High interlaboratory reproducibility of DNA sequence-based typing of bacteria in a multicenter study

Molecular Epidemiologic and Geo-Spatial Characterization of Staphylococcus aureus Cultured from Skin and Soft Tissue Infections from United States-Born and Immigrant Patients Living in New York City

(1) Background: With increasing international travel and mass population displacement due to war, famine, climate change, and immigration, pathogens, such as Staphylococcus aureus (S. aureus), can also spread across borders. Methicillin-resistant S. aureus (MRSA) most commonly causes skin and soft tissue infections (SSTIs), as well as more invasive infections. One clonal strain, S. aureus USA300, originating in the United States, has spread worldwide. We hypothesized that S. aureus USA300 would still be the leading clonal strain among US-born compared to non-US-born residents, even though risk factors for SSTIs may be similar in these two populations (2) Methods: In this study, 421 participants presenting with SSTIs were enrolled from six community health centers (CHCs) in New York City. The prevalence, risk factors, and molecular characteristics for MRSA and specifically clonal strain USA300 were examined in relation to the patients' self-identified country of birth. (3) Results: Patients born in the US were more likely to have S. aureus SSTIs identified as MRSA USA300. While being male and sharing hygiene products with others were also significant risks for MRSA SSTI, we found exposure to animals, such as owning a pet or working at an animal facility, was specifically associated with risk for SSTIs caused by MRSA USA300. Latin American USA300 variant (LV USA300) was most common in participants born in Latin America. Spatial analysis showed that MRSA USA300 SSTI cases were more clustered together compared to other clonal types either from MRSA or methicillin-sensitive S. aureus (MSSA) SSTI cases. (4) Conclusions: Immigrants with S. aureus infections have unique risk factors and S. aureus molecular characteristics that may differ from US-born patients. Hence, it is important to identify birthplace in MRSA surveillance and monitoring. Spatial analysis may also capture additional information for surveillance that other methods do not.

Staphylococcus aureus from Atopic Dermatitis Patients: Its Genetic Structure and Susceptibility to Phototreatment

We characterized the population of Staphylococcus aureus from patients with atopic dermatitis (AD) in terms of (i) genetic diversity, (ii) presence and functionality of genes encoding important virulence factors: staphylococcal enterotoxins (sea, seb, sec, sed), toxic shock syndrome 1 toxin (tsst-1), and Panton-Valentine leukocidin (lukS/lukF-PV) by spa typing, PCR, drug resistance profile determination, and Western blot. We then subjected the studied population of S. aureus to photoinactivation based on a light-activated compound called rose bengal (RB) to verify photoinactivation as an approach to effectively kill toxin-producing S. aureus. We have obtained 43 different spa types that can be grouped into 12 clusters, indicating for the first-time clonal complex (CC) 7 as the most widespread. A total of 65% of the tested isolates had at least one gene encoding the tested virulence factor, but their distribution differed between the group of children and adults, and between patients with AD and the control group without atopy. We detected a 3.5% frequency of methicillin-resistant strains (MRSA) and no other multidrug resistance. Despite genetic diversity and production of various toxins, all isolates tested were effectively photoinactivated (bacterial cell viability reduction ≥ 3 log10 units) under safe conditions for the human keratinocyte cell line, which indicates that photoinactivation can be a good option in skin decolonization. IMPORTANCE Staphylococcus aureus massively colonizes the skin of patients with atopic dermatitis (AD). It is worth noting that the frequency of detection of multidrug-resistant S. aureus (MRSA) in AD patients is higher than the healthy population, which makes treatment much more difficult. Information about the specific genetic background of S. aureus accompanying and/or causing exacerbations of AD is of great importance from the point of view of epidemiological investigations and the development of possible treatment options.

Clonal diversity of Staphylococcus aureus isolates in clinical specimens from selected health facilities in Ethiopia

Staphylococcus aureus is among the top three causative agents of nosocomial infection in Ethiopia. The majority of studies in Ethiopia have focused on the epidemiology of S. aureus in hospital settings, with limited molecular genotyping results. Molecular characterization of S. aureus is essential for identification of strains, and contributes to the control and prevention of S. aureus infection. The aim of the current study was to determine the molecular epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates recovered from clinical specimens in Ethiopia. A total of 161 MSSA and 9 MRSA isolates were characterized using pulsed-field gel electrophoresis (PFGE) and staphylococcal protein A (spa) typing. Based on the PFGE analysis, MSSA isolates were grouped into eight pulso-types groups (from A to I), while MRSA isolates clustered into three (A, B and C) pulso-types with more than 80% similarity. The spa typing analysis showed diversity of S. aureus with 56 distinct spa types. Spa type t355 was most prevalent (56/170, 32.9%), while eleven new spa types were detected including t20038, t20039, and t20042. The identified spa types were clustered into 15 spa-clonal complexes (spa-CCs) using BURP analysis; novel/unknown spa types were further subjected to MLST analysis. The majority of isolates belonged to spa-CC 152 (62/170, 36.4%), followed by spa-CC 121 (19/170, 11.2%), and spa-CC 005 (18 /170, 10.6%). Of the nine MRSA isolates, 2 (22.2%) were spa-CC 239 with staphylococcal cassette chromosome (SCC)mec III. These findings highlight the diversity of S. aureus strains in Ethiopia, as well as the presence of potentially epidemic strains circulating in the country necessitating further characterization of S. aureus for antimicrobial resistance detection and infection prevention purposes.

Gausemycin A-Resistant Staphylococcus aureus Demonstrates Affected Cell Membrane and Cell Wall Homeostasis

Antibiotic resistance is a significant and pressing issue in the medical field, as numerous strains of infectious bacteria have become resistant to commonly prescribed antibiotics. Staphylococcus aureus is a bacterium that poses a grave threat, as it is responsible for a large number of nosocomial infections and has high mortality rates worldwide. Gausemycin A is a new lipoglycopeptide antibiotic that has considerable efficacy against multidrug-resistant S. aureus strains. Although the cellular targets of gausemycin A have been previously identified, detailing the molecular processes of action is still needed. We performed gene expression analysis to identify molecular mechanisms that may be involved in bacterial resistance to gausemycin A. In the present study, we observed that gausemycin A-resistant S. aureus in the late-exponential phase showed an increased expression of genes involved in cell wall turnover (sceD), membrane charge (dltA), phospholipid metabolism (pgsA), the two-component stress-response system (vraS), and the Clp proteolytic system (clpX). The increased expression of these genes implies that changes in the cell wall and cell membrane are essential for the bacterial resistance to gausemycin A. In the stationary phase, we observed a decrease in the expression of genes involved in the phospholipid metabolism (mprF) and Clp proteolytic system (clpX).

Staphylococcus nasal colonization in three species of non-human primates

Bacterial nasal colonization is common in many mammals and Staphylococcus represents the main pathogen isolated. Staphylococcus nasal carriage in humans constitutes a risk factor for Staphylococcus infections pointing out the need for animal experimentation for nasal colonization studies, especially for vaccine development. A limitation in addressing this hypothesis has been a lack of appropriate animal model. Murine models do not mimic human nasal colonization studies. Non-human primates (NHP) remain the best classical models for nasal colonization studies. In this study, we analyzed nasal colonization between two species of Old World monkeys (cynomolgus and rhesus) and a New World monkey (squirrel monkey) from breeding colony at Fiocruz (Brazil). Sixty male and female NHP with the average age of 1-21 years old, comprising twenty animals of each species, were analyzed. Nine different Staphylococcus species (S. aureus, S. cohnii, S. saprophyticus, S. haemolyticus, S. xylosus, S. warneri, S. nepalensis, S. simiae, and S. kloosi) were identified by MALDI-TOF and 16S rRNA gene sequence analyses. Antibiotic resistance was not detected among the isolated bacterial population. S. aureus was the main isolate (19 strains), present in all species, predominant in cynomolgus monkeys (9/20) and squirrel monkeys (7/20). spa typing was used to examine the clonal structure and genetic profile of Staphylococcus aureus isolates. Eight (8) spa types were identified among the S. aureus strains. A major cluster was identified, corresponding to a new spa type t20455, and no spa types found in this study were seen before in Brazil.

In Vivo Pathogenicity of Methicillin-Susceptible Staphylococcus aureus Strains Carrying Panton-Valentine Leukocidin Gene

Toxin-producing Staphylococcus aureus strains posing a potential risk for public health have long been a topic of scientific research. Effects of Panton-Valentine leukocidin (PVL) on tissue destruction mechanisms and activities of inflammatory cells were presented in animal models of pneumonia and skin infections induced by PVL-producing S. aureus strains. This study aimed to demonstrate the in vivo pathogenicity of PVL-producing S. aureus strains isolated from some foodstuffs, which can be a potential risk to public health. PVL-positive methicillin-susceptible S. aureus (MSSA) strains M1 and YF1B-b isolated from different foodstuffs and a PVL-positive MSSA strain HT480 (positive control) were administered to New Zealand rabbits. Blood samples were harvested three and six hours after the intratracheal inoculation. Lung tissue samples were collected for gross and microscopic exams and immunohistochemical (IHC) demonstration of IL-6, IL8, IL-10, and TNF-α expressions. Serum cytokine levels were also measured by ELISA. The strains isolated from lung tissue samples were confirmed by pulsed-field gel electrophoresis. The development of acute necrotising pneumonia and a significant elevation in IL-6, IL-8, IL-10, and TNF-α expressions demonstrated the significance of foodborne PVL-positive MSSA strains in public health for the first time.

Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers

Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.

Prevalence, Infectious Characteristics and Genetic Diversity of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus (MRSA) in Two Raw-Meat Processing Establishments in Northern Greece

In the present study, we investigated the isolation frequency, the genetic diversity, and the infectious characteristics of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) from the incoming meat and the meat products, the environment, and the workers' nasal cavities, in two meat-processing establishments in northern Greece. The isolated S. aureus strains were examined for their resistance to antimicrobials, carriage of the mecA and mecC genes, carriage of genes encoding for the production of nine staphylococcal enterotoxins, carriage of the Panton-Valentine Leukocidin and Toxic Shock Syndrome genes, and the ability to form biofilm. The genetic diversity of the isolates was evaluated using Pulsed Field Gel Electrophoresis (PFGE) and spa typing. S. aureus was isolated from 13.8% of the 160 samples examined, while only one sample (0.6%) was contaminated by MRSA carrying the mecA gene. The evaluation of the antimicrobial susceptibility of the isolates revealed low antimicrobial resistance. The higher resistance frequencies were observed for penicillin (68.2%), amoxicillin/clavulanic acid (36.4%) and tetracycline (18.2%), while 31.8% of the isolates were sensitive to all antimicrobials examined. Multidrug resistance was observed in two isolates. None of the isolates carried the mecC or lukF-PV genes, and two isolates (9.1%) harbored the tst gene. Eight isolates (36.4%) carried the seb gene, one carried the sed gene, two (9.1%) carried both the sed and sei genes, and one isolate (4.5%) carried the seb, sed and sei genes. Twenty-one (95.5%) of the isolates showed moderate biofilm production ability, while only one (4.5%) was characterized as a strong biofilm producer. Genotyping of the isolates by PFGE indicates that S. aureus from different meat-processing establishments represent separate genetic populations. Ten different spa types were identified, while no common spa type isolates were detected within the two plants. Overall, our findings emphasize the need for the strict application of good hygienic practices at the plant level to control the spread of S. aureus and MRSA to the community through the end products.

Genomic analysis, antibiotic resistance, and virulence of Staphylococcus aureus from food and food outbreaks: A potential public concern

Transmission and outbreaks of Staphylococcus aureus among retail food highlights the need to comprehensive analysis the molecular characteristic of Staphylococcus aureus in foods. However, the information about Staphylococcus aureus in north China is limited. In this study, 97 and 28 S. aureus strains were isolated for analysis from 4262 samples of retail food and 61 samples food outbreaks with prevalence rate 2.28 % and 45.9 %, respectively in Jilin, China from 2014 to 2018. This study aimed to investigate the prevalence of S. aureus isolates and characterize by antimicrobial resistance testing, virulence profiles, spa typing, and multilocus sequence typing (MLST) analysis. 60 % (75/125) of the isolates contained at least enterotoxin genes including classic and new SEs genes as following: sea (40/125,32 %), see (36/125,28.8 %), sec (29/125,23.2 %), sell (29/125,23.2 %), seb (25/125,20 %), seh (22/125,17.6 %), sed (6/125,4.8 %), selq (6/125,4.8 %), and selk (6/125,4.8 %). In antimicrobial susceptibility tests, 59.2 % of the isolates (74/125) were considered as multi-drug-resistant isolates and four MRSA strains were all found with high multi-drug-resistance. Phenotype resistance to penicillin (94.4 %), erythromycin (84.2 %), clindamycin (63.9 %), and tetracycline (47.2 %) was observed which was corresponding with genotype resistance. The strains were classified to twenty-two sequence types (STs), fourteen clonal complexes (CCs), and forty-seven spa types. The predominant ST and spa types were ST1(22/125,17.6 %), ST25(20/125,16.00 %), ST398 (14/125,11.2 %) and t127 (20/125,16 %), t078 (14/125,11.2 %), t803 (7/125,5.6 %). The wgSNP analysis of these isolates in food represents showed close relatedness with food outbreaks which pose a potential health risk for consumers and warrants further attention.

Distribution and antibiotic-resistance of different Staphylococcus species identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) isolated from the oral cavity

BACKGROUND

The use of antibiotics in dentistry is associated with the emergence and spread of antibiotic-resistant microorganisms, including commensal staphylococci.

METHODS

A total of 367 oral samples were collected, from which staphylococci were isolated and identified by using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF). The antibiotic susceptibility of the isolates was determined and molecular characteristics for methicillin-resistant staphylococci was performed.

RESULTS

A total of 103 coagulase-negative staphylococci (CoNS), among them S. warneri, S. haemolyticus, S. saprophyticus, S. pasteuri, S. epidermidis, S. hominis, S. xylosus, S. equorum, S. kloosii, S. succinus, S. cohnii, and S. simulans, were confirmed by MALDI-TOF. Resistance to most tested antibiotics was statistically higher in CoNS than in S. aureus isolates (P-value < 0.05). CoNS isolates showed high resistance to penicillin (S. saprophyticus 88.9%), erythromycin (S. haemolyticus 84.6%), fusidic acid (S. saprophyticus 77.8%), co-trimoxazole (S. epidermidis 71.4%), gentamicin (S. warneri 63.8%), and tetracycline (S. saprophyticus 55.6%). Multidrug resistance was largely observed, especially among S. haemolyticus and S. saprophyticus species. Methicillin-resistance in S. haemolyticus (38.5%), S. saprophyticus (22.2%) and S. aureus (13.5%) was associated with the presence of the mecA gene and SCCmec type IV or V.

CONCLUSION

Coagulase-negative staphylococci, especially S. haemolyticus and S. saprophyticus, seem to be a reservoir of methicillin resistance and multidrug resistance in the oral cavity.

Relative virulence of Staphylococcus aureus bovine mastitis strains representing the main Canadian spa types and clonal complexes as determined using in vitro and in vivo mastitis models

Staphylococcus aureus is one of the main pathogens leading to both clinical and subclinical bovine mastitis in dairy cattle. Prediction of disease evolution based on the characteristics of Staph. aureus isolates that cause intramammary infections and understanding the host-pathogen interactions may improve management of mastitis in dairy herds. For this study, several strains were selected from each of the 6 major Canadian spa types associated with mastitis (t267, t359, t529, t605, t2445, and t13401). Adherence to host cells and intracellular persistence of these strains were studied using a bovine mammary gland epithelial cell line (MAC-T). Additionally, relative virulence and host response (cytokines production) were also studied in vivo using a mouse model of mastitis. Whole-genome sequencing was performed on all strains and associations between clonal complex, sequence type, and presence of certain virulence factors were also investigated. Results show that spa type t2445 was correlated with persistence in MAC-T cells. Strains from spa t359 and t529 showed better ability to colonize mouse mammary glands. The exception was strain sa3154 (spa t529), which showed less colonization of glands compared with other t359 and t529 strains but possessed the highest number of superantigen genes including tst. All strains possessed hemolysins, but spa types t529 and t2445 showed the largest diameter of β-hemolysis on blood agar plates. Although several spa types possessed 2 or 3 serine-aspartate rich proteins (Sdr) believed to be involved in many pathogenic processes, most t529 strains expressed only an allelic variant of sdrE. The spa types t605 (positive for the biofilm associated protein gene; bap+) and t13401 (bap-), that produced the largest amounts of biofilm in vitro, were the least virulent in vivo. Finally, strains from spa type t529 (ST151) elicited a cytokine expression profile (TNF-α, IL-1β and IL-12) that suggests a potential for severe inflammation. This study suggests that determination of the spa type may help predict the severity of the disease and the ability of the immune system to eliminate intramammary infections caused by Staph. aureus.

Molecular Characterization of Staphylococcus aureus Isolated from Raw Milk Samples of Dairy Cows in Manhiça District, Southern Mozambique

Staphylococcal infections are among the most common foodborne diseases. We performed the antibiotic susceptibility and molecular characterization of S. aureus from milk samples of dairy cows in Manhiça District. We observed a high frequency of S. aureus (41%, 58/143), in which 71% (41/58) were from commercial farms and 29% (17/58) from smallholder farms. Half of the isolates (50%, 29/58) were resistant to at least one antibiotic, with higher rates of resistance to penicillin (43%, 25/58), followed by tetracycline (16%, 9/58). Multidrug-resistant and methicillin-resistant S. aureus isolates were rare (5%, 3/58 and 3%, 2/58, respectively). The genetic diversity was low, with predominance of human-adapted strains being: ST1/CC1-t5388 (78%) and ST152-t1299 (10%), followed by ST8/CC8-t1476 (5%) and ST5/CC5-t002 (3%) and lastly, ST508/CC45-t331 and ST152-t355, with 2% each. The Panton–Valentine leukocidin (PVL) gene was detected among 14% (8/58) of the isolates, while genes encoding staphylococcal enterotoxins were scarce (3%, 2/58). Our findings revealed a high frequency of S. aureus, with high rates of resistance to the antibiotics commonly used in veterinary and human medicine. Further investigations focusing on the molecular epidemiology of S. aureus from cattle and farmers will provide detailed insights on the genetic relatedness between the strains.

Staphylococcus aureus Isolated from Ruminants with Mastitis in Northern Greece Dairy Herds: Genetic Relatedness and Phenotypic and Genotypic Characterization

Staphylococcus aureus is the most common mastitis-related pathogen in dairy cattle, goats, and sheep worldwide. However, the population structure and genomic characteristics of mastitis-associated S. aureus in small ruminants are limited. Furthermore, the genotypic and phenotypic characteristics involved in the pathogenicity of S. aureus have been thoroughly defined, yet their association with the severity of mastitis is not fully established. Here, we performed genotyping by pulsed-field gel electrophoresis (PFGE) and spa analyses to assess the genetic diversity and relatedness of 162 S. aureus strains recovered from clinical mastitis (CM) and subclinical mastitis (SCM) cases from goats, sheep, and bovines. PFGE analysis revealed 108 distinguishable pulsotypes and 3 main clusters that comprised isolates from the three host species, while according to spa typing, 32 different spa types were identified. Genotypic analysis revealed a spreading of genetically related or indistinguishable S. aureus strains among ovine, caprine, and bovine farms of distant geographical regions. In total, 28 different staphylococcal enterotoxin (SE) gene profiles were observed, revealing a diverse range of SE genes among isolates. By evaluating the antimicrobial resistance, we found low phenotypic antimicrobial resistance among all ruminant isolates. We also performed multiple correspondence analysis, which indicated that the presence of the sec gene, biofilm production, and high autoaggregation ability are associated with CM cases.

Presence of egc-positive major clones ST 45, 30 and 22 among methicillin-resistant and methicillin-susceptible oral Staphylococcus aureus strains

The oral cavity may comprise a significant reservoir for Staphylococcus aureus but the data on molecular epidemiology and clonal distribution of oral strains are really scarce. This study aimed to evaluate the clonal relatedness in S. aureus isolated from oral cavity and their relationship with carriage of virulence genes, and antimicrobial resistance profiles. A total of 139 oral S. aureus isolates were obtained from 2327 analysed oral samples of dental patients. Antimicrobial susceptibility testing was performed. Isolates were characterized using protein A gene (spa) typing, spa-CC clonal complexes, toxin genes and SCCmec typing for MRSA. High resistance rates for penicillin, tetracycline and gentamicin were detected, respectively 58.3%, 42.4%, and 35.2%. Twelve (8.6%) S. aureus isolates were identified as MRSA. All of MRSA isolates were mecA-positive and mecC-negative. SCCmec IV was the most common type (66.7%), which was typical for community-acquired MRSA (CA-MRSA). Overall, the enterotoxin gene cluster (egc) was the most frequent detected virulence factor (44.9%), both in MSSA and MRSA isolates. Presence of genes encoding for the enterotoxins (sea, seb, sec, seh, sek), exfoliative toxin A (eta), and toxic shock syndrome toxin-1 (tst) was also observed. Strains carrying lukS-PV/lukF-PV genes belonged to SCCmecV- spa type t437. The most prevalent spa types were t091, t015, t084, t002, t571, and t026 among all 57 identified. Spa types, including 3 new ones, grouped in 6 different spa-CC clonal complexes, with four major dominated; CC45, CC30, CC5, and CC15. This study demonstrated that both methicillin-susceptible and methicillin-resistant major European clones of S. aureus could be isolated from the oral cavity of dental patients, with the emergence of PVL-positive CA-MRSA strains. The oral cavity should be considered as a possible source of toxigenic egc-positive S. aureus strains, in terms of potential risk of cross-infection and dissemination to other body sites.

High Colonization Rate and Heterogeneity of ESBL- and Carbapenemase-Producing Enterobacteriaceae Isolated from Gull Feces in Lisbon, Portugal

In order to evaluate whether seagulls living on the Lisbon coastline, Portugal, might be colonized and consequently represent potential spreaders of multidrug-resistant bacteria, a total of 88 gull fecal samples were screened for detection of extended-spectrum β-lactamase (ESBL)- or carbapenemase-producing Enterobacteriaceae for methicillin-resistant Staphylococcus aureus (MRSA) and for vancomycin-resistant Enterococci (VRE). A large proportion of samples yielded carbapenemase- or ESBL-producing Enterobacteriaceae (16% and 55%, respectively), while only two MRSA and two VRE were detected. Mating-out assays followed by PCR and whole-plasmid sequencing allowed to identify carbapenemase and ESBL encoding genes. Among 24 carbapenemase-producing isolates, there were mainly Klebsiella pneumoniae (50%) and Escherichia coli (33%). OXA-181 was the most common carbapenemase identified (54%), followed by OXA-48 (25%) and KPC-2 (17%). Ten different ESBLs were found among 62 ESBL-producing isolates, mainly being CTX-M-type enzymes (87%). Co-occurrence in single samples of multiple ESBL- and carbapenemase producers belonging to different bacterial species was observed in some cases. Seagulls constitute an important source for spreading multidrug-resistant bacteria in the environment and their gut microbiota a formidable microenvironment for transfer of resistance genes within bacterial species.

Isolation and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) from milk of dairy goats under low-input farm management in Greece

The presence of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in raw milk is a challenge for veterinarians and public health professionals. In this study, we investigated the presence and clonality of S. aureus and MRSA in milk of individual dairy goats with subclinical mastitis reared under the low-input farming system in Greece and determined the isolates' enterotoxin gene carriage and their ability to form biofilms. S. aureus was isolated from 162 out of the 559 milk samples examined (29 %) and one isolate per S. aureus-positive sample was further characterized. S. aureus isolates were very closely related even among farms of distant geographical regions. Nine S. aureus isolates carried a functional mecA gene and were classified as MRSA. The S. aureus protein A (spa) typing in the MRSA isolates showed that four belonged to spa type t127 (44.4 %), three to t2049 (33.3 %) and two to t7947 (22.2 %). The spa type t7947 is reported for the first time in Greece. The MRSA isolates originated from two very distantly located farms, one located in the island of Skopelos and the other in Central Macedonia. Four of the MRSA isolates carried the staphylococcal enterotoxin genes sea or sec. Most of the isolates (92 % of S. aureus and 77.8 % of the MRSA) possessed moderate or weak biofilm-formation ability. Raw milk from low-input goat herds may serve as a potential vector of antimicrobial-resistant S. aureus to raw-milk consumers.

First report of mecC gene in clinical methicillin resistant S. aureus (MRSA) from tertiary care hospital Islamabad, Pakistan

BACKGROUND

Staphylococcus aureus (S. aureus) is one of the leading causes of community and hospital acquired infections globally. The objective of the study was to assess the prevalence, study the carriage of antibiotic resistance genes and evaluate the molecular typing of S. aureus isolates from a tertiary care hospital in Islamabad.

METHODS

A total of 1528 staphylococci isolates were included in this study. Standard microbiological procedures were applied to identify S. aureus. Antimicrobial susceptability was evaluated using the disk diffusion method and Minimum Inhibitory Concentrations (MICs) were determined using microbroth dilution method following Clinical and Laboratory Standards Institute (CLSI) guidelines. Multiplex PCR was used to detect antibiotic resistance genes, and molecular typing was performed using agr, SCCmec, spa, and Multi-Locus Sequence Typing (MLST) and clonal relatedness by Pulse Field Gel Electrophoresis (PFGE) methods.

RESULTS

Overall 65% were MRSA and 35% were methicillin sensitive Staphylococcus aureus (MSSA). Among MRSA isolates, 83% were multi-drug resistant and mecA was found in 54% isolates, mecC was in 3% while 1 MRSA carried both mecA and mecC genes. agrI (22%) was most prevalent group in MRSA, while agrIII (16%) was observed in MSSA. SCCmec types I, II, III, IV, and VI were detected, with high prevalence of type III while type V was absent. The prevelant spa type in MRSA was t657 with SCCmecIII elelments while in MSSA it was t021. One NEW spa type identified in MSSA isolates. In a subset of isolates, ST772 with SCCmecIV, ST1 carrying PVL marker, and ST1535 was reported first time from Pakistan.

CONCLUSIONS

The study presents a comprehensive analysis of prevalent S. aureus types and their antibiotic resistance profiles. It also reports for the first time SCCmec type VI and clinical MRSA isolates with mecC alone and in combination with mecA from Islamabad, Pakistan. This calls for further detailed investigations in other hospital settings in the region.

In vitro Antibiotic Susceptibility, Virulence Genes Distribution and Biofilm Production of Staphylococcus aureus Isolates from Bovine Mastitis in the Liaoning Province of China

Purpose

The aim of this study was to identify the subtype, characterize the antimicrobial resistance, determine the virulence gene distribution, and analyze the biofilm production of Staphylococcus aureus isolates from bovine mastitis milk samples in the Liaoning Province of China.

Materials and Methods

In total, 56 Staph. aureus isolates were collected and identified in this study; the isolates were divided into different spa types based on the sequence of the polymorphic X region of the spa gene. Additionally, antimicrobial susceptibility was investigated using the broth microdilution method, and 18 virulence genes were detected using PCR. Biofilm formation was measured by spectrophotometry with crystal violet staining and observed using confocal laser scanning microscopy.

Results

There were 12.12% (56/462) milk samples that were positive for Staph. aureus. These isolates were nonsusceptible to sulfamethoxazole (100%), penicillin (76.9%), daptomycin (76.79%), clindamycin (69.64%), and oxacillin (60.71%); however, the majority of the isolates (80.4%) were susceptible to amoxicillin/clavulanate. The predominant virulence genes encoded the cytotoxins, hla (94.64%) and hlb (89.29%), and the adhesion factors clfA (89.29%), clfB (89.29%), and fnbB (80.36%). Comparatively, virulence genes related to other adhesion factors such as cna (8.93%) and enterotoxins, such as seg (26.79%), sea (16.07%), seb (7.14%), and sec (7.14%) were detected at relatively lower rates. The following eight spa types were identified: t267 (35.84%), t730 (22.64%), t518 (15.09%), t1190 (11.32%), t1456 (9.43%), t224 (1.88%), t9129 (1.88%), and t177 (1.88%). The highest biofilm production was observed for t267. Staph. aureus exhibited various patterns of biofilm formation, with the biofilm often being associated with a tower-shaped structure or a thicker biofilm.

Conclusion

Our results indicated that Staph. aureus isolates from dairy cows with mastitis in the Liaoning Province of China were non-susceptible to sulfamethoxazole, penicillin, daptomycin, oxacillin, and clindamycin. Additionally, the most prevalent subtype was t267, which displayed resistance to multiple antimicrobial agents and harbored several virulence genes, including clfA, clfB, fnbB, hla, and hlb.

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories.

Epidemiology and antimicrobial resistance of methicillin-resistant Staphylococcus aureus isolates colonizing pigs with different exposure to antibiotics

Background

In 2016, very high rates of methicillin-resistant Staphylococcus aureus (MRSA)-ST398 (99%) were found in Portuguese pig farms that used colistin, amoxicillin, and zinc oxide as feed additives. Since then, farms A and B banned the use of colistin, and farm C banned the use of both antibiotics.

Objective

The aim of the present study was to evaluate the impact of the ban of colistin and amoxicillin on pig MRSA carriage rates, clonal types and antimicrobial resistance, compared to the results obtained in 2016.

Methods

In 2018, 103 pigs (52 from farm B using amoxicillin only as a feed additive and 51 from farm C where no antibiotics were included in the feed regimen) were nasally swabbed for MRSA colonization. Isolates were tested for antimicrobial susceptibility, and characterised by spa typing, SCCmec typing and MLST. Whole genome sequencing (WGS) was performed for representative isolates.

Results

Overall, 96% of the pigs swabbed in 2018 carried MRSA, mostly ST398-SCCmec V-spa types t011/t108. MRSA from pigs not receiving antibiotics in the feed regimen showed susceptibility to a higher number of antibiotics, namely erythromycin, ciprofloxacin, gentamicin, and chloramphenicol. Notably, most of these isolates (n = 52) presented an unusual erythromycin-susceptibility/clindamycin-resistance phenotype. WGS showed that these isolates lacked the erm and the lnu genes encoding resistance to macrolides and lincosamides, respectively, but carried the vgaA_LC gene encoding resistance to lincosamides, which is here firstly identified in S. aureus ST398.

Conclusion

After two years the ban of colistin and amoxicillin as feed additives had no significant impact on the MRSA nasal carriage rates. Nevertheless, the MRSA strains circulating in those farms showed resistance to a lower number of antibiotic classes.

Microarray based genetic profiling of Staphylococcus aureus isolated from abattoir byproducts of pork origin

Many parts of pork meat processing are currently not used for human consumption in Switzerland, although they are of great nutritional value. Therefore, data on the occurrence of pathogenic organisms on byproducts is extremely scarce and the prevalence and population structure of Staphylococcus aureus on meat processing sidestreams is unknown. Hence, abattoir byproducts of pork origin including ear, forefoot, heart, intestine, liver, rib bone, sternum, bladder, stomach, hind foot and tongue originating from six abattoirs were screened for S. aureus. The obtained isolates were investigated by spa typing and DNA microarray analysis to reveal their genomic profile and population structure. The prevalence of S. aureus was generally low with a mean of 8%. In total, 40 S. aureus strains were detected and assigned to 12 spa types (t015, t1491, t1778, t091, t337, t899, t2922, t7439, t1333, t208, t4049, t034) and seven clonal complexes (CC1, CC7, CC9, CC30, CC45, CC49, CC398). Detected enterotoxin genes included sea, seb, sec, seh, sel and egc encoded toxin genes seg, sei, sem, sen, seo, and seu. None of the isolates harbored genes conferring methicillin resistance, but blaZ/I/R genes causing penicillin resistance were frequently found. In addition, strains from CC398 exhibited tetM and tetK, conferring tetracycline resistance. Similarity calculations based on microarray profiles revealed no association of clonal complexes with particular body parts, but revealed a certain correspondence of clonal complex and originating abattoir.

Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - Experiences from the first inter-laboratory ring trial in four German speaking countries

Clostridium (Clostridioides) difficile is a major cause of nosocomial diarrhoea. A first inter-laboratory ring trial was performed in four European countries to evaluate the genotyping and antibiotic susceptibility testing (AST) accuracy. Six C. difficile isolates representing the epidemiologic important ribotypes (RT), RT001, RT002, RT010, RT014, RT027, and RT078 were blinded and send to 21 participating laboratories. Participants tested the samples with their genotyping and AST methods in use for concordance with reference. A total of 21 genotyping- and 14 antimicrobial susceptibility data sets were obtained. Ribotyping (11 participants) correctly identified most RTs (median 91% concordance rate) except for RT002, which was misidentified in 4/11 reports. However, this isolate was correctly asserted to RT002 after an update of a publicly available ribotyping database. Multilocus sequence typing, surface layer sequence typing, DNA microarray based genotyping, and whole genome sequencing, which were used by 1-3 participants, identified all six isolates correctly. AST was done by epsilometry by the participants and compared to agar dilution data determined by the coordinating reference centre. Susceptibilities against metronidazole, moxifloxacin, and vancomycin were correctly identified in 235 of 237 cases and in accordance to agar dilution as the gold standard. Genotyping of the C. difficile test strains revealed a remarkable high concordance on the level of ribotypes with a wide variety of methods. Epsilometry appears to be a reliable method for AST of C. difficile isolates in routine clinical microbiology laboratories.

Staphylococcus aureus nasal carriage among homeless population in Lisbon, Portugal

Methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage is a major risk factor for infection, namely among populations in the community with inherent prompting factors, such as the homeless. In Portugal, there are no data on S. aureus/MRSA nasal carriage among the homeless community. A total of 84 homeless individuals living in Lisbon (34 with no permanent address and 50 living in shelter) were nasally screened for S. aureus/ MRSA. All isolates were characterized to determine antimicrobial susceptibility and clonal type. A total of 43 (51.2%) S. aureus carriers were identified, including a single individual colonized with MRSA (1.2%). S. aureus carriage rate was higher among individuals with no permanent address (58.8% versus 46%), younger (45.7 ± 12.7 versus 52.5 ± 10.8 years), and with diagnosis of asthma (9% versus 0%). The single MRSA belonged to the EMRSA-15 clone (PFGE D, ST15-SCCmec IVh, and spa type t790). Almost half of the methicillin-susceptible S. aureus (MSSA) isolates (41.9%, n = 18) belonged to two major clones, ST398-t1451 (n = 13) and ST30-t399/t11980/t12808 associated with PFGE I (n = 5). A high proportion of isolates showed non-susceptibility to mupirocin (64%), erythromycin (45%), and fusidic acid (20%) and induced resistance to clindamycin (39%). None of the isolates harboured PVL. Our results suggest that the homeless population of Lisbon does not constitute a reservoir of MRSA in the community, but harbour the highly transmissible ST398-t1451 MSSA lineage.

Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in bulk tank milk, livestock and dairy-farm personnel in north-central and north-eastern Greece: Prevalence, characterization and genetic relatedness

Recently, there has been an increased tendency towards raw-milk consumption, which may pose a consumer risk, due to the possible presence of human pathogenic microorganisms, such as Staphylococcus aureus and even methicillin-resistant S. aureus (MRSA). The prevalence of S. aureus and methicillin-resistant S. aureus (MRSA) was investigated in 40 dairy (cattle, sheep and goat) farms in northern Greece. S. aureus and MRSA were detected in 47.8% and 4.1% of the 387 samples (raw milk, farmers and animal samples) tested, respectively. Most (81.3%) of the MRSA isolates harbored the mecA gene, whereas the mecC or Panton-Valentine Leucocidin (PVL) genes were not detected. Seven spa types were identified, with t127 being the most prevalent. Spa type t034 (CC398) was isolated for the first time from livestock in Greece. Staphylococcal enterotoxin genes were detected in 93.8% of the MRSA isolates. The MRSA isolates were genetically diverse and were all capable of biofilm production. Our results confirm the lurking threat of MRSA in raw milk and dairy farms and suggest the need for surveillance programs starting at the farm level.

Existence of multiple SCCmec elements in clinical isolates of methicillin-resistant Staphylococcus aureus

PURPOSE

Methicillin-resistant Staphylococcus aureus (MRSA) can be classified into hospital-acquired MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA), based on the associated epidemiological risk factors and their SCCmec types. We therefore studied the diversity and distribution of SCCmec elements among MRSA isolates in our region and also evaluated SCCmec typing as a tool for the classification of MRSA.

METHODOLOGY

Two hundred isolates of MRSA obtained from various clinical specimens were included. The clinical and demographic details of the patients and the epidemiological risk factors for MRSA acquisition were documented. Multiplex PCR was optimized for all the major SCCmec types (I to V). Subtyping of SCCmec type IV (IVb, IVc, IVd, IVh) was carried out by simplex PCR.

RESULTS

Based on epidemiological criteria, CA-MRSA constituted 57  % (114/200) of the the test isolates and HA-MRSA made up 43  % (86/200). The predominant SCCmec type found in our study was type III (62%), followed by type V (52.5%) and type I (47.5%), while type II was carried by a single isolate. Of the 200 isolates, 118 carried multiple SCCmec types and 3 were non-typable.

CONCLUSION

The existence of multiple SCCmec types in individual MRSA isolates resulted in our inability to categorize many of these isolates as either CA-MRSA or HA-MRSA as defined by the SCCmec type criterion.

LIMITATION

The major limitation of the study was that the SCC mec element of MRSA isolates exhibiting multiple types was not sequenced and hence this finding could not be confirmed.

A ten year study of prevalence, antimicrobial susceptibility pattern, and genotypic characterization of Methicillin resistant Staphylococcus aureus causing ocular infections in a tertiary eye care hospital in South India

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of vision threatening ocular infections. This study aimed to determine the prevalence and antimicrobial susceptibility pattern of MRSA and their genotypic characterization in ocular infections. The study period was from January 2007 to December 2017 in Aravind Eye Hospital, Madurai. Retrospective analysis of clinical records found a total of 1306 Staphylococcus aureus in various ocular infections. Among these, 274 (21%) were found to be MRSA with an increased incidence from 9% in 2007 to 38% in 2017 (P = .007). MRSA was isolated commonly from lacrimal sac infection 89 (32%), lid infection 55 (20%), keratitis 45 (16%) and orbital infection 34 (12%). MRSA isolates showed 100% sensitivity to vancomycin, 91% to chloramphenicol and majority of MRSA isolates were resistant to all fluoroquinolones. MSSA strains showed very minimal resistance to chloramphenicol (5%) and also there was no resistance to vancomycin. In case of the MSSA isolates, resistance to fluroquinolones (ciprofloxacin, gatifloxacin, moxifloxacin, ofloxacin and levofloxacin) was found to increase during study period. Methicillin-resistance is conferred by the carriage of Staphylococcal Cassette Chromosome mec (SCCmec) and most of our isolates were belonged to SCCmec type V and IV which is known to be community acquired MRSA. MLST sequencing on seven housekeeping genes revealed, sequence type ST772 was predominant followed by ST22. Agr typing identified most of the isolates (69) were agr type II (77%). By spa typing, there are 16 spa types were identified, among which 60% of the isolates had t657 spa type.

New Insight into Genotypic and Phenotypic Relatedness of Staphylococcus aureus Strains from Human Infections or Animal Reservoirs

Staphylococcus aureus is a common human and livestock opportunistic pathogen, and there is evidence of animal to human transmission. This paper aimed to recognize properties of the isolates from collections of human and livestock S. aureus strains and to estimate compatibility of results based on phenotypic tests, microarrays and the spa typing methods. The second goal was to study differences between human and animal isolates in terms of specificity of their hosts and the strain transmission among various hosts. Most strains showed multi-susceptible profiles and produced enzymes on a high level, and they were phenotypically and genetically similar. However, in contrast to the Polish bovine mastitis strains, the Slovakian strains were multi-resistant. In this research, the strains showed significant differences in terms of their phenotypic manifestations and the presence of hemolysins genes; however, other enzyme-encoding genes correlated to a higher extent with the microarrays results. Interestingly, there was a lack of enterotoxin genes in human Poultry-like protein A+ strains in comparison to other human strains. Our study showed that differences between virulence profiles of the human and animal strains correlated with their origin rather than their hosts, and any trait allowed clearly distinguishing between them based on the microarray results.

Staphylococcus aureus is a common human and livestock opportunistic pathogen, and there is evidence of animal to human transmission. This paper aimed to recognize properties of the isolates from collections of human and livestock S. aureus strains and to estimate compatibility of results based on phenotypic tests, microarrays and the spa typing methods. The second goal was to study differences between human and animal isolates in terms of specificity of their hosts and the strain transmission among various hosts. Most strains showed multi-susceptible profiles and produced enzymes on a high level, and they were phenotypically and genetically similar. However, in contrast to the Polish bovine mastitis strains, the Slovakian strains were multi-resistant. In this research, the strains showed significant differences in terms of their phenotypic manifestations and the presence of hemolysins genes; however, other enzyme-encoding genes correlated to a higher extent with the microarrays results. Interestingly, there was a lack of enterotoxin genes in human Poultry-like protein A+ strains in comparison to other human strains. Our study showed that differences between virulence profiles of the human and animal strains correlated with their origin rather than their hosts, and any trait allowed clearly distinguishing between them based on the microarray results.

Staphylococcus aureus Infecting and Colonizing Experimental Animals, Macaques, in a Research Animal Facility

An outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infections on the skin and soft tissues of experimental macaques in the vivarium of The Rockefeller University, New York, triggered this observational and interventional study. We screened 14 macaques in the colony (samples from head, nares, and rectum) and their housing (40 environmental surfaces) four times in 1 year, for S. aureus colonization or contamination, while implementing enhanced decolonization and decontamination procedures. A total of 114 isolates of S. aureus were recovered and characterized (antibiograms, spa typing, multilocus sequence typing, pulsed-field gel electrophoresis [PFGE], mecA, Panton-Valentine Leukocidin, and arginine catabolic mobile element). Based on these results, six strains of S. aureus were identified: two MRSA strains (t16708/ST3862/PFGE-A, t16709/ST3862/PFGE-C) and one methicillin-sensitive S. aureus (t8397/ST3884/PFGE-D) were characterized for the first time in this study; strains belonging to spa types t189 and t4167 have been identified in primates in previous studies. None of these strains was common to the neighboring New York City human community. Thus, it seems probable that the animals were already colonized upon arrival to the University. We suggest screening primates for S. aureus carriage upon arrival to University vivaria and possible implementation of extensive decolonization procedures before any surgical interventions.

Prevalence, antimicrobial susceptibility and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus isolated from dairy industries in north-central and north-eastern Greece

Staphylococcus aureus is an important cause of food intoxication, whereas methicillin-resistant S. aureus (MRSA) constitutes a serious public-health concern due to its ability to colonize and infect humans and animals. S. aureus and MRSA have often been isolated from milk and dairy products. The objectives of this study were to estimate the prevalence and the antimicrobial resistance of S. aureus and MRSA in four Greek dairy industries, to identify virulence factors of MRSA isolates and to describe their genetic diversity, in order to identify possible epidemiological links and evaluate the risk of MRSA dissemination to the community. S. aureus was isolated from 67 out of 305 (22.0%) dairy industry samples (bulk-tank milk, dairy products, employee nasal swabs and equipment/surface swabs). Almost all (99%) of the 227 corresponding S. aureus isolates (approximately 4 isolates per positive sample) were resistant to at least one antimicrobial and 22% were multi-drug resistant (MDR). MRSA were isolated from 11 different samples (3.6%) originating from three of the dairy plants. All MRSA isolates were capable of forming biofilms, while staphylococcal enterotoxin (SE) genes were detected in 91% of the MRSA isolates, with sec being the most frequent. All of the MRSA isolates harbored the mecA gene but the mecC and Pandon-Valentine leucocidin (PVL) genes were not detected. Pulse-Field Gel Electrophoresis (PFGE) analysis showed genetic diversity among the MRSA isolates and indicated clonal circulation in one of the dairy plants. Seven spa types were identified among the MRSA isolates with the most prevalent (t065) isolated only in one dairy plant. Certain spa types (t065, t337 and t3536) were isolated for the first time in Greece. The presence of MDR, biofilm-forming and enterotoxigenic MRSA strains in dairy plant facilities may lead to their dissemination to the community, but also to staphylococcal food poisoning, when conditions are favorable. The study's findings highlight the need for continuous monitoring of the dairy production chain, the need for re-evaluating the implemented cleaning and sanitizing processes and the adoption of preventive strategies in order to minimize public-health risks.

Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes: A New Insight Into Daptomycin Resistance

Objectives: Daptomycin (DAP) resistance in Staphylococcus aureus is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant S. aureus isolates investigated carried mutations in the mprF gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible S. aureus (MSSA) isolates (DAP-susceptible and DAP-resistant). Additionally, the activity of genes previously associated with DAP resistance was assessed.

Materials and Methods: Two MSSA isolates from patient with left-sided endocarditis were analyzed by whole genome sequencing (WGS) and reverse transcription-quantitative real-time PCR (RT-qPCR). The first isolate, DAP-susceptible, was obtained before initiation of treatment and the second isolate, DAP-resistant, was recovered after 4 weeks of DAP therapy.

Results: Comparison of complete genomes of DAP-susceptible and its DAP-resistant variant identified two non-synonymous and one synonymous mutations. The non-synonymous mutations consisted of a S829L substitution in mprF and a T331I substitution in vraS. The RT-qPCR experiments revealed an increased expression of vraS, dltA, mprF, and sceD genes in DAP-resistant variant. Strikingly, the expression of dltA and mprF genes was significantly downregulated by DAP.

Conclusion: The mprF and vraS genes were previously associated with DAP resistance, however, none of the mutations described in this study had been previously identified and linked to DAP resistance. Moreover, we provide a new insight into the DAP action on S. aureus, in which the expression of key genes in DAP resistance is decreased by the antibiotic.

Phenotypic and Molecular Characterisation of Staphylococcus Aureus with Reduced Vancomycin Susceptibility Derivated in Vitro

Vancomycin has been the primary agent used to treat serious Methicillin-resistant Staphylococcus aureus (MRSA) infection for many years. However, the rise of MRSA infection rates and the extensive use of vancomycin have led to the emergence of reduced vancomycin susceptibility. Therefore, four typical Staphylococcus aureus (S. aureus) strains from different clinical specimens were derivated by vancomycin in vitro to better clarify their phenotypic and molecular characteristics. Some experiments, such as stepwise selection of vancomycin-resistant strains, pulsed-field gel electrophoresis (PFGE), antimicrobial susceptibility test, population analysis profile-area under the curve (PAP-AUC), molecular typing, transmission electron microscopy, δ-hemolysin expression, autolysis assay, biofilm assay and quantitative real-time polymerase chain reaction (qPCR) for gene expression were carried out to compare the derivated bacteria with their parental strains. Results showed that the observed phenotypes of vancomycin-resistant strains such as hemolysin, autolysis and biofilm significantly reduced, which were associated with vancomycin resistance capability of the selected strain. The changes of phenotype and regulatory genes expression were inversely proportional to the vancomycin minimum inhibitory concentration (MICvan). Most heterogeneous vancomycin intermediate Staphylococcus aureus (hVISA) or VISA strains belonged to spa type t570 and agr group II. In summary, the clinical isolated vancomycin susceptible Staphylococcus aureus (VSSA), hVISA and VISA could be derivated into high vancomycin-resistant VISA in vitro, but it was difficult for them to develop into vancomycin resistant Staphylococcus aureus (VRSA). VISA and hVISA could gradually adapt to the environment with the vancomycin concentration that continuously elevates.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

Frequent MRSA nasal colonization among hospitalized children and their parents in Angola and São Tomé and Príncipe

BACKGROUND

The prevalence of nosocomial meticillin-resistant Staphylococcus aureus (MRSA) was previously estimated as 23% in a paediatric hospital in Luanda, Angola and 18% in a general hospital in São Tomé and Príncipe.

AIM

To evaluate the prevalence of S. aureus/MRSA colonization among hospitalized children and their parents at two hospitals in Angola and São Tomé and Príncipe.

METHODS

In 2017, 127 hospitalized children and 129 of their parents had nasal swabs for S. aureus/MRSA carriage in the two countries. The isolates were tested for the presence of the mecA and Panton-Valentine leukocidin (PVL) genes, and characterized by pulsed-field gel electrophoresis (PFGE), spa typing, multi-locus sequence typing and SCCmec typing.

FINDINGS

Twenty of 127 children (15.7%) and 13 of 129 parents (10.1%) were MRSA nasal carriers. Three lineages comprised 88% of the MRSA isolates: (i) PFGE A-ST5-SCCmec IVa (N=15; 45%), associated with spa type t105, recovered in Angola alone; (ii) PFGE N-ST8-IV/V (N=7; 21%), associated with spa types t008/t121, recovered in São Tomé and Príncipe alone; and (iii) PFGE B-ST88-IVa (N=7; 21%), associated with spa types t325/t786, present in both countries. Fifteen child/guardian pairs were colonized with identical MRSA (N=8) or meticillin-susceptible S. aureus (N=7) strains. PVL was detected in 25% of isolates, including two MRSA (ST30-V and ST8-IVa).

CONCLUSION

Hospitalized children and their parents are important reservoirs of MRSA. Infection control measures should focus on parents in order to minimize the spread of MRSA to the community.

Livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) among human MRSA isolates, European Union/European Economic Area countries, 2013

Currently, surveillance of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) in humans in Europe is not systematic but mainly event-based. In September 2014, the European Centre for Disease Prevention and Control (ECDC) initiated a questionnaire to collect data on the number of LA-MRSA from human samples (one isolate per patient) from national/regional reference laboratories in European Union/European Economic Area (EU/EEA) countries in 2013. Identification of LA-MRSA as clonal complex (CC) 398 by multilocus sequence typing (MLST) was preferred, although surrogate methods such as spa-typing were also accepted. The questionnaire was returned by 28 laboratories in 27 EU/EEA countries. Overall, LA-MRSA represented 3.9% of 13,756 typed MRSA human isolates, but it represented ≥ 10% in five countries (Belgium, Denmark, Spain, the Netherlands and Slovenia). Seven of the reference laboratories did not type MRSA isolates in 2013. To monitor the dispersion of LA-MRSA and facilitate targeted control measures, we advocate periodic systematic surveys or integrated multi-sectorial surveillance.

Carriage of Staphylococcus aureus among Portuguese nursing students: A longitudinal cohort study over four years of education

Background

Staphylococcus aureus is a major human pathogen that can colonize healthy people mainly in the anterior nares. The aim of the present study was to evaluate S. aureus nasal colonization over time among Portuguese nursing students, including methicillin-resistant S. aureus (MRSA).

Methods and findings

In this longitudinal cohort study, we collected 280 nasal swabs from nursing students at 14 time points over four years of schooling (2012–2016). The isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, multilocus sequence typing (MLST), and SCCmec typing for MRSA.

Among 47 students, 20 (43%) carried methicillin-susceptible S. aureus (MSSA) at admission, but none was colonized with MRSA. A total of 19 students (40%) became colonized after exposure during the nursing training, out of which five carried MRSA. Overall, 39 students (83%) had S. aureus detected at least once during the study period. Among the 97 MSSA isolates, most (65%) belonged to four clones: PFGE A-ST30 (21%), B-ST72 (20%), C-ST508 (13%), and D-ST398 (11%). Three of the five MRSA carriers were colonized with the predominant clone circulating in Portuguese hospitals (ST22-IVh) and two with ST3162-II. Colonization of nursing students was highly dynamic with continuous appearance of strains with distinct PFGE types in the same individual.

Conclusions

A considerable proportion of students became colonized by S. aureus, including MRSA, during the nursing education, evidencing this population represents an important reservoir of S. aureus. Therefore, education on infection control measures in nursing schools is of major importance.

MALDI-TOF MS typing of a nosocomial methicillin-resistant Staphylococcus aureus outbreak in a neonatal intensive care unit

BACKGROUND

The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods have a high discriminatory power but their availability remains restricted. In this study, we aimed to challenge matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a typing tool of a nosocomial MRSA outbreak in a neonatal intensive care unit.

METHODS

Over a 2-year period, 15 MRSA isolates were recovered from patients (n = 14) and health care workers (n = 1) at the neonatal intensive care unit. Five reference strains were included for comparison. Identification was performed by MALDI-TOF MS and susceptibility profiles determined by automated broth microdilution. Typing analysis by MALDI-TOF MS included mean spectrum profiles and subsequent dendrogram creation using BioNumerics software. Results were compared with spa typing and pulsed-field gel electrophoresis (PFGE).

RESULTS

Our study showed good concordance (93%) between PFGE, spa typing, and MALDI-TOF MS for the outbreak-related MRSA strains. MALDI-TOF MS typing showed excellent typeability and discriminatory power but showed poor reproducibility.

CONCLUSIONS

This study is one of the first to document the potential usefulness of MALDI-TOF MS with standardized data analysis as a typing tool for investigating a nosocomial MRSA outbreak. A concordance of 93% compared to reference typing techniques was observed. However, because of poor reproducibility, long-term follow-up of prospective isolated strains is not practical for routine use. Further studies are needed to confirm our observations.

Healthy Bovines as Reservoirs of Major Pathogenic Lineages of Staphylococcus aureus in Portugal

The nosocomial prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Portugal is close to 50% and remains one of the highest in Europe. MRSA reservoirs in the animal setting in Portugal have been very poorly investigated, namely among animal husbandry. A total of 52 samples (nasal, inguinal region, and milk) were obtained from bovine animals and analyzed for the presence of S. aureus. The isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, SCCmec typing, and multilocus sequence typing and tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants. Overall, 54% of the screened animals were colonized with S. aureus in at least one body site. Notably, S. aureus nasal carriage followed an increasing trend with animal age (p = 0.0006). None of the isolates harbored the mecA or mecC genes. Resistance to penicillin, rifampicin, and tetracycline was observed in 24%, 18%, and 6% of the isolates, respectively. The isolates were distributed into three clonal lineages: PFGE type A, spa type t1166, ST1247-CC133 (43%), PFGE B-t267-ST352-CC97 (30%), and PFGE C-t091-ST7-CC7 (27%). CC133 was associated to older animals (p = 0.0025), whereas CC97 was isolated from calves (p = 0.0016). Virulence determinants commonly found in mastitis were widely detected in carriage isolates: lukDE and hlgv (100%), hlb (76%), and lukM (35%). Although healthy bovines do not represent a MRSA reservoir in Portugal, they are mainly colonized with S. aureus pathogenic lineages associated to mastitis in cattle (CC97 and CC133).

Frequent isolation of methicillin resistant Staphylococcus aureus (MRSA) ST398 among healthy pigs in Portugal

Background

Although livestock-associated ST398 methicillin-resistant Staphylococcus aureus (MRSA) has been widely reported in different geographic regions, MRSA carriage studies among healthy pigs in Portugal are very limited.

Methods and findings

In total, 101 swine nasal samples from two Portuguese farms were screened for MRSA. In addition five swine workers (including one veterinary and one engineer) and four household members were nasally screened. The isolates were characterized by spa typing, SCCmec typing and MLST. All isolates were tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants.

MRSA prevalence in swine was 99% (100/101), 80% (4/5) in swine workers and 25% (1/4) in household members. All isolates belonged to ST398 distributed over two spa types–t011 (57%) and t108 (42%). SCCmec type V was present in most of the isolates (n = 95; 82%) while 21 isolates amplified the mecA gene only and were classified as nontypeable. The majority of the isolates were resistant to tetracycline (100%), clindamycin (97%), erythromycin (96%), chloramphenicol (84%) and gentamycin (69%). Notably, 12% showed resistance to quinupristin-dalfopristin (MICs 3–8 μg/mL). Beta-hemolysin (81%) and gamma-hemolysin (74%) were the unique virulence determinants detected. None of the isolates harboured PVL or mecC gene.

Conclusions

This study showed a massive occurrence of ST398-MRSA in two independent swine farms, highlighting its establishment among healthy pigs in Portugal.

Livestock-associated Staphylococcus aureus on Polish pig farms

BACKGROUND

Livestock-associated Staphylococcus aureus (LA-SA) draws increasing attention due to its particular ability to colonize farm animals and be transmitted to people, which in turn leads to its spread in the environment. The aim of the study was to determine the dissemination of LA-SA on pig farms selected throughout Poland, characterize the population structure of identified S. aureus, and assess the prevalence of LA-SA carriage amongst farmers and veterinarians being in contact with pigs.

METHODS AND FINDINGS

The study was conducted on 123 pig farms (89 farrow-to-finish and 34 nucleus herds), located in 15 out of 16 provinces of Poland. Human and pig nasal swabs, as well as dust samples were analyzed. S. aureus was detected on 79 (64.2%) farms from 14 provinces. Amongst these farms LA-SA-positive farms dominated (71/79, 89.9%, 95% CI [81.0%, 95.5%]). The prevalence of LA-MRSA-positive farms was lower than LA-MSSA-positive (36.6% of LA-SA-positive farms, 95% CI [25.5%, 48.9%] vs. 74.6%, 95% CI [62.9%, 84.2%]). In total, 190 S. aureus isolates were identified: 72 (38%) MRSA and 118 (62%) methicillin-susceptible S. aureus (MSSA), of which 174 (92%) isolates were classified to three livestock-associated lineages: CC398 (73%), CC9 (13%), and CC30/ST433 (6%). All CC398 isolates belonged to the animal clade. Four LA-MRSA clones were detected: ST433-IVa(2B) clone (n = 8, 11%), described to the best of our knowledge for the first time, and three ST398 clones (n = 64, 89%) with the most prevalent being ST398-V(5C2&5)c, followed by ST398-V(5C2), and ST398-IVa(2B). Nasal carriage of LA-SA by pig farmers was estimated at 13.2% (38/283), CC398 carriage at 12.7% (36/283) and ST398-MRSA carriage at 3.2% (9/283), whereas by veterinarians at 21.1% (8/38), 18.4% (7/38) and 10.5% (4/38), respectively.

CONCLUSIONS

The prevalence of LA-MRSA-positive pig farms in Poland has increased considerably since 2008, when the first MRSA EU baseline survey was conducted in Europe. On Polish pig farms CC398 of the animal clade predominates, this being also reflected in the prevalence of CC398 nasal carriage in farmers and veterinarians. However, finding a new ST433-IVa(2B) clone provides evidence for the continuing evolution of LA-MRSA and argues for further monitoring of S. aureus in farm animals.

Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname

We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial

Today, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing. The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using 250-bp paired-end chemistry for library preparation in a single sequencing run on an Illumina MiSeq sequencer. The run acceptance criteria were sequencing outputs >5.6 Gb and Q30 read quality scores of >75%. Subsequently, spa typing, multilocus sequence typing (MLST), ribosomal MLST, and core genome MLST (cgMLST) were performed by the participants. Moreover, discrepancies in cgMLST target sequences in comparisons with the included and also published sequence of the quality control strain ATCC 25923 were resolved using Sanger sequencing. All five laboratories fulfilled the run acceptance criteria in a single sequencing run without any repetition. Of the 400 total possible typing results, 394 of the reported spa types, sequence types (STs), ribosomal STs (rSTs), and cgMLST cluster types were correct and identical among all laboratories; only six typing results were missing. An analysis of cgMLST allelic profiles corroborated this high reproducibility; only 3 of 183,927 (0.0016%) cgMLST allele calls were wrong. Sanger sequencing confirmed all 12 discrepancies of the ring trial results in comparison with the published sequence of ATCC 25923. In summary, this ring trial demonstrated the high reproducibility and accuracy of current next-generation sequencing-based bacterial typing for molecular surveillance when done with nearly completely locked-down methods.

Multiple-locus variable-number tandem repeat fingerprinting as a method for rapid and cost-effective typing of animal-associated Staphylococcus aureus strains from lineages other than sequence type 398

In veterinary medicine, Staphylococcus aureus is associated with a range of mild to severe infections. The high density of livestock in intensive farming systems increases the risk of disease spread and hampers its control and measures of prevention, making S. aureus one of the most important animal pathogens. Multiple-locus variable-number tandem repeat fingerprinting (MLVF) has been successfully applied to the characterization of livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) ST398 but not to the characterization of a wide range of other animal isolates. The objective of the current study was to examine the effectiveness of MLVF for studying S. aureus strains isolated from households, farms and exotic animals in three regions of Poland. MLVF, random amplification of polymorphic DNA (RAPD), spa typing and diagnostic microarrays were compared to determine the most suitable combination of methods for veterinary purposes. MLVF generated results consistent with host and geographic origins, reflecting population structures with a high concordance to spa typing results. MLVF has been proven to be a rapid, highly discriminatory and cost-effective method suitable for molecular typing in veterinary settings.

Differences in prevalence of community-associated MRSA and MSSA among U.S. and non-U.S. born populations in six New York Community Health Centers

BACKGROUND

Staphylococcus aureus is the most common cause of Skin and Soft Tissue Infections (SSTIs) in the community in the United States of America. Community Health Centers (CHC) serve as primary care providers for thousands of immigrants in New York.

METHODS

As part of a research collaborative, 6 New York City-area CHCs recruited patients with SSTIs. Characterization was performed in all S. aureus isolates from wounds and nasal swabs collected from patients. Statistical analysis examined the differences in wound and nasal cultures among immigrant compared to native-born patients.

RESULTS

Wound and nasal specimens were recovered from 129 patients and tested for antibiotic susceptibility. 40 patients were immigrants from 15 different countries. Although not statistically significant, immigrants had lower rates of MRSA infections (n = 15) than did native-born participants, and immigrants showed significantly higher rates of MSSA wound cultures (n = 11) (OR = 3.5, 95% CI: 1.3, 9.7).

CONCLUSIONS

In our study, immigrants were more likely to present with SSTIs caused by MSSA than US-born patients. Immigants also reported lower frequencies of antibiotic prescription or consumption in the months prior to SSTI infection. This suggests that antibiotic resistance may vary regionally and that immigrants presenting with SSTIs may benefit from a broader range of antibiotics.

Identification of Infantile Diarrhea Caused by Breast Milk-Transmitted Staphylococcus aureus Infection

Staphylococcus aureus is a well-known organism which is responsible for a variety of human infectious diseases including skin infections, pneumonia, bacteremia, and endocarditis. Few of the microorganisms can be transmitted from mother to the newborn or infant by milk breastfeeding. This study aims to identify transmission of S. aureus from healthy, lactating mothers to their infants by breastfeeding. Stool specimens of diarrheal infants and breast milk of their mother (totally three pairs) were collected and six Staphylococcus aureus isolates were cultured positively. Homology and molecular characters of isolated strains were tested using pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing. Furthermore, toxin genes detection was also performed. Each pair of isolates has the same PFGE type and spa type. Four Sequence types (STs) were found among all the isolates; they are ST15, ST188, and ST59, respectively. Among the strains, seb, sec, and tst genes were found, and all were negative for pvl gene. The homology of the S. aureus strains isolated from the infants' stool and the mothers' milk was genetically demonstrated, which indicated that breastfeeding may be important in the transmission of S. aureus infection, and the character of S. aureus needed to be further evaluated.