL wear that was significantly associated with A. agilis contamination was cleaning the CL case with tap water (P value = 0.04).

Conclusions

This is the first study focusing on the association between the culture selected microbial community on the CL surface and compehensive behavioural characteristics. Environmental contamination was the main source of microbes found on CL surfaces. An emphasis in patient education should be placed on careful handling during the CL care routine and managing the hygiene of the surroundings.

Assessing the Bacterial Community Composition of Bivalve Mollusks Collected in Aquaculture Farms and Respective Susceptibility to Antibiotics

Aquaculture is a growing sector, providing several products for human consumption, and it is therefore important to guarantee its quality and safety. This study aimed to contribute to the knowledge of bacterial composition of Crassostrea gigas, Mytilus spp. and Ruditapes decussatus, and the antibiotic resistances/resistance genes present in aquaculture environments. Two hundred and twenty-two bacterial strains were recovered from all bivalve mollusks samples belonging to the Aeromonadaceae, Bacillaceae, Comamonadaceae, Enterobacteriaceae, Enterococcaceae, Micrococcaceae, Moraxellaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Staphylococcaceae, Streptococcaceae, Vibrionaceae, and Yersiniaceae families. Decreased susceptibility to oxytetracycline prevails in all bivalve species, aquaculture farms and seasons. Decreased susceptibilities to amoxicillin, amoxicillin/clavulanic acid, cefotaxime, cefoxitin, ceftazidime, chloramphenicol, florfenicol, colistin, ciprofloxacin, flumequine, nalidixic acid and trimethoprim/sulfamethoxazole were also found. This study detected six qnrA genes among Shewanella algae, ten qnrB genes among Citrobacter spp. and Escherichia coli, three oqxAB genes from Raoultella ornithinolytica and bla_TEM-1 in eight E. coli strains harboring a qnrB19 gene. Our results suggest that the bacteria and antibiotic resistances/resistance genes present in bivalve mollusks depend on several factors, such as host species and respective life stage, bacterial family, farm’s location and season, and that is important to study each aquaculture farm individually to implement the most suitable measures to prevent outbreaks.