Whole-genome sequencing of staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species

Multi-metal-resistant Staphylococcus warneri strain TWSL_1: revealing heavy metal-resistant genomic features by whole-genome sequencing and analysis

This study explores the genomic basis of heavy metal resistance in Staphylococcus warneri strain TWSL_1, isolated from industrial textile effluent. The strain exhibited strong resistance to Cd²+, Pb²+ and Cu²+, with MICs of 50, 1,200 and 75 mg l-1, respectively. Whole-genome sequencing revealed a 2.66 Mb genome with 2,567 CDSs and a 99.81% average nucleotide identity to S. warneri WS479. Comparative genomic analysis at the genus level revealed that S. warneri strain TWSL_1 possesses a unique and expanded repertoire of heavy metal resistance genes, including the cadmium efflux system accessory protein and cadmium resistance protein, which are absent in pathogenic Staphylococcus sp. used for the comparison. Phylogenetic analysis confirmed its classification within S. warneri, with strong bootstrap support (100). Functional annotation highlighted metabolic versatility and stress response capabilities, supporting its adaptation to metal-rich environments. S. warneri TWSL_1 demonstrated high Pb²+ removal efficiency, reducing concentrations by over 70%. These findings highlight S. warneri TWSL_1 as a promising candidate for heavy metal bioremediation with potential applications in environmental detoxification and monitoring strategies.

MRSA Profiles Reveal Age- and Gender-Specificity in a Tertiary Care Hospital: High Burden in ICU Elderly and Emerging Community Patterns in Youth

Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating global health concern. Hypervirulent strains are on the rise, causing morbidities and mortalities worldwide. In tertiary care hospitals, critically ill patients, those undergoing invasive procedures, and pediatric and geriatric patients are at risk. It is not fully clear how strains adapt and specialize in humans and emerge despite the well-established commonality of the S. aureus genome from humans and animals. This study investigates the influence of age-, gender-, and source-specific profiles (clinical, intensive care unit (ICU vs. non-ICU)) on the evolution of hospital-associated (HA)-MRSA versus community-associated (CA)-MRSA lineages. A total of 253 non-duplicate S. aureus isolates were obtained from May 2023 to March 2025. The patients were stratified by age and gender in ICUs and non-ICUs. Standard microbiology methods and Clinical and Laboratory Standards Institute (CLSI) guidelines were used for identification and susceptibility testing, with cefoxitin and oxacillin disk diffusions and molecular diagnosis confirming MRSA. Mann-Whitney U and Chi-square tests assessed the demographic distributions, clinical specimen sources, and MRSA/methicillin-sensitive S. aureus (MSSA) prevalence. Of 253, 41.9% originated from ICUs (71% male; 29% female) and 58.1% from non-ICU wards (64% male; 36% female). In both settings, MRSA colonized the two extremes of age (10-29 and 70+) for males and females, with different mid-life peaks or declines by gender. However, the overall demographic distribution did not differ significantly between the ICU and non-ICU groups (p = 0.287). Respiratory specimens constituted 37% and had the highest MRSA rate (42%), followed by blood (24.5%) and wounds (10.3%). In contrast, MSSA dominated wounds (20.3%). Overall, 73.9% were resistant to cefoxitin and cefotaxime, whereas vancomycin, linezolid, daptomycin, and tigecycline remained highly effective. Younger non-ICU patients (10-29) had higher MSSA, whereas older ICU ones showed pronounced HA-MRSA profiles. By the virtue of methicillin resistance, all MRSA were classified as multidrug resistance. Thus, MRSA colonization of the two extremes of life mostly in ICU seniors and the dominance of invasive MSSA and CA-MRSA patterns in non-ICU youth imply early age- and gender-specific adaptations of the three lineages. MRSA colonizes both ICU and non-ICU populations at extremes of age and gender specifically. High β-lactam resistance underscores the importance of robust stewardship and age- and gender-specific targeting in screening. These findings also indicate host- and organ-specificity in the sequalae of MSSA, CA-MRSA, and HA-MRSA evolutionary dynamics, emphasizing the need for continued surveillance to mitigate MRSA transmission and optimize patient outcomes in tertiary care settings.

Genomic and phenotypic characterization of multidrug-resistant Staphylococcus haemolyticus isolated from burn patients in Chongqing, southwestern China

Staphylococcus hemolyticus is one of the frequently isolated nosocomial pathogens in immunocompromised patients; however, its genotypic and phenotypic characteristics in burn patients remain largely unknown. In this study, 146 S. haemolyticus strains were collected from the burn unit of a tertiary hospital in Chongqing, southwestern China. Whole genome sequencing was applied to determine the molecular characteristics of these S. haemolyticus isolates. Results showed that sequence type 1 (ST1; 26.7%, 39/146) was the most prevalent lineage, followed by clones ST42 (17.8%, 25/146), ST3 (15.8%, 23/146), ST25 (9.6%, 14/146), ST29 (4.8%, 7/146), and newly emerged ST152 (6.2%, 9/146). In terms of phenotypes, 90.4% (132/146) of the S. haemolyticus isolates were multidrug-resistant (MDR), and more than 90% strains exhibited resistance to penicillin, erythromycin, oxacillin, and levofloxacin. A total of 145 out of 146 S. haemolyticus isolates harbored at least 10 virulence factor genes. The tested strains with ST1, ST3, ST25, and ST42 presented similar hemolytic activities and biofilm formation capabilities. All detected ST152 isolates were MDR, corresponding to the number of their antimicrobial resistance genes being the largest among all tested STs. Moreover, ST152 isolates had increased hemolytic capacity and biofilm formation capability compared with their counterpart ST29 strains, the parent lineage of ST152 with a single locus variation. Overall, this study showed the genomic and phenotypic characteristics of 146 S. haemolyticus strains isolated in Chongqing and found the newly emerged ST152 MDR lineage with hypervirulence, which may call attention to the control of infections caused by MDR S. haemolyticus strains in hospitals.IMPORTANCEStaphylococcus haemolyticus is a common opportunistic pathogen with multidrug resistance in clinical infections. In this study, we analyzed the molecular epidemiological characteristics of 146 S. haemolyticus strains isolated from the burn patients of a tertiary hospital in Chongqing between 2017 and 2023. The results demonstrated that the phylogenetic evolution of S. haemolyticus strains was diverse and plastic. The majority of the isolates were multidrug-resistant (MDR). The virulence genes, resistance elements, and phenotypes, such as hemolysis and biofilm formation, were determined. A new lineage (ST152) that harbored the highest number of resistance genes was characterized to be 100% (9/9) MDR. The prevalence of ST152 S. haemolyticus strains suggests a new health threat in terms of control and treatment of coagulase-negative staphylococcal infections in Chongqing. This study provides information for clinical control of S. haemolyticus dissemination and infection in hospitals.

DeepES: deep learning-based enzyme screening to identify orphan enzyme genes

MOTIVATION

Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions.

RESULTS

Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria.

AVAILABILITY AND IMPLEMENTATION

DeepES is available at https://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).

Epidemiology of Staphylococcus haemolyticus nosocomial bacteraemia in neonatal intensive care units, France, 2019 to 2023: predominance of the ST29 (CC3) multidrug-resistant lineage

BackgroundStaphylococcus haemolyticus (SH) is an opportunistic pathogen associated with nosocomial infections, particularly bacteraemia in neonates. Epidemiological trends and genetic diversity of these infections worldwide are largely unknown.AimTo investigate an increase in SH vascular catheter-related bacteraemia in neonates and describe the molecular epidemiology in France between 2019 and 2023.MethodsWe analysed clinical and microbiological surveillance data from the French national surveillance network for central catheter-related (venous and umbilical) infections between 2019 and 2023. We also performed genomic and phylogenetic analyses of 496 strains isolated both inside (n = 383 from neonates, staff and environmental samples) and outside (n = 113 from adults) the neonatal intensive care unit (NICU) settings.ResultsThe proportion of SH among the 474 reported cases of nosocomial bacteraemia increased from about 20% to 30% over 5 years, mainly affecting very low birth weight preterm neonates (≤ 1,500 g). The ST29 sequence type (ST) not prevalent in previous studies was predominant, accounting for 74% of NICU strains. ST29 was characterised by phenotypic multidrug resistance to at least six classes of antibiotics (oxacillin, quinolones, gentamicin, cotrimoxazole, clindamycin and rifampicin), which distinguished it with good sensitivity and specificity from other prevalent multidrug-resistant STs identified (ST1 and ST25). ST29 strains more frequently harboured the drfG, vga-LC and mupA genes and a triple point mutation (D471E, I527M and S532N) in the rpoB gene.ConclusionsThe present study highlights the success of a highly resistant ST29 lineage in French NICUs mainly affecting very low birth weight premature neonates.

From Farm to Community: Dispersal of Potentially Pathogenic Staphylococcus and Mammaliicoccus Species and Antimicrobial Resistance Across Shared Environments

Staphylococcaceae are a diverse bacterial family with important implications for human and animal health. This study highlights the One Health relevance of their environmental dispersal, particularly, by identifying closely related or genetically identical strains circulating between farm and community environments. Environmental Staphylococcaceae strains were isolated from animal farms and interconnected areas within a university setting, both influenced by anthropogenic activities. Genetic diversity analysis via GTG5-PCR revealed that specific strains circulated across these environments, likely facilitated by human interaction, supporting the potential for cross-environmental bacterial transfer. The strains were further tested for antimicrobial resistance against a panel of antibiotics, biofilm formation, and the presence of resistance-associated genes. We identified a wide array of Staphylococcaceae species (n = 16), with over half being pathogenic to humans and animals, including S. aureus, S. epidermidis, S. haemolyticus, and S. saprophyticus. Notably, 55.5% of the strains exhibited multidrug resistance, and 15.9% harbored the methicillin resistance gene mecA, underscoring the challenges these infections might pose to treatment. Biofilm-forming capabilities further enhance the environmental persistence of these strains. These findings underscore the critical need for surveillance and targeted intervention strategies in a One Health framework to mitigate antimicrobial resistance across shared environments.

Codon usage analysis in selected virulence genes of Staphylococcal species

The Staphylococcus genus, composed of Gram-positive bacteria, includes several pathogenic species such as Staphylococcus aureus, S. epidermidis, S. haemolyticus, and S. saprophyticus, each implicated in a range of infections. This study investigates the codon usage patterns in key virulence genes, including Autolysin (alt), Elastin Binding protein (EbpS), Lipase, Thermonuclease, Intercellular Adhesion Protein (IcaR), and V8 Protease, across four Staphylococcus species. Using metrics such as the Effective Number of Codons (ENc), Relative Synonymous Codon Usage (RSCU), Codon Adaptation Index (CAI), alongside neutrality and parity plots, we explored the codon preferences and nucleotide composition biases. Our findings revealed a pronounced AT-rich codon preference, with AT-rich genomes likely aiding in energy-efficient translation and bacterial survival in host environments. These insights provide a deeper understanding of the evolutionary adaptations and translational efficiency mechanisms that contribute to the pathogenicity of Staphylococcus species. This knowledge could pave the way for novel therapeutic interventions targeting codon usage to disrupt virulence gene expression.

Coagulase-Negative Staphylococci phages panorama: Genomic diversity and in vitro studies for a therapeutic use

Coagulase-negative staphylococci (CoNS) are commensal bacteria of the human skin and mucosal membranes. The incidence of nosocomial infections caused by these species is on the rise, leading to a potential increase in antibiotic tolerance and resistance. Phages are emerging as a promising alternative to combat CoNS infections. Scientists are isolating phages infecting CoNS with a particular interest in S. epidermidis. This review compiles and analyses CoNS phages for several parameters including source, geographical location, host species, morphological diversity, and genomic diversity. Additionally, recent studies have highlighted the potential of these phages based on host range, in vitro evaluation of performance and stability, and interaction with biofilms. This comprehensive analysis enables a better understanding of the steps involved in using these phages for therapeutic purposes.

Emergence of multidrug-resistant Staphylococcus haemolyticus in neonatal intensive care unit in Southern France, a genomic study

An emergence of multidrug-resistant (MDR) Staphylococcus haemolyticus has been observed in the neonatal intensive care unit (NICU) of Nîmes University Hospital in southern France. A case-control analysis was conducted on 96 neonates, to identify risk factors associated with S. haemolyticus infection, focusing on clinical outcomes. Forty-eight MDR S. haemolyticus strains, isolated from neonates between October 2019 and July 2022, were investigated using routine in vitro procedures and whole-genome sequencing. Additionally, five S. haemolyticus isolates from adult patients were sequenced to identify clusters circulating within the hospital environment. The incidence of neonatal S. haemolyticus was significantly associated with low birth weight, lower gestational age, and central catheter use (p < 0.001). Sepsis was the most frequent clinical manifestation in this series (20/46, 43.5%) and was associated with five deaths. Based on whole-genome analysis, three S. haemolyticus genotypes were predicted: ST1 (6/53, 11%), ST25 (3/53, 5.7%), and ST29 (44/53, 83%), which included the subcluster II-A, predominantly emerging in the neonatal department. All strains were profiled in silico to be resistant to methicillin, erythromycin, aminoglycosides, and fluoroquinolones, consistent with in vitro antibiotic susceptibility tests. Moreover, in silico prediction of biofilm formation and virulence-encoding genes supported the association of ST29 with severe clinical outcomes, while the persistence in the NICU could be explained by the presence of antiseptic and heavy metal resistance-encoding genes. The clonality of S. haemolyticus ST29 subcluster II-A isolates confirms healthcare transmission causing severe infections. Based on these results, reinforced hygiene measures are necessary to eradicate the nosocomial transmission of MDR strains.

Detection and genetic characterization of multidrug-resistant staphylococci isolated from public areas in an international airport

The environmental realm has been acknowledged as a pivotal arena for the emergence and propagation of antimicrobial resistance. To further explore insight into antimicrobial resistance dynamics beyond clinical and veterinary settings, we embarked on an environmental surveillance initiative targeting the prevalence of antibiotic-resistant bacteria within the bustling confines of an international airport in Japan. Our findings illuminate a high prevalence of methicillin-resistant staphylococci (46.3%) on frequently contacted surfaces in the public domain. Notably, Staphylococcus haemolyticus and S. epidermidis emerged as the preeminent carriers of the mecA gene. Intriguingly, we encountered a virulent strain of livestock-associated MRSA harboring a PVL-positive ST1232 clone, CC398 lineage. Further scrutiny unveiled a repertoire of resistance mechanisms, the methicillin-resistant isolates exhibited two or more resistance genes conferring resistance against different types of antibiotics, including beta-lactams, macrolides, lincosamides, aminoglycosides, chloramphenicol, and fosfomycin. Revealing multidrug-resistant CoNS and a LA-MRSA across various surfaces in urban public areas unearths a looming public health hazard. Thus, implementation of molecular surveillance is imperative, augmenting our capacity for early detection and mitigation of the insidious spread and potential transfer of antibiotic resistance genes and virulence factors amidst urban settings, notably within pivotal nodes such as airports.

Current types of staphylococcal cassette chromosome mec (SCCmec) in clinically relevant coagulase-negative staphylococcal (CoNS) species

Coagulase-negative staphylococci (CoNS) colonize human skin and mucosal membranes, which is why they are considered harmless commensal bacteria. Two species, Staphylococcus epidermidis and Staphylococcus haemolyticus belong to the group of CoNS species and are most frequently isolated from nosocomial infections, including device-associated healthcare-associated infections (DA-HAIs) and local or systemic body-related infections (FBRIs). Methicillin resistance, initially described in Staphylococcus aureus, has also been reported in CoNS species. It is mediated by the mecA gene within the staphylococcal cassette chromosome (SCCmec). SCCmec typing, primarily using PCR-based methods, has been employed as a molecular epidemiological tool. However, the introduction of whole genome sequencing (WGS) and next-generation sequencing (NGS) has enabled the identification and verification of new SCCmec types. This review describes the current distribution of SCCmec types, subtypes, and variants among CoNS species, including S. epidermidis, S. haemolyticus, and S. capitis. The literature review focuses on recent research articles from the past decade that discuss new combinations of SCCmec in coagulase-negative Staphylococcus. The high genetic diversity and gaps in CoNS SCCmec annotation rules underscore the need for an efficient typing system. Typing SCCmec cassettes in CoNS strains is crucial to continuously updating databases and developing a unified classification system.

Whole genome sequence analysis of multi-drug resistant and biofilm-forming Staphylococcus haemolyticus isolated from bovine milk

BACKGROUND

Milk is an excellent growth medium for microorganisms due to its nutritive composition. Microorganisms have been implicated in bovine mastitis (BM) in dairy cows as well as causing infections in animals and humans. Despite extensive endeavours to manage BM, this condition continues to persist as the most prevalent and economically burdensome problem affecting dairy cattle on a global scale. Non-aureus staphylococci (NAS) species such as Staphylococcus haemolyticus, S. epidermidis, and S. xylosus are currently the predominant microbiological agents identified as the main cause of subclinical udder infections and are also considered opportunistic pathogens in cases of clinical mastitis in dairy cows. Therefore, it is crucial to elucidate the genetic profile of these species. The primary objective of this study was to characterise three phenotypically determined multidrug-resistant NAS environmental strains (NWU MKU1, NWU MKU2, and NWU MKS3) obtained from dairy cows milk via whole-genome sequencing.

RESULTS

The results confirmed that the three isolates were S. haemolyticus with genome sizes of 2.44, 2.56, and 2.56 Mb and a G + C content of 32.8%. The genomes contained an array of antibiotic resistance genes that may potentially confer resistance to a range of antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, cephalosporins, tetracyclines, peptides, and phenicol. Furthermore, all the genomes carried virulence genes, which are responsible for several functions, such as adhesion, enzyme and toxin production. The genomes of these organisms contained signatures encoding mobile genetic elements such as prophages and insertion sequences.

CONCLUSION

These findings indicate there is a need for diligent monitoring with improved management practices and quality control strategies on farms to safeguard milk production systems and human health.

Characterization of staphylococcal cassette chromosome mec in Staphylococcus haemolyticus ST3 and ST42 isolates from bovine mastitis milk: identification of novel variant in class C1 mec complex

BACKGROUND

Methicillin-resistant Staphylococcus haemolyticus (MRSH) is an important pathogenic agent of bovine mastitis. Among the prominent clone lineages in dairy cows are MRSH sequence types ST3 and ST42. Little information is available on the complete characterization of SCCmec elements in MRSH.

OBJECTIVE

In this study, two clinical isolates of MRSH ST3 and ST42 from bovine mastitis milk were selected, and their nontypable SCCmec structures were compared.

METHODS

Two MRSH strains, MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1, were identified from bovine mastitis milk in Thailand in 2022. Minimum inhibitory concentration was used to screen for antimicrobial resistance susceptibility. Oxford Nanopore Technologies and Illumina sequencing were performed in combination to complete the genome. Their gene organization and structure of SCCmec types were analysed and compared with the whole sequences of other strains in the same sequence types.

RESULTS

Both MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1 possessed the class C1 mec complex but lacked the ccr gene complex. Notably, MRSH-ST42 strain M81.1 contained a novel variant of C1 mec complex, which consisted of IS431-mecA-ISSha1-paaZ-upgQ-IS431, with IS431 organized in the same orientation. Apart from class C1 mec and the heavy metal-resistant cluster, the gene composition and order of the SCCmec element varied. In ST3, variations in the SCCmec type, gene content and organization were observed.

CONCLUSIONS

The distinct evolution of the MRSH lineage was indicated by the various SCCmec elements. The insertion of ISSha1 resulted in a unique variant of class C1 mec complex that demonstrated the important role of the insertion sequence in SCCmec diversification.

CSER: a gene regulatory network construction method based on causal strength and ensemble regression

Introduction

Gene regulatory networks (GRNs) reveal the intricate interactions between and among genes, and understanding these interactions is essential for revealing the molecular mechanisms of cancer. However, existing algorithms for constructing GRNs may confuse regulatory relationships and complicate the determination of network directionality.

Methods

We propose a new method to construct GRNs based on causal strength and ensemble regression (CSER) to overcome these issues. CSER uses conditional mutual inclusive information to quantify the causal associations between genes, eliminating indirect regulation and marginal genes. It considers linear and nonlinear features and uses ensemble regression to infer the direction and interaction (activation or regression) from regulatory to target genes.

Results

Compared to traditional algorithms, CSER can construct directed networks and infer the type of regulation, thus demonstrating higher accuracy on simulated datasets. Here, using real gene expression data, we applied CSER to construct a colorectal cancer GRN and successfully identified several key regulatory genes closely related to colorectal cancer (CRC), including ADAMDEC1, CLDN8, and GNA11.

Discussion

Importantly, by integrating immune cell and microbial data, we revealed the complex interactions between the CRC gene regulatory network and the tumor microenvironment, providing additional new biomarkers and therapeutic targets for the early diagnosis and prognosis of CRC.

Prevalence and molecular characterization of multidrug-resistant coagulase negative staphylococci from urban wastewater in Delhi-NCR, India

Antimicrobial resistance (AMR) is global health concern escalating rapidly in both clinical settings and environment. The effluent from pharmaceuticals and hospitals may contain diverse antibiotics, exerting selective pressure to develop AMR. To study the aquatic prevalence of drug-resistant staphylococci, sampling was done from river Yamuna (3 sites) and wastewater (7 sites) near pharmaceutical industries in Delhi-NCR, India. 59.25% (224/378) were considered presumptive staphylococci while, methicillin resistance was noted in 25% (56/224) isolates. Further, 23 methicillin-resistant coagulase negative staphylococci (MR-CoNS) of 8 different species were identified via 16S rRNA gene sequencing. Multidrug resistance (MDR) was noted in 60.87% (14/23) isolates. PCR based detection of antibiotic resistance genes revealed the number of isolates containing mecA (7/23), blaZ (6/23), msrA (10/23), aac(6')aph (2") (2/23), aph(3')-IIIa (2/23), ant(4')-Ia (1/23), dfrG (4/23), dfrA(drfS1) (3/23), tetK (1/23) and tetM (1/23). The current research highlights the concerning prevalence of MDR-CoNS in aquatic environment in Delhi.

Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants

Background

Previous studies of infants born to HIV-positive mothers have linked HIV exposure to poor outcomes from gastrointestinal and respiratory illnesses, and to overall increased mortality rates. The mechanism behind this is unknown, but it is possible that differences in the nasopharyngeal (NP) microbiome between infants who are HIV-unexposed or HIV-exposed could play a role in perpetuating some outcomes.

Methods

We conducted a longitudinal analysis of 170 NP swabs of healthy infants who are HIV-exposed (n=10) infants and their HIV(+) mothers, and infants who are HIV-unexposed, uninfected (HUU; n=10) .and their HIV(-) mothers. These swabs were identified from a sample library collected in Lusaka, Zambia between 2015 and 2016. Using 16S rRNA gene sequencing, we characterized the maturation of the microbiome over the first 14 weeks of life to determine what quantifiable differences exist between HIV-exposed and HUU infants, and what patterns are reflected in the mothers' NP microbiomes.

Results

In both HIV-exposed and HUU infants, Staphylococcus and Corynebacterium began as primary colonizers of the NP microbiome but were in time replaced by Dolosigranulum, Streptococcus, Moraxella and Haemophilus. When evaluating the interaction between HIV exposure status and time of sampling among infants, the microbe Staphylococcus haemolyticus showed a distinctive high association with HIV exposure at birth. When comparing infants to their mothers with paired analyses, HIV-exposed infants' NP microbiome composition was only slightly different from their HIV(+) mothers at birth or 14 weeks, including in their carriage of S. pneumoniae, H. influenzae, and S. haemolyticus.

Conclusions

Our analyses indicate that the HIV-exposed infants in our study exhibit subtle differences in the NP microbial composition throughout the sampling interval. Given our results and the sampling limitations of our study, we believe that further research must be conducted in order to confidently understand the relationship between HIV exposure and infants' NP microbiomes.

Vendors' handling practices of edible long-horned grasshoppers (Ruspolia differens) products and implications on microbial safety

Edible grasshopper, Ruspolia ruspolia, has nutritional and cherished cultural and economic importance to people from diverse cultures, particularly in over 20 African countries. It is consumed at home or commercially traded as sautéed, deep-fried, or boiled products. However, there is limited information on the hygiene practices of the vendors and the implications on the microbial safety of the final product. This research aimed at assessing the food safety knowledge, handling practices and shelf life of edible long-horned grasshopper products among vendors and the microbial safety of ready-to-eat products sold in 12 different markets in Uganda. Samples of raw, deep-fried and boiled grasshoppers were randomly collected from 74 vendors (62% street and 38% market vendors) and subjected to microbial analysis. Over 85% of the vendors surveyed had no public health food handler's certificate and >95% had limited post-harvest handling knowledge. Total aerobic bacteria (7.30-10.49 Log10 cfu/g), Enterobacteriaceae (5.53-8.56 Log10 cfu/g), yeasts and molds (4.96-6.01 Log10 cfu/g) total counts were significantly high and above the acceptable Codex Alimentarius Commission and Food Safety Authority of Ireland (FSAI) limits for ready-to-eat food products. Eight key pathogenic bacteria responsible for foodborne diseases were detected and these isolates were characterized as Bacillus cereus, Hafnia alvei, Serratia marcescens, Staphylococcus aureus, S. xylosus, S. scuiri, S. haemolyticus, and Pseudomonas aeruginosa. Findings from this study highlight the urgent need to create local and national food safety policies for the edible grasshopper "nsenene" subsector to regulate and guide street and market vending along the value chain, to prevent the transmission of foodborne diseases to consumers.

Staphylococcus haemolyticus: An updated review on nosocomial infections, antimicrobial resistance, virulence, genetic traits, and strategies for combating this emerging opportunistic pathogen

Staphylococcus haemolyticus, a key species of the Staphylococcus genus, holds significant importance in healthcare-associated infections, due to its notable resistance to antimicrobials, like methicillin, and proficient biofilms-forming capabilities. This coagulase-negative bacterium poses a substantial challenge in the battle against nosocomial infections. Recent research has shed light on Staph. haemolyticus genomic plasticity, unveiling genetic elements responsible for antibiotic resistance and their widespread dissemination within the genus. This review presents an updated and comprehensive overview of the clinical significance and prevalence of Staph. haemolyticus, underscores its zoonotic potential and relevance in the one health framework, explores crucial virulence factors, and examines genetics features contributing to its success in causing emergent and challenging infections. Additionally, we scrutinize ongoing studies aimed at controlling spread and alternative approaches for combating it.

AM, Doster E, Fernandes L, Calles VF, Bauman C, Godden S, Heins B, Pinedo P, Machado VS, Caixeta LS, Noyes NR. Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives

The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).

IMPORTANCE

Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.

Serine-rich repeat proteins: well-known yet little-understood bacterial adhesins

Serine-rich-repeat proteins (SRRPs) are large mucin-like glycoprotein adhesins expressed by a plethora of pathogenic and symbiotic Gram-positive bacteria. SRRPs play major functional roles in bacterial-host interactions, like adhesion, aggregation, biofilm formation, virulence, and pathogenesis. Through their functional roles, SRRPs aid in the development of host microbiomes but also diseases like infective endocarditis, otitis media, meningitis, and pneumonia. SRRPs comprise shared domains across different species, including two or more heavily O-glycosylated long stretches of serine-rich repeat regions. With loci that can be as large as ~40 kb and can encode up to 10 distinct glycosyltransferases that specifically facilitate SRRP glycosylation, the SRRP loci makes up a significant portion of the bacterial genome. The significance of SRRPs and their glycans in host-microbe communications is becoming increasingly evident. Studies are beginning to reveal the glycosylation pathways and mature O-glycans presented by SRRPs. Here we review the glycosylation machinery of SRRPs across species and discuss the functional roles and clinical manifestations of SRRP glycosylation.

Staphylococcus borealis - A newly identified pathogen of bovine mammary glands

Twelve Staphylococcus borealis strains, isolated in Canada and Poland from milk of cows with intramammary infections, were characterized phenotypically (biochemical reactions on ID 32 STAPH and Biolog Phenotype MicroArrays™ PM1 and PM2A, ability of biofilm production) and genotypically (random amplified polymorphic DNA). In addition, a genomic comparison was done with S. borealis strains of human and porcine origin using the multilocus sequence typing (MLST) technique. The bovine isolates showed a high degree of phenotypic and genotypic diversity, however, they could be differentiated from human strains by the negative test for urease (found in all but one bovine isolate examined with ID 32 STAPH) and positive reaction for D-galactose (on Biolog phenotype microarray PM1) and D-lactose (on both commercial systems). The MLST method, utilizing six concatenated genes of the total length of ∼2930 bp, revealed that bovine strains (irrespective of the country of origin) show a distinctly greater degree of mutual relationship than to the strains of human and porcine origin, suggesting that S. borealis has evolved independently in these hosts. In conclusion, bovine-specific S. borealis can be involved in intramammary infections in cattle.

Antibacterial activity and antibacterial mechanism of flavaspidic acid BB against Staphylococcus haemelyticus

BACKGROUND

Staphylococcus haemolyticus (S. haemolyticus) is the main etiological factor in skin and soft tissue infections (SSTI). S. haemolyticus infections are an important concern worldwide, especially with the associated biofilms and drug resistance. Herein, we investigated the inhibitory effect of Flavaspidic acid BB obtained from plant extractions on clinical S. haemolyticus strains and their biofilms. Moreover, we predicted its ability to bind to the protein-binding site by molecular simulation. Since the combination of Hsp70 and RNase P synthase after molecular simulation with flavaspidic acid BB is relatively stable, enzyme-linked immunosorbent assay (ELISA) was used to investigate Hsp70 and RNase P synthase to verify the potential antimicrobial targets of flavaspidic acid BB.

RESULTS

The minimum inhibitory concentrations (MIC) of flavaspidic acid BB on 16 clinical strains of S. haemolyticus was 5 ~ 480 µg/mL, and BB had a slightly higher inhibitory effect on the biofilm than MUP. The inhibitory effect of flavaspidic acid BB on biofilm formation was better with an increase in the concentration of BB. Molecular simulation verified its ability to bind to the protein-binding site. The combination of ELISA kits showed that flavaspidic acid BB promoted the activity of Hsp70 and inhibited the activity of RNase P, revealing that flavaspidic acid BB could effectively inhibit the utilization and re-synthesis of protein and tRNA synthesis, thus inhibiting bacterial growth and biofilm formation to a certain extent.

CONCLUSIONS

This study could potentially provide a new prospect for the development of flavaspidic acid BB as an antibacterial agent for resistant strains.

Molecular basis and evolutionary cost of a novel macrolides/lincosamides resistance phenotype in Staphylococcus haemolyticus

Staphylococcus haemolyticus (S. haemolyticus) is a coagulase-negative Staphylococcus that has become one of the primary causes of nosocomial infection. After a long period of antibiotic use, S. haemolyticus has developed multiple resistance phenotypes for macrolides and lincosamides. Herein, we evaluated four S. haemolyticus clinical isolates, of which three had antibiotic resistance patterns reported previously. The fourth isolate was resistant to both erythromycin and clindamycin in the absence of erythromycin induction. This novel phenotype, known as constitutive macrolides-lincosamides-streptogramins resistance, has been reported in other bacteria but has not been previously reported in S. haemolyticus. Investigation of the isolate demonstrated a deletion in the methyltransferase gene ermC, upstream leader peptide. This deletion resulted in constitutive MLS resistance based on whole-genome sequencing and experimental verification. Continuous expression of ermC was shown to inhibit the growth of S. haemolyticus, which turned out to be the fitness cost with no MLS pressure. In summary, this study is the first to report constitutive MLS resistance in S. haemolyticus, which provides a better understanding of MLS resistance in clinical medicine. IMPORTANCE This study identified a novel phenotype of macrolides/lincosamides resistance in Staphylococcus haemolyticus which improved a better guidance for clinical treatment. It also clarified the mechanistic basis for this form of antibiotic resistance that supplemented the drug resistance mechanism of Staphylococcus. In addition, this study elaborated on a possibility that continuous expression of some resistance genes was shown to inhibit the growth of bacteria themselves, which turned out to be the fitness cost in the absence of antibiotic pressure.

Staphylococcus brunensis sp. nov. isolated from human clinical specimens with a staphylococcal cassette chromosome-related genomic island outside of the rlmH gene bearing the ccrDE recombinase gene complex

Novel species of coagulase-negative staphylococci, which could serve as reservoirs of virulence and antimicrobial resistance factors for opportunistic pathogens from the genus Staphylococcus, are recognized in human and animal specimens due to advances in diagnostic techniques. Here, we used whole-genome sequencing, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize five coagulase-negative strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds, and bile. Based on the results of polyphasic taxonomy, we propose the species Staphylococcus brunensis sp. nov. (type strain NRL/St 16/872T = CCM 9024T = LMG 31872T = DSM 111349T). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCIccrDE integrated into the ribosomal protein L7 serine acetyltransferase gene rimL. SbCIccrDE has a cassette chromosome recombinase (ccr) gene complex with a typical structure found in SCCs. Based on nucleotide and amino acid identity to other known ccr genes and the distinct integration site that differs from the canonical methyltransferase gene rlmH exploited by SCCs, we classified the ccr genes as novel variants, ccrDE. The comparative genomic analysis of SbCIccrDE with related islands shows that they can accumulate virulence and antimicrobial resistance factors creating novel resistance elements, which reflects the evolution of SCC. The spread of these resistance islands into established pathogens such as Staphylococcus aureus would pose a great threat to the healthcare system. IMPORTANCE The coagulase-negative staphylococci are important opportunistic human pathogens, which cause bloodstream and foreign body infections, mainly in immunocompromised patients. The mobile elements, primarily the staphylococcal cassette chromosome mec, which confers resistance to methicillin, are the key to the successful dissemination of staphylococci into healthcare and community settings. Here, we present a novel species of the Staphylococcus genus isolated from human clinical material. The detailed analysis of its genome revealed a previously undescribed genomic island, which is closely related to the staphylococcal cassette chromosome and has the potential to accumulate and spread virulence and resistance determinants. The island harbors a set of conserved genes required for its mobilization, which we recognized as novel cassette chromosome recombinase genes ccrDE. Similar islands were revealed not only in the genomes of coagulase-negative staphylococci but also in S. aureus. The comparative genomic study contributes substantially to the understanding of the evolution and pathogenesis of staphylococci.

Lethal and mutagenic effects of different LET radiations on Bacillus subtilis spores

New, useful microorganism resources have been generated by ionizing radiation breeding technology. However, the mutagenic effects of ionizing radiation on microorganisms have not been systematically clarified. For a deeper understanding and characterization of ionizing radiation-induced mutations in microorganisms, we investigated the lethal effects of seven different linear energy transfer (LET) radiations based on the survival fraction (SF) and whole-genome sequencing analysis of the mutagenic effects of a dose resulting in an SF of around 1% in Bacillus subtilis spores. Consequently, the lower LET radiations (gamma [surface LET: 0.2 keV/µm] and 4He2+ [24 keV/µm]) showed low lethality and high mutation frequency (MF), resulting in the major induction of single-base substitutions. Whereas higher LET radiations (12C5+ [156 keV/µm] and 12C6+ [179 keV/µm]) showed high lethality and low MF, resulting in the preferential induction of deletion mutations. In addition, 12C6+ (111) ion beams likely possess characteristics of both low- and high-LET radiations simultaneously. A decrease in the relative biological effectiveness and an evaluation of the inactivation cross section indicated that 20Ne8+ (468 keV/µm) and 40Ar13+ (2214 keV/µm) ion beams had overkill effects. In conclusion, in the mutation breeding of microorganisms, it should be possible to regulate the proportions, types, and frequencies of induced mutations by selecting an ionizing radiation of an appropriate LET in accordance with the intended purpose.

Phenotypic and Genotypic Characterization of Methicillin Resistance in Staphylococci Isolated from an Egyptian University Hospital

Methicillin-resistant in Staphylococci is a serious public health issue. It is mostly encoded by the mecA gene. The mecC gene is a new mecA analog responsible for resistance to methicillin in some Staphylococcal clinical isolates. This mecC gene is still underestimated in Egypt. The aim of the current study was to detect mecA and mecC genes in clinical Staphylococci isolates from a tertiary care university hospital in Egypt compared to the different phenotypic methods. A total of 118 Staphylococcus aureus (S. aureus) and 43 coagulase-negative Staphylococci (CoNS) were identified from various hospital-acquired infections. Methicillin resistance was identified genotypically using the PCR technique and phenotypically using the cefoxitin disc diffusion test, oxacillin broth microdilution and the VITEK2 system in all Staphylococcal isolates. The mecA gene was detected in 82.2% of S. aureus and 95.3% of CoNS isolates, while all of the isolates tested negative for the mecC gene. Interestingly, 30.2% of CoNS isolates showed the unique character of inducible oxacillin resistance, being mecA-positive but oxacillin-susceptible (OS-CoNS). The dual use of genotypic and phenotypic methods is highly recommended to avoid missing any genetically divergent strains.

Spontaneous Genomic Variation as a Survival Strategy of Nosocomial Staphylococcus haemolyticus

Staphylococcus haemolyticus is one of the most important nosocomial human pathogens frequently isolated in bloodstream and medical device-related infections. However, its mechanisms of evolution and adaptation are still poorly explored. To characterize the strategies of genetic and phenotypic diversity in S. haemolyticus, we analyzed an invasive strain for genetic and phenotypic stability after serial passage in vitro in the absence and presence of beta-lactam antibiotics. We performed pulsed-field gel electrophoresis (PFGE) of the culture and analyzed five colonies at seven time points during stability assays for beta-lactam susceptibility, hemolysis, mannitol fermentation, and biofilm production. We compared their whole genomes and performed phylogenetic analysis based on core single-nucleotide polymorphisms (SNPs). We observed a high instability in the PFGE profiles at the different time points in the absence of antibiotic. Analysis of WGS data for individual colonies showed the occurrence of six large-scale genomic deletions within the oriC environ, smaller deletions in non-oriC environ regions, and nonsynonymous mutations in clinically relevant genes. The regions of deletion and point mutations included genes encoding amino acid and metal transporters, resistance to environmental stress and beta-lactams, virulence, mannitol fermentation, metabolic processes, and insertion sequence (IS) elements. Parallel variation was detected in clinically significant phenotypic traits such as mannitol fermentation, hemolysis, and biofilm formation. In the presence of oxacillin, PFGE profiles were overall stable over time and mainly corresponded to a single genomic variant. Our results suggest that S. haemolyticus populations are composed of subpopulations of genetic and phenotypic variants. The maintenance of subpopulations in different physiological states may be a strategy to adapt rapidly to stress situations imposed by the host, particularly in the hospital environment. IMPORTANCE The introduction of medical devices and antibiotics into clinical practice have substantially improved patient quality of life and contributed to extended life expectancy. One of its most cumbersome consequences was the emergence of medical device-associated infections caused by multidrug-resistant and opportunistic bacteria such as Staphylococcus haemolyticus. However, the reason for this bacterium's success is still elusive. We found that in the absence of environmental stresses, S. haemolyticus can spontaneously produce subpopulations of genomic and phenotypic variants with deletions/mutations in clinically relevant genes. However, when exposed to selective pressures, such as the presence of antibiotics, a single genomic variant will be recruited and become dominant. We suggest that the maintenance of these cell subpopulations in different physiological states is an extremely effective strategy to adapt to stresses imposed by the host or the infection environment and might contribute for S. haemolyticus survival and persistence in the hospital.

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.

Molecular Epidemiology of Neonatal-Associated Staphylococcus haemolyticus Reveals Endemic Outbreak

Staphylococcus haemolyticus is a major cause of late-onset sepsis in neonates, and endemic clones are often multidrug-resistant. The bacteria can also act as a genetic reservoir for more pathogenic bacteria. Molecular epidemiology is important in understanding bacterial pathogenicity and preventing infection. To describe the molecular epidemiology of S. haemolyticus isolated from neonatal blood cultures at a Swedish neonatal intensive care unit (NICU) over 4 decades, including antibiotic resistance genes (ARGs), virulence factors, and comparison to international isolates. Isolates were whole-genome sequenced, and single nucleotide polymorphisms in the core genome were used to map the relatedness. The occurrence of previously described ARGs and virulence genes were investigated. Disc diffusion and gradient tests were used to determine phenotypic resistance. The results revealed a clonal outbreak of S. haemolyticus at this NICU during the 1990s. Multidrug resistance was present in 28 (82%) of all isolates and concomitant resistance to aminoglycoside and methicillin occurred in 27 (79%). No isolates were vancomycin resistant. Genes encoding ARGs and virulence factors occurred frequently. The isolates in the outbreak were more homogenous in their genotypic and phenotypic patterns. Genotypic and phenotypic resistance combinations were consistent. Pathogenic traits previously described in S. haemolyticus occurred frequently in the present isolates, perhaps due to the hospital selection pressure resulting in epidemiological success. The clonal outbreak revealed by this study emphasizes the importance of adhering to hygiene procedures in order to prevent future endemic outbreaks. IMPORTANCE This study investigated the relatedness of Staphylococcus haemolyticus isolated from neonatal blood and revealed a clonal outbreak in the 1990s at a Swedish neonatal intensive care unit. The outbreak clone has earlier been isolated in Japan and Norway. Virulence and antibiotic resistance genes previously associated with clinical S. haemolyticus were frequently occuring in the present study as well. The majority of the isolates were multidrug-resistant. These traits should be considered important for S. haemolyticus epidemiological success and are probably caused by the hospital selection pressure. Thus, this study emphasizes the importance of restrictive antibiotic use and following the hygiene procedures, to prevent further antibiotic resistance spread and future endemic outbreaks.

Internal and external microbiota of home-caught Anopheles coluzzii (Diptera: Culicidae) from Côte d'Ivoire, Africa: Mosquitoes are filthy

Over the past 10 years, studies using high-throughput 16S rRNA gene sequencing have shown that mosquitoes harbor diverse bacterial communities in their digestive system. However, no previous research has examined the total bacteria community inside versus outside of mosquitoes and whether bacteria found on the outside could represent a potential health threat through mechanical transfer. We examined the bacterial community of the external surface and internal body of female Anopheles coluzzii adults collected from homes in Côte d'Ivoire, Africa, by Illumina sequencing of the V3 to V4 region of 16S rRNA gene. Anopheles coluzzii is in the Anopheles gambiae sensu lato (s.l.) species complex and important in the transmission of malaria. The total 16S rRNA reads were assigned to 34 phyla, 73 orders, 325 families, and 700 genera. At the genus level, the most abundant genera inside and outside combined were Bacillus, Staphylococcus, Enterobacter, Corynebacterium, Kocuria, Providencia, and Sphingomonas. Mosquitoes had a greater diversity of bacterial taxa internally compared to the outside. The internal bacterial communities were similar between homes, while the external body samples were significantly different between homes. The bacteria on the external body were associated with plants, human and animal skin, and human and animal infections. Internally, Rickettsia bellii and Rickettsia typhi were found, potentially of importance, since this genus is associated with human diseases. Based on these findings, further research is warranted to assess the potential mechanical transmission of bacteria by mosquitoes moving into homes and the importance of the internal mosquito microbiota in human health.

Molecular Characterisation of Antibiotic Resistance in Staphylococcus haemolyticus Isolates from Chennai, South India

Staphylococcus haemolyticus is a highly resistant opportunistic pathogen having close genomic relatedness with other virulent species of staphylococci. However, compared to Staphylococcus aureus and Staphylococcus epidermidis, little is known about the resistance genes of S. haemolyticus. The purpose of this study was to characterise antibiotic resistance genes in S. haemolyticus isolates. Standard microbiological techniques were used to identify and confirm 104 S. haemolyticus isolates included in the study. Antibiotic susceptibility testing and D-test were performed, followed by PCR amplification of various resistance determinants (mecA, ermA, ermC, msrA, aac(6′)-Ie-aph(2″), ant(4′)-Ia,aph(3′)-IIIa, tetK, tetM, dfrA, fusB, fusC, fusD and mupA). Methicillin resistance was observed in 93.3% of study isolates. The maximum number of isolates showed resistance to erythromycin (n=79, 76%), followed by ciprofloxacin (n=66, 63.5%) and cotrimoxazole (n=58, 55.8%). In the D-test, 8 isolates showed inducible (iMLSB) and 11 showed constitutive (cMLSB) resistance. Among the resistance determinants, mecA gene (93.3%) was the most prevalent, followed by dfrA (50.5%). Furthermore, aac(6’)-Ie-aph(2’’) and aph(3’)-IIIa combination was observed in 26.9% of isolates, and aac(6’)-Ie-aph(2’’) alone was present in 3.8% of isolates. Among the study isolates, 17.3% exhibited tetK gene, whereas only 1% exhibited tetM; a combination of tetK and tetM was observed in one isolate. The fusB and fusC were present in 11.5% of isolates, and 12.5% of the isolates were positive for mupA. In conclusion, the present study underlines the concern of increasing antibiotic resistance among S. haemolyticus isolates. Avoiding misuse/overuse of antibiotics along with continuous surveillance programs can reduce the spread of antibiotic resistance.

Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs

Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis are common coagulase-negative staphylococcus opportunistic pathogens. In Thailand, the clinical strains S. haemolyticus 1864 and 48 and S. hominis subsp. hominis 384 and 371 have been recovered from sick dogs. These strains were methicillin resistant with the nontypeable staphylococcal cassette chromosome mec (NT-SCCmec). The SCCmec element distribution in the clinical isolates from dogs was analyzed using whole-genome sequencing, which revealed the presence of different SCCmec composite islands (CIs) and gene structure. The SCCmec-CIs of ψSCCmec1864 (13 kb) and ψSCC1864 (11 kb) with a class C1 mec complex but no ccr gene were discovered in S. haemolyticus 1864. The CIs of ψSCCmec48 with a C1 mec complex (28 kb), SCC48 with ccrA4B4 (23 kb), and ψSCC48 (2.6 kb) were discovered in S. haemolyticus 48. In SCC48, insertion sequence IS256 contained an aminoglycoside-resistant gene [aph(2″)-Ia]. Two copies of IS431 containing the tetracycline-resistant gene tet(K) were found downstream of ψSCC48. In S. hominis subsp. hominis, the SCCmec-CI in strain 384 had two separate sections: ψSCCmec384 (20 kb) and SCCars (23 kb). ψSCCmec384 lacked the ccr gene complex but carried the class A mec complex. Trimethoprim-resistant dihydrofolate reductase (dfrC) was discovered on ψSCCmec384 between two copies of IS257. In strain 371, SCCmec VIII (4A) (37 kb) lacking a direct repeat at the chromosomal end was identified. This study found SCCmec elements in clinical isolates from dogs that were structurally complex and varied in their genetic content, with novel organization. IMPORTANCE In Thailand, the staphylococcal cassette chromosome mec (SCCmec) element, which causes methicillin resistance through acquisition of the mec gene, has been studied in clinical coagulase-negative Staphylococcus isolates from various companion animals, and Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis were found to have the most nontypeable (NT)-SCCmec elements. These species are more prone to causing illness and more resistant to a variety of antimicrobials than other coagulase-negative staphylococci. However, full characterization of NT-SCCmec in clinical S. haemolyticus and S. hominis subsp. hominis isolates from such animals has been limited. Our findings support the use of full nucleotide sequencing rather than PCR designed for Staphylococcus aureus in further research of novel SCCmec elements. Moreover, several antimicrobial resistance and heavy metal resistance genes were identified on the SCCmec elements; these are important as they could limit the therapeutic options available in veterinary medicine.

The Emergence of a Multidrug-Resistant and Pathogenic ST42 Lineage of Staphylococcus haemolyticus from a Hospital in China

Staphylococcus haemolyticus is an opportunistic pathogen associated with hospital-acquired infections. However, the genetic diversity of S. haemolyticus among the patients and the hospital environment is largely unknown. Here, we isolated 311 S. haemolyticus strains from different sampling sites of patients and hospital environment. Genomic analysis showed that ST42 is an emerging clone widely disseminated in the hospital. S. haemolyticus ST42 strains exhibited decreased susceptibilities for multiple antibiotics compared with other STs and carried significantly more antibiotic resistance genes (ARGs). Furthermore, ST42 strains harbored more virulence genes per isolate than in other STs, and the capsular biosynthesis genes capDEFG were more prevalent in ST42 strains. Using the Galleria mellonella infection model, we demonstrated that ST42 strains are highly virulent compared with non-ST42 strains. Taken together, our data identified an emerging ST42 clone of S. haemolyticus with aggregated ARGs and virulence determinants in the hospital, representing a significant health threat in terms of both disease and treatment. IMPORTANCES. haemolyticus is an emerging opportunistic pathogen with a high burden of antimicrobial resistance. We performed molecular epidemiological analysis of S. haemolyticus that was isolated from a hospital, and found that the phylogenetic lineages are diverse accompanied by a dominant epidemic clonal lineage ST42. We demonstrated that S. haemolyticus ST42 strains have been disseminated among patients and the hospital environment. The data provide mechanistic insight and indicate that S. haemolyticus ST42 strains are multidrug-resistance and virulent clones via accumulating more ARGs and virulence genes.

Clinical Infections, Antibiotic Resistance, and Pathogenesis of Staphylococcus haemolyticus

Staphylococcus haemolyticus (S. haemolyticus) constitutes the main part of the human skin microbiota. It is widespread in hospitals and among medical staff, resulting in being an emerging microbe causing nosocomial infections. S. haemolyticus, especially strains that cause nosocomial infections, are more resistant to antibiotics than other coagulase-negative Staphylococci. There is clear evidence that the resistance genes can be acquired by other Staphylococcus species through S. haemolyticus. Severe infections are recorded with S. haemolyticus such as meningitis, endocarditis, prosthetic joint infections, bacteremia, septicemia, peritonitis, and otitis, especially in immunocompromised patients. In addition, S. haemolyticus species were detected in dogs, breed kennels, and food animals. The main feature of pathogenic S. haemolyticus isolates is the formation of a biofilm which is involved in catheter-associated infections and other nosocomial infections. Besides the biofilm formation, S. haemolyticus secretes other factors for bacterial adherence and invasion such as enterotoxins, hemolysins, and fibronectin-binding proteins. In this review, we give updates on the clinical infections associated with S. haemolyticus, highlighting the antibiotic resistance patterns of these isolates, and the virulence factors associated with the disease development.

Molecular Epidemiology and Comparative Genome Analysis of Clinically-isolated MRSA Strains in Indonesia

Objective

Most strains of methicillin-resistant Staphylococcus aureus (MRSA) analyzed to date have been from industrialized countries, with information lacking on the epidemiology of MRSA in other regions of the world. The present study describes the molecular epidemiology of MRSA strains collected at a referral hospital in Surabaya City, Indonesia in 2015-2016. The similarity of strains isolated in Indonesia to known lineages of MRSA was investigated.

Materials

Of 45 MRSA strains isolated in Surabaya, 10 were selected by antibiotic resistance patterns and clinical features, while excluding duplicates. Methods: Whole genome sequencing was performed using a next-generation sequencer, and the complete genome sequence of one of these 10 strains was also determined by the PacBio system. The strains were subjected to molecular epidemiological analyses, including the presence of drug-resistance and virulence-related genes, the determination of sequence types and staphylococcal cassette chromosome mec (SCCmec) types and mutual phylogenetic relationships, using standard analytical tools.

Results

The molecular types of these MRSA strains showed significant diversity. Complete sequencing of the genome of strain IDSA1 showed that it belonged to the ST239 group, while also having unique mobile genetic elements. Conclusions: Despite the small number of MRSA strains collected in a limited area and over a short period of time, these strains were found to have arisen in many other regions of the world, suggesting that they had migrated into Indonesia through human movement. These strains also showed molecular differentiation after migrating into Indonesia.

Epidemiology and Drug Resistance of Neonatal Bloodstream Infection Pathogens in East China Children's Medical Center From 2016 to 2020

Introduction

To analyze the pathogen distribution and drug resistance of newborns with bloodstream infection (BSI) to help clinicians choose the appropriate empirical antibiotic therapy for clinical infection control.

Methods

A total of 707 neonatal BSI cases were retrospectively analyzed. The bacteria in blood culture-positive samples were cultured, identified, and analyzed for drug sensitivity by routine methods. Statistical software was used to compare and analyze the basic data, pathogenic information, and drug resistance of the main bacteria.

Results

The 5-year average positive rate of neonatal blood culture was 2.50%. The number of specimens submitted for inspection in 2020 significantly decreased. The top five infectious pathogens with the highest proportion were coagulase-negative Staphylococcus (67.35%), of which Staphylococcus epidermidis had the highest proportion (31.26%), followed by Escherichia coli (12.87%), Klebsiella pneumoniae (9.05%), Streptococcus agalactiae (8.63%), and Staphylococcus aureus (3.25%). Gram-positive (G+) bacteria were dominant, accounting for 69.45%. The main G+ bacteria had a higher rate of resistance to erythromycin and penicillin G. The main Gram-negative (G-) bacteria had a high resistance rate to a variety of antibacterial drugs, especially cephalosporin antibiotics. The overall resistance of K. pneumoniae was higher than that of E. coli. The top two fungi detected were Candida parapsilosis and Candida albicans. C. parapsilosis did not appear to be resistant to antibiotics, while C. albicans was resistant to multiple antibiotics. The type of microbial infection had a statistically significant difference in the positive rate among the age at delivery and wards (p < 0.05). There were significant differences in the detection of fungi among these groups (p < 0.05). The positive rate of G+ bacteria in the term newborns was significantly higher than that in the preterm newborns (p < 0.05). Preterm newborns are more susceptible to pneumonia.

Conclusion

G+ bacteria are the main pathogens of neonatal BSI. Preterm newborns are more likely to be infected with G- bacteria. E. coli and K. pneumoniae are the most common G- bacteria, and both have a high resistance rate to a variety of antibacterial drugs. According to the distribution characteristics and drug resistance, it is very important to select antibiotics reasonably.

Staphylococcus taiwanensis sp. nov., isolated from human blood

A novel coagulase-negative Staphylococcus strain (NTUH-S172T) was isolated from human blood culture in Taiwan with preliminary identification of Staphylococcus saprophyticus . 16S rRNA gene analysis and multilocus sequence analysis (MLSA) showed that NTUH-S172T was most closely related to Staphylococcus haemolyticus . The average nucleotide identity and digital DNA–DNA hybridization values with the whole genome sequence were <95 % and<70 % when compared to the related species. Strain NTUH-S172T could be distinguished from S. haemolyticus by urease production and from Staphylococcus borealis by nitrate reduction. In addition, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) spectrum of NTHU-S172T was significantly different from that of S. haemolyticus , which could be used in clinical identification. In conclusion, it is proposed that this isolate represents a novel species, named Staphylococcus taiwanensis sp. nov., with type strain NTUH-S172T (=BCRC 81315T=JCM 34726T).

Novel insights into the role of the mobilome in ecological diversification and success of Staphylococcus haemolyticus as an opportunistic pathogen

Staphylococcus haemolyticus is a species of coagulase-negative staphylococci that has primarily been studied as a human skin microbiome member and an emerging nosocomial pathogen. Here, we present the first complete genome of S. haemolyticus strains SE3.9, SE3.8 and SE2.14 reported as an endophyte of rice seed. Detailed investigation of the genome dynamics of strains from diverse origins revealed an expanded genome size in clinical isolates, and a role of many insertion sequence (IS) elements in strain diversification. Interestingly, several of the IS elements are also unique or enriched in a particular habitat. Comparative studies also revealed the potential movement of mobile elements from rice endophytic S. haemolyticus to strains from other pathogenic species such as Staphylococcus aureus. The study highlights the importance of ecological studies in the systematic understanding of genome plasticity and management of medically important Staphylococcus species.

Oxacillin (Methicillin) Resistant Staphylococci in Domestic Animals in the Czech Republic

The aim of this study was to describe the prevalence of different Staphylococcus species isolated from pathological processes and lesions in domestic animals in the Czech Republic and to detect and describe oxacillin (methicillin)-resistant strains (MRS). During the years 2019–2020, a total of 5218 veterinary clinical samples from the Czech Republic were tested. Testing was performed by culture methods and typing by molecular phenotypic methods MALDI-TOF MS and PCR. Antimicrobial susceptibility testing of the strains was performed by the disk diffusion method. A total of 854 staphylococci strains were identified (16.37% prevalence), out of which 43 strains of 6 species of staphylococci were MRS (n = 43; 0.82% prevalence). Of the MRS strains, the most prevalent species were Staphylococcus pseudintermedius (n = 24; 0.46% prevalence) and Staphylococcus aureus (n = 7; 0.13% prevalence). Susceptibility testing showed resistance to beta-lactam antibiotics and, depending on the species, also to trimethoprim/sulfamethoxazole, gentamicin, tetracycline, erythromycin, clindamycin, and enrofloxacin. For further characterization of MRS, PCR assay for virulence factor genes was performed. Seven of the 14 target genes were observed only in S. aureus, except for the eno gene encoding laminin-binding protein, which was also detected in other staphylococci. It is necessary to emphasize the issue of correct using of antimicrobials in practice and antibiotic policy in university teaching and to create stricter legislation that would prevent the widespread use of antimicrobials in veterinary medicine, especially in livestock to reduce the emergence and spread of antimicrobial resistance.

Successful endovascular coiling of infectious cerebral aneurysm following Staphylococcus haemolyticus endocarditis

Recent reports suggest that Staphylococcus haemolyticus can cause infective endocarditis (IE). However, no data are available regarding infectious intracranial aneurysm (IIA) following S. haemolyticus endocarditis. Endovascular coiling is a challenging approach for the treatment of IIA. We describe the case of a 63-year-old woman who suddenly developed aphasia and dysarthria following an acute cerebral infarction in her left insular and temporal cortex. After a total hysterectomy at the age of 39, the patient had suffered from recurrent bacterial pyomyositis in her legs. At admission, there was no evidence of cerebral aneurysm, as assessed by magnetic resonance angiography, and no vegetation, as assessed by transesophageal echocardiography (TEE), resulting in an incorrect diagnosis. However, subarachnoid hemorrhage and development of cerebral aneurysm in the left middle cerebral artery occurred within 1 week of hospitalization. Continuous positive blood culture results and a second TEE finally revealed that IE was caused by S. haemolyticus. Coil embolization of the IIA was successful on day 26 after symptom onset; after this procedure, the patient began to recover. This case demonstrates that S. haemolyticus-induced endocarditis can cause IIA. Endovascular coiling is a potentially effective approach to treat IIA.

Antibiotic Resistance and Pathogenomics of Staphylococci Circulating in Novosibirsk, Russia

A total of 394 strains of staphylococci found in humans and pets in Novosibirsk, Siberian Russia, were characterized in terms of antibiotic resistance and corresponding genes. Two coagulase-positive and 17 coagulase-negative species were identified. The majority of isolates, with the exception of S. haemolyticus and hospital S. epidermidis isolates, were sensitive to most of the tested antibiotics, and isolates from pets displayed the lowest level of resistance. Nevertheless, methicillin-resistant (MRS) and/or multidrug-resistant (MDR) isolates were found in all prevailed species, including coagulase-negative. A set of genes corresponding to the detected resistance was identified: mecA (beta-lactam resistance), aac(6')-Ie-aph(2″)-Ia, aph(3')-IIIa,&nbsp;ant(4')-Ia (aminoglycoside-modifying enzymes), ermA/ermC, and msrA (macrolide resistance). Complete genome analysis for ten MDR S. epidermidis and five MDR S. haemolyticus isolates revealed additional antibiotic resistance genes mphC, qacA/qacB, norA, dfrC/dfrG, lnuA, BseSR, and fosB. NorA, dfrC, and fosB were present in all S. epidermidis genomes, whereas mphC and msrA were identified in all S. haemolyticus ones. All investigated MDR S. epidermidis and four of five S. haemolyticus strains were moderate or strong biofilm producers, whereas multiple genes responsible for this function and for virulence and pathogenicity were identified mostly in S. epidermidis, but were less frequently represented in S. haemolyticus.

Prevalence of Methicillin-Resistant Staphylococcus Species Among Filarial Lymphedema Patients in Ahanta West District of Ghana

Background

Filarial pathologies such as lymphedema may be associated with complications such as chronic non-healing wounds. Nonetheless, the role of bacterial population colonizing the lymphedematous legs has been posited to worsen the conditions of those living with the infection. These bacteria are usually composed of staphylococcal species partly because they are commensals. Thus, this present study sought to type the methicillin-resistant Staphylococcus aureus (MRSA) prevalence among individuals presenting with filarial lymphedema, particularly as MRSA tends to affect treatments options.

Methods

We recruited individuals (n = 321) with stages I–VII of lymphedema in a cross-sectional study in the Ahanta West district of the Western Region of Ghana. Swabs from lymphedematous limb ulcers, pus, and cutaneous surfaces were cultured using standard culture-based techniques. The culture isolates were later identified using Matrix-assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometry.

Results

A total of 192 Staphylococci species were isolated, with an overall prevalence of 39.7% (95% CI: 35%–44%; N = 483). S. hominis was the most prevalent species (23.95%), followed by S. haemolyticus (20.83%), S. epidermidis (15.10%), S. aureus (10.41%), and S. saprophyticus (9.32%). The remaining 20.34% were distributed among S. wanneri, S. sciuri, S. pasteuri, S. xylosus, S. simulans, S. cohnii, S. caprae, S. lugdunensis, and S. capitis. MRSA, containing mecA gene, was detected in 21 out of 31 Staphylococci isolates tested, with an overall prevalence of 68% (95% CI: 51%–84%). In addition, a virulent gene, Panton–Valentine leukocidin (PVL), which is usually associated with S. aureus, was detected in 20/31 (64.5%) S. aureus in the study.

Conclusion

These results suggest that MRSA species may pose a challenge to the treatment of filarial lymphedema with antibiotics particularly, as doxycycline is currently being piloted in some endemic areas to treat the infection. Thus, intensive antimicrobial resistance surveillance should be conducted in endemic areas by health authorities to forestall the dilemma of multidrug resistance not only against lymphatic filariasis (LF) infection but other diseases.

Characterization of New Staphylococcus haemolyticus ST42 Populations in Northern Taiwan

Introduction: Staphylococcus haemolyticus is an acquired opportunistic pathogen causing nosocomial infections. Our previous studies of S. haemolyticus showed a group of isolates that produced a significantly higher disease severity than the others. Further molecular typing showed that the sequence type (ST) 42 was the major clone among the isolates. The main aim of this study was to characterize ST42. Materials and Methods: Sixty-one and 36 isolates were collected from burn and nonburn patients, respectively. Molecular typing, antibiotic susceptibility assays, and phenotypic characterizations were performed. Results: Thirteen STs, including seven new STs, were established (ST42 to ST48). ST42 was prevalent in burn and nonburn patients, and all the pulsotype C isolates were ST42. Four of the novel STs originated from ST3, suggesting that these clonal lineages evolved locally. ST3 and ST42 showed a significant difference in clindamycin susceptibility; molecular typing showed only one MLST locus variation among seven loci in SH1431, which has been reportedly involved in the regulation of biofilm formation through Zn ²⁺ binding affinities. Conclusions: Seven novel S. haemolyticus STs were identified; phylogenetic analysis suggested the presence of locally evolved clonal lineages. The predominant ST42 showed weak biofilm formation abilities; other factors that cause the clonal lineage change still need further investigation.

Pathogenesis of Staphylococcus haemolyticus on primary human skin fibroblast cells

STAPHYLOCOCCUS HAEMOLYTICUS

(S. haemolyticus) is one of the Coagulase-negative staphylococci (CoNS) that inhabits the skin as a commensal. It is increasingly implicated in opportunistic infections, including diabetic foot ulcer (DFU) infections. In contrast to the abundance of information available for S. aureus and S. epidermidis, little is known about the pathogenicity of S. haemolyticus, despite the increased prevalence of this pathogen in hospitalized patients. We described, for the first time, the pathogenesis of different clinical isolates of S. haemolyticus isolated from DFU on primary human skin fibroblast (PHSF) cells. Virulence-related genes were investigated, adhesion and invasion assays were carried out using Giemsa stain, transmission electron microscopy (TEM), MTT and flowcytometry assays. Our results showed that most S. haemolyticus carried different sets of virulence-related genes. S. haemolyticus adhered to the PHSF cells to variable degrees. TEM showed that the bacteria were engulfed in a zipper-like mechanism into a vacuole inside the cell. Bacterial internalization was confirmed using flowcytometry and achieved high intracellular levels. PHSF cells infected with S.haemolyticus suffered from amarked decrease in viability and increased apoptosis when treated with whole bacterial suspensions or cell-free supernatants but not with heat-treated cells. After co-culture with PBMCs, S. haemolyticus induced high levels of pro-inflammatory cytokines. This study highlights the significant development of S. haemolyticus, which was previously considered a contaminant when detected in cultures of clinical samples. Their high ability to adhere, invade and kill the PHSF cells illustrate the severe damage associated with DFU infections.

ABBREVIATIONS

CoNS, coagulase-negative staphylococci; DFU, diabetic foot ulcer; DM, diabetes mellitus; DMEM, Dulbecco's Modified Eagle Medium; MTT, 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide; PBMCs,peripheral blood mononuclear cells; PHSF, primary human skin fibroblast; CFU, colony-forming unit.

A bacteriocin-based treatment option for Staphylococcus haemolyticus biofilms

Bacteriocins are ribosomally-synthesized antimicrobial peptides, showing great potential as novel treatment options for multidrug-resistant pathogens. In this study, we designed a novel hybrid bacteriocin, Hybrid 1 (H1), by combing the N-terminal part and the C-terminal part of the related bacteriocins enterocin K1 (K1) and enterocin EJ97 (EJ97), respectively. Like the parental bacteriocins, H1 used the membrane-bound protease RseP as receptor, however, it differed from the others in the inhibition spectrum. Most notably, H1 showed a superior antimicrobial effect towards Staphylococcus haemolyticus—an important nosocomial pathogen. To avoid strain-dependency, we further evaluated H1 against 27 clinical and commensal S. haemolyticus strains, with H1 indeed showing high activity towards all strains. To curtail the rise of resistant mutants and further explore the potential of H1 as a therapeutic agent, we designed a bacteriocin-based formulation where H1 was used in combination with the broad-spectrum bacteriocins micrococcin P1 and garvicin KS. Unlike the individual bacteriocins, the three-component combination was highly effective against planktonic cells and completely eradicated biofilm-associated S. haemolyticus cells in vitro. Most importantly, the formulation efficiently prevented development of resistant mutants as well. These findings indicate the potential of a bacteriocins-based formulation as a treatment option for S. haemolyticus.

Coagulase-Negative Staphylococci Clones Are Widely Distributed in the Hospital and Community

Coagulase-negative staphylococci (CoNS) may be considered contaminants when isolated from clinical specimens but may also be a cause of true infection. This study aimed to compare the clonality and SCCmec type of a collection of CoNS isolated from blood cultures of inpatients, nasal swabs of healthy individuals, and patients with chronic wounds, all from the same community, using SCCmec typing, pulsed-field gel electrophoresis (PFGE), and MLST. Staphylococcus epidermidis, exhibited high clonal diversity, but hospital and community clusters were observed. Nosocomial S. epidermidis clones belonged to sequence types ST2, ST6, and ST23. Some Staphylococcus haemolyticus clones were found to circulate in the hospital and community, while Staphylococcus saprophyticus exhibited very high clonal diversity. Staphylococcus lugdunensis, Staphylococcus warneri, and Staphylococcus capitis revealed several isolates belonging to the same clone in the hospital and community. The detection of different SCCmec types within the same cluster indicated high diversity. S. epidermidis was associated with SCCmec I and III, S. haemolyticus with I and II, S. capitis with type V, Staphylococcus hominis with mec complex type A and ccr1, and S. warneri and S. saprophyticus with SCCmec I. The generation of elements and new combinations of cassette genes were highly associated with CoNS isolates, suggesting that SCCmec may not be a good marker of clonality in these bacteria.

Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus

A pervasive pest of stored leguminous products, the bean beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) associates with a simple bacterial community during adulthood. Despite its economic importance, little is known about the compositional stability, heritability, localization, and metabolic potential of the bacterial symbionts of C. maculatus. In this study, we applied community profiling using 16S rRNA gene sequencing to reveal a highly conserved bacterial assembly shared between larvae and adults. Dominated by Firmicutes and Proteobacteria, this community is localized extracellularly along the epithelial lining of the bean beetle's digestive tract. Our analysis revealed that only one species, Staphylococcus gallinarum (phylum Firmicutes), is shared across all developmental stages. Isolation and whole-genome sequencing of S. gallinarum from the beetle gut yielded a circular chromosome (2.8 Mb) and one plasmid (45 kb). The strain encodes complete biosynthetic pathways for the production of B vitamins and amino acids, including tyrosine, which is increasingly recognized as an important symbiont-supplemented precursor for cuticle biosynthesis in beetles. A carbohydrate-active enzyme search revealed that the genome codes for a number of digestive enzymes, reflecting the nutritional ecology of C. maculatus. The ontogenic conservation of the gut microbiota in the bean beetle, featuring a "core" community composed of S. gallinarum, may be indicative of an adaptive role for the host. In clarifying symbiont localization and metabolic potential, we further our understanding and study of a costly pest of stored products. IMPORTANCE From supplementing essential nutrients to detoxifying plant secondary metabolites and insecticides, bacterial symbionts are a key source of adaptations for herbivorous insect pests. Despite the pervasiveness and geographical range of the bean beetle Callosobruchus maculatus, the role of microbial symbioses in its natural history remains understudied. Here, we demonstrate that the bean beetle harbors a simple gut bacterial community that is stable throughout development. This community localizes along the insect's digestive tract and is largely dominated by Staphylococcus gallinarum. In elucidating symbiont metabolic potential, we highlight its possible adaptive significance for a widespread agricultural pest.

Bacterial Contamination in Health Care Centers: Differences between Urban and Rural Settings

This study aims to assess the airborne bioburden of rural and urban Portuguese Primary Health Care Centers (PHCC) using active and passive sampling methods and identify the potential differences in airborne microbiota between both environments. The highest total aerobic mesophilic bacterial load in indoor air were found in the Vaccination Room (448 CFU.m−3) in the Rural PHCC and in the Waiting Room (420 CFU.m−3) for Urban PHCC. The total coliforms contamination level in indoor air was detected only in the Cleaning Supplies Room (4 CFU.m−3) in the Urban PHCC. The most frequent bacteria genera identified was Micrococcus (21% Rural PHCC; 31% Urban PHCC). The surface samples showed a highest total aerobic mesophilic bacterial contamination in the Treatment Room (86 × 103 CFU.m−2) from the Rural PHCC and in the Front Office (200 × 103 CFU.m−2) from the Urban PHCC. The electrostatic dust cloth (EDC) samples showed a highest bacterial load in the Urban PHCC. Total aerobic mesophilic bacterial load in settled dust and in the Heating, Ventilating and Air Conditioning (HVAC) filter samples in the Urban PHCC (8 CFU.g−1 and 6 × 103 CFU.m−2) presented higher values compared with the Rural PHCC (1 CFU.g−1 and 2.5 × 103 CFU.m−2). Urban PHCC presented higher bacterial airborne contamination compared with the Rural PHCC for the majority of sampling sites, and when compared with the indoor air quality (IAQ) Portuguese legislation it was the Rural PHCC in two sampling places who did not comply with the established criteria.

First Case of Staphylococci Carrying Linezolid Resistance Genes from Laryngological Infections in Poland

Linezolid is currently used to treat infections caused by multidrug-resistant Gram-positive cocci. Both linezolid-resistant S. aureus (LRSA) and coagulase-negative staphylococci (CoNS) strains have been collected worldwide. Two isolates carrying linezolid resistance genes were recovered from laryngological patients and characterized by determining their antimicrobial resistance patterns and using molecular methods such as spa typing, MLST, SCCmec typing, detection of virulence genes and ica operon expression, and analysis of antimicrobial resistance determinants. Both isolates were multidrug resistant, including resistance to methicillin. The S. aureus strain was identified as ST-398/t4474/SCCmec IVe, harboring adhesin, hemolysin genes, and the ica operon. The S. haemolyticus strain was identified as ST-42/mecA-positive and harbored hemolysin genes. Linezolid resistance in S. aureus strain was associated with the mutations in the ribosomal proteins L3 and L4, and in S. haemolyticus, resistance was associated with the presence of cfr gene. Moreover, S. aureus strain harbored optrA and poxtA genes. We identified the first case of staphylococci carrying linezolid resistance genes from patients with chronic sinusitis in Poland. Since both S. aureus and CoNS are the most common etiological factors in laryngological infections, monitoring of such infections combined with surveillance and infection prevention programs is important to decrease the number of linezolid-resistant staphylococcal strains.