Plasmid-Encoded Transferable mecB-Mediated Methicillin Resistance in Staphylococcus aureus

Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants

In Staphylococcus aureus, resistance to β-lactamase stable β-lactam antibiotics is mediated by the penicillinbinding protein 2a, encoded by mecA or by its homologues mecB or mecC. However, a substantial number of meticillin-resistant isolates lack known mec genes and, thus, are called meticillin resistant lacking mec (MRLM). This study aims to identify the genetic mechanisms underlying the MRLM phenotype. A total of 141 MRLM isolates and 142 meticillin-susceptible controls were included in this study. Oxacillin and cefoxitin minimum inhibitory concentrations were determined by broth microdilution and the presence of mec genes was excluded by PCR. Comparative genomics and a genome-wide association study (GWAS) approach were applied to identify genetic polymorphisms associated with the MRLM phenotype. The potential impact of such mutations on the expression of PBP4, as well as on cell morphology and biofilm formation, was investigated. GWAS revealed that mutations in gdpP were significantly associated with the MRLM phenotype. GdpP is a phosphodiesterase enzyme involved in the degradation of the second messenger cyclic-di-AMP in S. aureus. A total of 131 MRLM isolates carried truncations, insertions or deletions as well as amino acid substitutions, mainly located in the functional DHH-domain of GdpP. We experimentally verified the contribution of these gdpP mutations to the MRLM phenotype by heterologous complementation experiments. The mutations in gdpP had no effect on transcription levels of pbp4; however, cell sizes of MRLM strains were reduced. The impact on biofilm formation was highly strain dependent. We report mutations in gdpP as a clinically relevant mechanism for β-lactam resistance in MRLM isolates. This observation is of particular clinical relevance, since MRLM are easily misclassified as MSSA (meticillin-susceptible S. aureus), which may lead to unnoticed spread of β-lactam-resistant isolates and subsequent treatment failure.

Screening for multi-drug-resistant Gram-negative bacteria: what is effective and justifiable?

Effectiveness is a key criterion in assessing the justification of antibiotic resistance interventions. Depending on an intervention’s effectiveness, burdens and costs will be more or less justified, which is especially important for large scale population-level interventions with high running costs and pronounced risks to individuals in terms of wellbeing, integrity and autonomy. In this paper, we assess the case of routine hospital screening for multi-drug-resistant Gram-negative bacteria (MDRGN) from this perspective. Utilizing a comparison to screening programs for Methicillin-Resistant Staphylococcus aureus (MRSA) we argue that current screening programmes for MDRGN in low endemic settings should be reconsidered, as its effectiveness is in doubt, while general downsides to screening programs remain. To accomplish justifiable antibiotic stewardship, MDRGN screening should not be viewed as a separate measure, but rather as part of a comprehensive approach. The program should be redesigned to focus on those at risk of developing symptomatic infections with MDRGN rather than merely detecting those colonised.

Comparative analysis of Methicillin-Resistant Staphylococcus aureus (MRSA) and Borderline Oxacillin Resistant Staphylococcus aureus (BORSA) in community and food of animal origin

The aim of this study was to illustrate the relative pervasiveness of Borderline Oxacillin Resistant Staphylococcus aureus (BORSA) and Methicillin-Resistant Staphylococcus aureus (MRSA) in community and food of animal origin and their relationship with other genetic determinants. Staphylococcus aureus isolates were subjected to E-test using the antibiotics: oxacillin, ceftriaxone, cotrimoxazole, vancomycin, genotypic tests for the genes mecA, vanA, blaZ, pvl gene and SCCmec typing. The prevalence of S. aureus (MRSA) in the food of animal origin and community settings was 21% (1.8% MRSA) and 21.9% (7.4% MRSA), respectively. SCCmec type V was prevalent among the food of animal origin, while SCCmec type IVa among the community isolates. The likelihood of MRSA presence among community isolates was three times more than in isolates from chicken and milk samples. Likewise, the likelihood of detecting pvl positive MRSA (pvl+MRSA) isolates was 4-fold higher in the community setting than in the food of animal origin. The mecA negative BORSA (mecA-BORSA) was a frequently observed phenotype among S. aureus isolates. Also, co-detection of pvl and cotrimoxazol resistance was reported in this study although there was no noteworthy correlation of cotrimoxazol resistance with the type of sample. Isolates from milk and community settings exhibit higher minimum inhibitory concentration to vancomycin (Vancomycin MIC creep, 2-4 µg/mL).

SIGNIFICANCE

Current study provides the information on the statistical relationship between the genetic determinants of S. aureus with respect to sample type, and additionally the correlation that exists between the pvl and MRSA, pvl and cotrimoxazol resistance, vancomycin MIC and MRSA/Methicillin-Susceptible S. aureus (MSSA).

Prevalence and Antimicrobial Susceptibility Profile of Staphylococcus aureus in Milk and Traditionally Processed Dairy Products in Addis Ababa, Ethiopia

Staphylococcus aureus is a contagious pathogen that can cause various diseases in both humans and animals. Antimicrobial-resistant S. aureus is becoming an extremely important global health problem. A cross-sectional study was conducted from December 2019 to May 2020 to assess the occurrence of S. aureus and its antimicrobial susceptibility profiles in milk and traditionally processed dairy products in selected subcities of Addis Ababa. A total of 255 dairy product samples (175 raw milk and 80 traditionally processed dairy products) were collected from farms and retail markets. Samples were cultured for S. aureus according to standard microbiology techniques, and the Kirby-Bauer disk diffusion method was used to assess antimicrobial susceptibility of isolates to a panel of 12 antimicrobials. Susceptibility to methicillin was determined based on the sensitivity of isolates to cefoxitin, and resistant isolates were investigated for the presence of mecA and mecC genes using PCR. Staphylococcus aureus was isolated from 43 (24.6%) of milk, 7 (17.5%) of yogurt, and 2 (5%) of cottage cheese. A significantly higher rate of contamination with S. aureus was recorded among milk samples compared to yogurt and cottage cheese (p = 0.019). Out of 52 S. aureus isolates investigated for susceptibility to 12 antimicrobials, 49 (94.2%) of the isolates were resistant to ampicillin and 42 (80.8%) to amoxicillin+clavulanic acid. Twenty (38.5%) of the isolates were methicillin-resistant S. aureus (MRSA) based on susceptibility to cefoxitin. However, only one of these isolates (5%) was positive for mecA gene, and none of them were positive for the mecC gene. There was no significant difference (p > 0.05) in the rate of occurrence of MRSA among isolates from different sources. In conclusion, this study demonstrated a significant level of contamination of milk and dairy products with S. aureus and most isolates were multidrug resistant. The occurrence of MRSA in raw milk and dairy products signifies a serious public health threat as the practice of consuming raw dairy products in the study area is widespread. The lack of agreement between phenotypic and genotypic detection of MRSA suggests the need for further study to identify the genetic basis for the observed resistance phenotype.

Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids-who's mimicking whom?

In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-conjugative plasmids have been identified that contain mimics of each. The relaxasome accessory factor SmpO, encoded by each conjugative plasmid, determines specificity for its cognate oriT. Here we characterized the binding of SmpO proteins to each oriT. SmpO proteins predominantly formed tetramers in solution and bound 5′-GNNNNC-3′ sites within each oriT. Four of the five SmpO proteins specifically bound their cognate oriT. An F7K substitution in pWBG749 SmpO switched oriT-binding specificity in vitro. In vivo, the F7K substitution reduced but did not abolish self-transfer of pWBG749. Notably, the substitution broadened the oriT subtypes that were mobilized. Thus, this substitution represents a potential evolutionary intermediate with promiscuous DNA-binding specificity that could facilitate a switch between oriT specificities. Phylogenetic analysis suggests pWBG749-family plasmids have switched oriT specificity more than once during evolution. We hypothesize the convergent evolution of oriT specificity in distinct branches of the pWBG749-family phylogeny reflects indirect selection pressure to mobilize plasmids carrying non-cognate oriT-mimics.

Antimicrobial Resistance Profiles and Genes of Staphylococci Isolated from Mastitic Cow's Milk in Kenya

Increasing numbers of potentially zoonotic multidrug-resistant (MDR) staphylococci strains, associated with mastitis in dairy cows, are being reported globally and threaten disease management in both animal and human health. However, the prevalence and antimicrobial resistance profiles of these strains, including methicillin-resistant staphylococci (MRS), in Kenya is not well known. This study investigated the drug resistance profiles and genes carried by 183 staphylococci isolates from 142 dairy cows representing 93 farms recovered from mastitis milk of dairy cows in two selected counties in Kenya. Staphylococci isolates were characterized by phenotypic characteristics, polymerase chain reaction (PCR) amplification, partial sequencing and susceptibility testing for 10 antimicrobial drugs. Detection of seven resistance genes to the various antimicrobial drugs was conducted using PCR. Overall, phenotypic resistance among the staphylococci ranged between 66.1% for ampicillin and 3.5% for fluoroquinolones. Twenty-five percent (25%) of S. aureus and 10.8% of the coagulase-negative staphylococci (CoNS) isolates, were methicillin-resistant staphylococci phenotypically (defined as resistance to cefoxitin disk diffusion). The most common genes found in S. aureus and CoNS were blaZ and strB at 44.3% and 26%, and 78% and 50%, respectively. MDR was observed in 29.67% and 16.3% of S. aureus and CoNS, respectively. These findings pose a threat to bovine mastitis treatment and management as well as human health.

The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus

OBJECTIVES

To analyse macrolide resistance in a Macrococcus canis strain isolated from a dog with an ear infection, and determine whether the resistance mechanism is also present in other bacteria, and associated with mobile genetic elements.

METHODS

The whole genome of M. canis Epi0082 was sequenced using PacBio and Illumina technologies. Novel macrolide resistance determinants were identified through bioinformatic analysis, and functionality was demonstrated by expression in Staphylococcus aureus. Mobile genetic elements containing the novel genes were analysed in silico for strain Epi0082 as well as in other bacterial strains deposited in GenBank.

RESULTS

M. canis Epi0082 contained a 3212 bp operon with the novel macrolide resistance genes mef(F) and msr(G) encoding a efflux protein and an ABC-F ribosomal protection protein, respectively. Cloning in S. aureus confirmed that both genes individually confer resistance to the 14- and 15-membered ring macrolides erythromycin and azithromycin, but not the 16-membered ring macrolide tylosin. A reduced susceptibility to the streptogramin B pristinamycin IA was additionally observed when msr(G) was expressed in S. aureus under erythromycin induction. Epi0082 carried the mef(F)-msr(G) operon together with the chloramphenicol resistance gene fexB in a novel 39 302 bp plasmid pMiCAN82a. The mef(F)-msr(G) operon was also found in macrolide-resistant Macrococcus caseolyticus strains in the GenBank database, but was situated in the chromosome as part of a novel 13 820 bp or 13 894 bp transposon Tn6776.

CONCLUSIONS

The identification of mef(F) and msr(G) on different mobile genetic elements in Macrococcus species indicates that these genes hold potential for further dissemination of resistance to the clinically important macrolides in the bacterial population.

What's new in mechanisms of antibiotic resistance in bacteria of clinical origin?

The discovery, commercialization and administration of antibiotics revolutionized the world of medicine in the middle of the last century, generating a significant change in the therapeutic paradigm of the infectious diseases. Nevertheless, this great breakthrough was soon threatened due to the enormous adaptive ability that bacteria have, through which they are able to develop or acquire different mechanisms that allow them to survive the exposure to antibiotics. We are faced with a complex, multifactorial and inevitable but potentially manageable threat. To fight against it, a global and multidisciplinary approach is necessary, based on the support, guidance and training of the next generation of professionals. Nevertheless, the information published regarding the resistance mechanisms to antibiotics are abundant, varied and, unfortunately, not always well structured. The objective of this review is to structure the, in our opinion, most relevant and novel information regarding the mechanisms of resistance to antibiotics that has been published from January 2014 to September 2019, analysing their possible clinical and epidemiological impact.

Antimicrobial Resistance and Genetic Lineages of Staphylococcus aureus from Wild Rodents: First Report of mecC-Positive Methicillin-Resistant S. aureus (MRSA) in Portugal

The frequent carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), by wild animals along with its zoonotic potential poses a public health problem. Furthermore, the repeated detection of the mecA gene homologue, mecC, in wildlife raises the question whether these animals may be a reservoir for mecC-MRSA. Thus, we aimed to isolate S. aureus and MRSA from wild rodents living in port areas and to characterize their antimicrobial resistance and genetic lineages. Mouth and rectal swab samples were recovered from 204 wild rodents. The samples were incubated in BHI broth with 6.5% of NaCl and after 24 h at 37 °C the inoculum was seeded onto Baird-Parker agar, Mannitol Salt agar and ORSAB (supplemented with 2 mg/L of oxacillin) plates. Species identification was confirmed by MALDI-TOF MS. The antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method against 14 antibiotics. The presence of virulence and resistance genes was performed by PCR. The immune evasion cluster (IEC) system was investigated in all S. aureus. All isolates were characterized by MLST, spa- and agr typing. From 204 samples, 38 S. aureus were isolated of which six MRSA were detected. Among the six MRSA isolates, three harbored the mecC gene and the other three, the mecA gene. All mecC-MRSA isolates were ascribed to sequence type (ST) 1945 (which belongs to CC130) and spa-type t1535 whereas the mecA isolates belonged to ST22 and ST36 and spa-types t747 and t018. Twenty-five S. aureus were susceptible to all antibiotics tested. S. aureus isolates were ascribed to 11 MLST and 12 spa-types. S. aureus presents a great diversity of genetic lineages in wild rodents. This is the first report of mecC-MRSA in Portugal.

Virulence Factors in Staphylococcus Associated with Small Ruminant Mastitis: Biofilm Production and Antimicrobial Resistance Genes

Small ruminant mastitis is a serious problem, mainly caused by Staphylococcus spp. Different virulence factors affect mastitis pathogenesis. The aim of this study was to investigate virulence factors genes for biofilm production and antimicrobial resistance to β-lactams and tetracyclines in 137 staphylococcal isolates from goats (86) and sheep (51). The presence of coa, nuc, bap, icaA, icaD, blaZ, mecA, mecC, tetK, and tetM genes was investigated. The nuc gene was detected in all S. aureus isolates and in some coagulase-negative staphylococci (CNS). None of the S. aureus isolates carried the bap gene, while 8 out of 18 CNS harbored this gene. The icaA gene was detected in S. aureus and S. warneri, while icaD only in S. aureus. None of the isolates carrying the bap gene harbored the ica genes. None of the biofilm-associated genes were detected in 14 isolates (six S. aureus and eight CNS). An association was found between Staphylococcus species and resistance to some antibiotics and between antimicrobial resistance and animal species. Nine penicillin-susceptible isolates exhibited the blaZ gene, questioning the reliability of susceptibility testing. Most S. aureus isolates were susceptible to tetracycline, and no cefazolin or gentamycin resistance was detected. These should replace other currently used antimicrobials.

Detection of Antimicrobial Resistance of Bacteria Staphylococcus chromogenes Isolated from Sheep's Milk and Cheese

Antimicrobial and multidrug resistance is detected in nonaureus staphylococci, including Staphylococcus chromogenes, which commonly causes intramammary infections. Recent clinical studies point to the presence of methicillin-resistant S. chromogenes. Therefore, this study aims to determine the prevalence of this species in samples of sheep‘s milk and cheeses made from them. Isolates were identified by polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF). A total of 208 staphylococcal isolates were identified. Of these, 18% were identified as S. chromogenes. The antimicrobial resistance of the identified isolates was determined using the agar dilution method against penicillin, ceftaroline, teicoplanin, gentamicin, erythromycin, tetracycline, and ofloxacin. The highest resistance was found to penicillin (95%), tetracycline (86%), and oxacillin (81%). The highest sensitivity was confirmed for gentamicin (55%). The study also confirmed the presence of methicillin resistant staphylococcal isolates (30%) based on the phenotypic manifestation of antimicrobial resistance and detection of the presence of the mecA gene. The study shows that the tested isolates (62%) were multidrug resistant. Resistance to two antibiotics was most often found (39%).

Antimicrobial resistance and virulence characteristics in 3 collections of staphylococci from bovine milk samples

Mastitis is a prevalent disease in dairy cattle, and staphylococci are among the most common causative pathogens. Staphylococci can express resistance to a range of antimicrobials, of which methicillin resistance is of particular public health concern. Additionally, Staphylococcus aureus carries a variety of virulence factors, although less is understood about the virulence of non-aureus staphylococci (NAS). The aim of our study was to identify and characterize 3 collections of staphylococcal isolates from bovine milk samples regarding antimicrobial resistance, with emphasis on methicillin resistance, and their carriage of virulence genes typically displayed by Staph. aureus. A total of 272 staphylococcal isolates collected in Norway and Belgium in 2016 were included, distributed as follows: group 1, Norway, 100 isolates; group 2, Flanders, Belgium, 64 isolates; group 3, Wallonia, Belgium, 108 isolates. Species identification was performed by use of MALDI-TOF mass spectrometry. Phenotypic resistance was determined via disk diffusion, and PCR was used for detection of methicillin resistance genes, mecA and mecC, and virulence genes. Antimicrobial resistance was common in Staphylococcus epidermidis and Staphylococcus haemolyticus from all different groups, with resistance to trimethoprim-sulfonamide frequently occurring in Staph. epidermidis and Staph. haemolyticus as well as in Staph. aureus. Resistance to penicillin was most frequently observed in group 1. Ten Belgian isolates (1 from group 2, 9 from group 3) carried the methicillin resistance determinant mecA: 5 Staph. aureus from 2 different farms and 5 NAS from 3 different farms. Almost all Staph. aureus isolates were positive for at least 3 of the screened virulence genes, whereas, in total, only 8 NAS isolates harbored any of the same genes. Our study contributes to the continuous need for knowledge regarding staphylococci from food-producing animals as a basis for better understanding of occurrence of resistance and virulence traits in these bacteria.

Diversity and genetic lineages of environmental staphylococci: a surface water overview

Antimicrobial resistance in the environmental dimension is one of the greatest challenges and emerging threats. The presence of resistant bacteria and resistance genes in the environment, especially in aquatic systems, has been a matter of growing concern in the past decade. Monitoring the presence of antimicrobial resistance species, in this particular case, Staphylococcus spp., in natural water environments could lead to a better understanding of the epidemiology of staphylococci infections. Thus, the investigation of natural waters as a potential reservoir and vehicle for transmission of these bacteria is imperative. Only a few studies have investigated the prevalence, antimicrobial resistance and genetic lineages of staphylococci in natural waters. Those studies reported a high diversity of staphylococci species and lineages in surface waters. Methicillin-resistant S. aureus were relatively prevalent in surface waters and, as expected, often presented a multidrug-resistant profile. There was a high diversity of S. aureus lineages in surface waters. The presence of S. aureus CC8 and CC5 suggests a human origin. Among the coagulase-negative staphylococci, the most frequently found in natural waters was S. warneri and S. epidermidis. These studies are extremely important to estimate the contribution of the aquatic environment in the spread of pathogenic bacteria.

Characterization of Antibiotic Resistance and Virulence Traits Present in Clinical Methicillin-Resistant Staphylococcus aureus Isolates

Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious superbug which poses serious health threats to humanity. The severity of the infections depends on the prevalence of virulence factors and antibiotic resistance. In this study, attempts have been made to nominate the two most virulent and multidrug-resistant MRSA isolates demonstrating the preliminary features of intestinal adhesion for the futuristic applications of probiotics and postbiotics as antagonists to combat MRSA infections. In this context, six clinical isolates of MRSA were polyphasically characterized for their identity, multidrug resistance, and few selected virulence determinates such as hemolytic activity and production of coagulase, nuclease, and capsule. The gut colonizing ability of MRSA isolates was assessed by mucoadhesion, auto-aggregation, and cell surface hydrophobicity. An antibiogram of MRSA isolates suggested the resistance towards several antibiotics with multiple antibiotic resistance (MAR) index >0.5 (12/241, 12/206, and 5/255) as well as their genome portraying mecA mediated methicillin resistance. Besides exhibiting strong biofilm formation ability, all the isolates exhibited positive responses towards tested virulence assays coupled with their genome displaying Coa, NucA, and CapE genes. On the other hand, isolates exhibited different levels of auto-aggregation (37.90 ± 1.8 to 51.53 ± 3.1%) and mucin adhesion ability (68.93 ± 0.61% to 86.62 ± 1.96%) with a significant (P ≤ 0.05) variation in adhesion to different hydrocarbons. Finally, multivariate Principal Component Analysis and Hierarchical Cluster Analysis (HCA) heatmap using Euclidean distance measurement indicated MRSA 12/206 and 5/255 as most resistant and virulent isolates with the potential to adhere to the hydrophobic gut niche.

Characterization of staphylococci sampled from diabetic foot ulcer of Jordanian patients

AIMS

The aim of this study was to isolate and characterize staphylococcal isolates from diabetic foot ulcers (DFU) in Jordanian patients.

METHODS AND RESULTS

Selected aerobic pathogens recovered from DFU specimens and patients' nares with a focus on staphylococci were investigated. Antimicrobial susceptibilities and the prevalence of methicillin-resistant staphylococci (MRS) were determined. SCCmec types and toxigenic characteristics were analysed and spa typing was performed for methicillin-resistant Staphylococcus aureus (MRSA) isolates. The relationship between toxigenic characteristics of MRSA and the Wagner ulcer grading system was statistically analysed. A total number of 87 DFU patients were recruited for the study. The DFU cultures were polymicrobial. Members of the genus Staphylococcus were the most common among DFU-associated isolates found in 48·3% (n = 42) of all patients enrolled. Coagulase-negative staphylococci (CoNS) comprised 63·3% of staphylococci isolated from DFUs predominated by Staphylococcus epidermidis in both DFU (7·6%) and nares (39·2%). Staphylococcus aureus was isolated from DFUs and nares in 14·2 and 9·8%, respectively, while 93 and 70% of these isolates were MRSA. Most of MRSA carried SCCmec type IV (76·2%) while SCCmec elements were non-typeable in most methicillin resistant coagulase negative staphylococci (MR-CoNS) (61·9%). The most frequent MRSA spa type was t386 (23·8%). Most MRSA and MR-CoNS exhibited resistance towards aminoglycosides, fluoroquinolones and macrolides and susceptibility towards vancomycin, mupirocin and linezolid. No association was found between the possession of pvl, tst, sea and hlg toxins and Wagner ulcer grading system (P value >0·05).

CONCLUSIONS

This analysis of Jordanian DFU culture demonstrated its polymicrobial nature with predominance of Staphylococcus sp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first of its type to assess the microbiology of DFU among Jordanian patients. The results will help in the appropriate application of antimicrobial chemotherapy in the management of DFU.

Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins

Most methicillin resistant Staphylococcus aureus (MRSA) isolates harboring mecC gene belong to clonal complex CC130. This lineage has traditionally been regarded as animal-associated as it lacks the human specific immune evasion cluster (IEC), and has been recovered from a broad range of animal hosts. Nevertheless, sporadic mecC-MRSA human infections have been reported, with evidence of zoonotic transmission in some cases. The objective of this study was to investigate the whole-genome sequences of 18 S. aureus CC130 isolates [13 methicillin-resistant (mecC-MRSA) and five methicillin-susceptible (MSSA)] from different sequences types, obtained from a variety of host species and origins (human, livestock, wild birds and mammals, and water), and from different geographic locations, in order to identify characteristic markers and genomic features. Antibiotic resistance genes found among MRSA-CC130 were those associated with the SSCmecXI element. Most MRSA-CC130 strains carried a similar virulence gene profile. Additionally, six MRSA-CC130 possessed scn-sak and one MSSA-ST130 had lukMF'. The MSSA-ST700 strains were most divergent in their resistance and virulence genes. The pan-genome analysis showed that 29 genes were present solely in MRSA-CC130 (associated with SCCmecXI) and 21 among MSSA-CC130 isolates (associated with phages). The SCCmecXI, PBP3, GdpP, and AcrB were identical at the amino acid level in all strains, but some differences were found in PBP1, PBP2, PBP4, and YjbH proteins. An examination of the host markers showed that the 3' region of the bacteriophage φ3 was nearly identical to the reference sequence. Truncated hlb gene was also found in scn-negative strains (two of them carrying sak-type gene). The dtlB gene of wild rabbit isolates included novel mutations. The vwbp gene was found in the three MSSA-ST700 strains from small ruminants and in one MSSA-ST130 from a red deer; these strains also carried a scn-type gene, different from the human and equine variants. Finally, a phylogenetic analysis showed that the three MSSA-ST700 strains and the two MSSA-ST130 strains cluster separately from the remaining MRSA-CC130 strains with the etD2 gene as marker for the main lineage. The presence of the human IEC cluster in some mecC-MRSA-CC130 strains suggests that these isolates may have had a human origin.

Comparison of the Staphylococcal Chromosome Cassette (SCC) mec in Methicillin-Resistant Staphylococcus aureus (MRSA) and Non-aureus Staphylococci (MRNAS) from Animals and Humans

Methicillin-resistant Staphylococcus aureus (MRSA) and non-aureus staphylococci (MRNAS) cause different infections in animals, including mastitis, in livestock and humans. This study aimed to identify and compare the staphylococcal chromosome cassette mec (SCCmec) types of MRSA or MRNAS isolated from several animal species and humans in different countries. Of 1462 S. aureus and non-aureus staphylococci, 68 grew on Chrom MRSA ID^® agar, were phenotypically resistant to cefoxitin and tested positive with the PCR for the mecA gene. These 60 MRSA and 8 MRNAS were isolated in Belgium mainly from cows (livestock-associated (LA) MRS) and humans (community-acquired (CA) MRS) and in Japan from dogs and cats. The SCCmec cassettes were identified by multiplex PCR in 52 MRSA and 7 MRNAS and by whole genome sequencing (WGS) in 8 additional MRSA. The SCCmec types IV and V were the most frequent in Belgian LA-MRS and CA-MRS, while the SCCmec type II was identified in four of the five Japanese MRSA. The remaining isolate was a bovine S. haemolyticus in which no SCCmec was identified. These results confirm the high prevalence of the SCCmec types IV and V in LA-MRS and CA-MRS in Belgium, emphasizing the possible public health hazard of the former, and the absence of SCCmec in some MRNAS.

The Prevalence of Staphylococcus aureus and Methicillin Resistant Staphylococcus aureus in Processed Food Samples in Riyadh, Saudi Arabia

Staphylococcus aureus mainly Methicillin Resistant Staphylococcus aureus(MRSA) is a life-threatening infection that occurring in food and caused a public health concern. This study designed to examine the prevalence of S. aureus and MRSA in different types of processed food. Food samples were screened for the recovered strains of S. aureus and MRSA, and they were examined for antimicrobial susceptibility and by molecular characterization of mecA and staphylococcal cassette chromosome mec(SCCmec). Detection of virulence factors like Panton-Valentine Leukocidin (PVL), Staphylococcus aureus protein A(spa) and Staphylococcal enterotoxins(SEs) by PCR using specific primers. Among the 150 collected processed food samples, 62.7% were contaminated by S. aureus bacteria, 56.4% of which were proved as MRSA. 17% of MRSA isolates were positive for mecA genes with the SCCmec type IVb and V (11.1% each) as the solely existing types of SCCmec. None of the MRSA isolates carried mecC or mecB genes. Most of MRSA isolates were multidrug resistance and 33.3% of MRSA-mecA positive isolates also carried vancomycin resistance genes (i.e., vanB). In addition, spa gene was found among 7.5% of MRSA isolates; none of which were positive for PVL gene. Further, there were variant presence of SEs among MRSA isolates and the highest presence was from type SEH (49.1%). Generally, our results confirmed that processed foods in Saudi Arabia (Riyadh) are potential vehicles for multidrug resistant S. aureus and MRSA transmission; which are serious public health risks, and underlined the need for good hygiene practices.

Truncation of GdpP mediates β-lactam resistance in clinical isolates of Staphylococcus aureus

OBJECTIVES

High-level β-lactam resistance in MRSA is mediated in the majority of strains by a mecA or mecC gene. In this study, we identified 10 mec gene-negative MRSA human isolates from Austria and 11 bovine isolates from the UK showing high levels of β-lactam resistance and sought to understand the molecular basis of the resistance observed.

METHODS

Different antimicrobial resistance testing methods (disc diffusion, Etest and VITEK® 2) were used to establish the β-lactam resistance profiles for the isolates and the isolates were further investigated by WGS.

RESULTS

A number of mutations (including novel ones) in PBPs, AcrB, YjbH and the pbp4 promoter were identified in the resistant isolates, but not in closely related susceptible isolates. Importantly, a truncation in the cyclic diadenosine monophosphate phosphodiesterase enzyme, GdpP, was identified in 7 of the 10 Austrian isolates and 10 of the 11 UK isolates. Complementation of four representative isolates with an intact copy of the gdpP gene restored susceptibility to penicillins and abolished the growth defects caused by the truncation.

CONCLUSIONS

This study reports naturally occurring inactivation of GdpP protein in Staphylococcus aureus of both human origin and animal origin, and demonstrates clinical relevance to a previously reported association between this truncation and increased β-lactam resistance and impaired bacterial growth in laboratory-generated mutants. It also highlights possible limitations of genomic determination of antibiotic susceptibility based on single gene presence or absence when choosing the appropriate antimicrobial treatment for patients.

Multidrug-Resistant Coagulase-Negative Staphylococci Isolated from Bloodstream in the uMgungundlovu District of KwaZulu-Natal Province in South Africa: Emerging Pathogens

Coagulase-negative staphylococci (CoNS) are increasingly associated with nosocomial infections, especially among the immunocompromised and those with invasive medical devices, posing a significant concern. We report on clinical multidrug-resistant CoNS from the uMgungundlovu District, KwaZulu-Natal Province, South Africa, as emerging pathogens. One hundred and thirty presumptive CoNS were obtained from blood cultures. Culture, biochemical tests, and the Staphaurex™ Latex Agglutination Test were used for the initial identification of CoNS isolates; confirmation and speciation were undertaken by the VITEK 2 system. Susceptibilities of isolates against a panel of 20 antibiotics were determined using the Kirby-Bauer disk diffusion method, and the multiple antibiotic resistance (MAR) indices of the isolates were determined. The polymerase chain reaction (PCR) was used to amplify the mecA gene to confirm methicillin resistance. Overall, 89/130 presumptive CoNS isolates were confirmed as CoNS by the VITEK 2 system. Of these, 68 (76.4%) isolates were putatively methicillin-resistant by the phenotypic cefoxitin screen test and 63 (92.6%) were mecA positive. Staphylococcus epidermidis (19.1%), S. hominis ssp. hominis (15.7%), and S. haemolyticus (16.9%) were the most common CoNS species. Isolates showed high percentage resistance against penicillin (100.0%), erythromycin (74.2%), and azithromycin (74.2%) while displaying high susceptibilities to linezolid (95.5%), gentamicin (95.5%), and tigecycline (94.4%). Multidrug resistance (MDR) was observed in 76.4% of isolates. MAR index calculation revealed 71.9% of isolates with MAR index >0.2 and 20.2% >0.5. Isolates with the highest MAR indices (0.7 and 0.8) were recovered from the neonatal intensive care unit. Fifty-one MDR antibiograms were observed. The high prevalence of methicillin resistance and multidrug resistance in several species of CoNS necessitates surveillance of this emerging pathogen, currently considered a contaminant of microbial cultures.

Livestock-Associated Methicillin-Resistant Staphylococcus aureus and Related Risk Factors in Holdings of Veal Calves in Northwest Italy

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) have emerged worldwide as zoonotic pathogens. Data on LA-MRSA in veal calf production in Italy are lacking; the aim of this survey was to fill current knowledge gaps in its prevalence and characteristics. Between February 2012 and January 2013 nasal swabs were taken from 1650 three- to six-month-old veal calves on 55 farms in Piedmont (northwest Italy), including gathering-related epidemiological data. S. aureus were screened for methicillin resistance by phenotypic and molecular (mecA gene detection) methods. MRSA were further genotyped by multilocus sequence typing. About 30% of the herds tested positive for MRSA: three different clonal complexes (CC398, CC97, and CC1) and staphylococcal cassette chromosome mec types (IVa, IVb, and V) were detected. Multilevel logistic regression model indicated poor cleaning, importation from Austria, and animal age as risk factors and coagulase-negative staphylococci colonization as a predictive factor for the occurrence of MRSA. The detection of CCs circulating in pigs and dairy cattle in Italy underscores the ability of the LA-MRSA clones to spread among animal production systems. In addition to maintaining preventive control measures for human health, better cleaning procedures need to be implemented, especially after new calves have been introduced into the herd.

Antimicrobial resistance of Staphylococcus spp. isolated from organic and conventional Minas Frescal cheese producers in São Paulo, Brazil

The genus Staphylococcus is recognized worldwide as a cause of bacterial infections in humans and animals. Antibiotics used in dairy cattle combined with ineffective control can increase antimicrobial resistance. The objective of this study was to characterize 95 Staphylococcus strains isolated from organic and conventional Minas Frescal cheese production regarding antibiotic resistance (phenotype and genotype), presence of sanitizer-resistant genes and biofilm-formation genes, and SCCmec typing. Most strains (25.3%) showed higher resistance to penicillin, followed by oxacillin (21.1%) and clindamycin (11.6%). Among antibiotic resistance genes, the most prevalent were blaZ (25.3%), mecA (13.7%), lsaB (6.3%), msrA (4.2%), ant4 (3.2%), and tetM (2.1%); among sanitizer-resistance genes they were qacA/B (5.3%) and qacC (6.3%); and among biofilm, bap (4.2%), icaA (29.5%), icaD (41.1%). However, there was no statistically significant difference between organic and conventional dairy products, possibly due to the lack of synthetic antibiotic use on conventional farms during the sample collection period. Methicillin-resistant Staphylococcus aureus (MRSA) had their SCCmec identified as types I and IVc, and the methicillin-resistant coagulase-negative staphylococci had nontypeable SCCmec. These results suggest that there are antibiotic-resistant strains in both organic and conventional Minas Frescal cheese production in the state of São Paulo, Brazil. This supports the idea that improved quality control is needed from the milking stage up to the final product.

Multidrug resistant staphylococci isolated from pigs with exudative epidermitis in North eastern Region of India

Exudative epidermatitis or greasy pig disease (GPD) is a contagious disease of pig and endemic worldwide caused by toxigenic strains under genus Staphylococcus. The present study reported an outbreak of GPD in Champhai district of Mizoram adjoining to the southern border of Myanmar. A total of 60 samples were collected from 22 clinically affected animals and processed for isolation and identification of Staphylococcus spp. All the isolates were subjected to antimicrobial sensitivity assay, biofilm production assay and detection of virulence genes, biofilm genes and mec genes followed by cloning and sequencing for phylogenetic analysis. A total of 44 staphylococci belonged to four species (S. sciuri, S. aureus,S. lentus, and S. hyicus) were isolated. Majority of the isolates were multidrug resistant with maximum resistance against ampicillin, penicillin including vancomycin. None of the S. hyicus isolates was methicillin resistant (MRSH) but 66·67% isolates were MRSA. By PCR, mecA gene was detected in S. aureus (n = 2), S. sciuri (n = 4) and S. lentus (n = 3). Biofilm associated gene icaD was detected in S. aureus (n = 3), S. sciuri (n = 5), S. hyicus (n = 4) and S. lentus (n = 6). The exfoliative toxin genes (ehxB, shetA and tsst1) were detected in S. hyicus (n = 3) and S. aureus (n = 1) isolates. All the isolates were closely related with the isolates from pigs of China, Germany, Japan and USA. The pathogens might be transmitted through illegal migration of pigs from Myanmar to India.

Characterization of Enterococci- and ESBL-Producing Escherichia coli Isolated from Milk of Bovides with Mastitis in Egypt

This study aimed to investigate the prevalence and antimicrobial resistance of enterococci- and ESBL-producing E. coli isolated from milk of bovine mastitis cases in Egypt. Fifty milk samples of dairy animals were collected from localities in the Nile Delta region of Egypt. Isolates were identified using MALDI-TOF MS, and antibiotic susceptibility testing was performed by the broth microdilution method. PCR amplifications were carried out, targeting resistance-associated genes. Seventeen Enterococcus isolates and eight coliform isolates could be cultivated. Vancomycin resistance rate was high in Ent. faecalis. The VITEK 2 system confirmed all E. coli isolates as ESBL-producing. All Ent. faecalis isolates harbored erm(B), tetL and aac-aphD genes. The vanA gene was detected in Ent. faecalis isolate, vanB was found in other Enterococcus, while one isolate of E. casseliflavus exhibited the vanA gene. E. coli isolates exhibited high prevalence of erm(B) and tetL. E. coli isolates were analyzed by DNA microarray analysis. Four isolates were determined by O-serotyping as O8 (n = 1), O86 (n = 2) and O157 (n = 1). H-serotyping resulted in H11, H12, H21 (two isolates each) and one was of H16 type. Different virulence-associated genes were detected in E. coli isolates including lpfA, astA, celB, cmahemL, intI1 and intI2, and the iroN gene was identified by DNA microarray analysis.

Methicillin-Resistant Staphylococci and Macrococci at the Interface of Human and Animal Health

The global impact of methicillin-resistant Staphylococcus aureus (MRSA) clonal lineages on human and animal health continues, even considering the decreasing MRSA rates in some parts of the world [...].

Detection, molecular characterization, and antibiogram of multi-drug resistant and methicillin-resistant Staphylococcus aureus (MRSA) isolated from pets and pet owners in Malaysia

BACKGROUND

The emergence of multidrug-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Staphylococcus aureus (MDRSA) in animals and humans with continuous contact are a great zoonotic concern.

AIMS

This cross-sectional study was performed to investigate the carriage rate, genotypic characteristics, and to determine the antibiogram of S. aureus isolated from pets and pet owners in Malaysia.

METHODS

Nasal and oral swab samples from 40 cats, 30 dogs, and 70 pet owners were collected through convenient sampling. Presumptive colonies on mannitol salt agar were subjected to biochemical identification. S. aureus and MRSA were confirmed by PCR detection of nuc and mecA genes, respectively. Molecular profiles for antimicrobial resistance and virulence genes in S. aureus were also determined. The antibiogram was carried out via Kirby-Bauer test using 18 antibiotics.

RESULTS

17.5% of cats, 20% of dogs, and 27% of pet owners were S. aureus positive. MRSA was also detected in dogs, and pet owners. S. aureus isolates displayed high resistance against penicillin (72.7%), and amoxicillin/clavulanate (66.7%). 39.4% of S. aureus isolates showed multidrug-resistance traits, phenotypically. Molecular characterization of S. aureus revealed the presence of mecA, tetk, tetL, ermA, ermB, ermC, msrA, scn, chp, sak, sep, and sea genes.

CONCLUSION

This study showed the emergence of MRSA and MDRSA in pets and pet owners in Malaysia. The antibiogram findings showed resistance of S. aureus to multiple antibiotics. Furthermore, molecular analysis of immune evasion cluster (IEC) strongly suggests the spread of animal-adapted S. aureus lineages among pets and pet owners.

Species Distribution, Antimicrobial Resistance, and Enterotoxigenicity of Non-aureus Staphylococci in Retail Chicken Meat

Non-aureus staphylococci (NAS), including coagulase-negative staphylococci, have emerged as important causes of opportunistic infections in humans and animals and a potential cause of staphylococcal food poisoning. In this study, we investigated (i) the staphylococcal species profiles of NAS in in retail chicken meat, (ii) the phenotypic and genotypic factors associated with antimicrobial resistance in the NAS isolates, and (iii) the prevalence of classical and newer staphylococcal enterotoxin (SE) genes. A total of 58 NAS of nine different species were isolated from retail raw chicken meat samples. The occurrence of multidrug resistance in the NAS, particularly S. agnetis and S. chromogenes, with high resistance rates against tetracycline or fluoroquinolones were confirmed. The tetracycline resistance was associated with the presence of tet(L) in S. chromogenes and S. hyicus or tet(K) in S. saprophyticus. The occurrence of fluoroquinolone resistance in S. agnetis and S. chromogenes was usually associated with mutations in the quinolone resistance determining regions (QRDR) of gyrA and parC. In addition, the frequent presence of SE genes, especially seh, sej, and sep, was detected in S. agnetis and S. chromogenes. Our findings suggest that NAS in raw chicken meat can have potential roles as reservoirs for antimicrobial resistance and enterotoxin genes.

Technological Applications of Macrococcus caseolyticus and its Impact on Food Safety

Macrococcus spp. are Gram-positive cocci that belong to the Staphylococcaceae family; they are closely related to staphylococci, but, unlike staphylococci, they are not considered as human pathogens. Macrococcus spp. are recognized as relevant veterinary pathogens, and their presence has been reported in food products of animal origin. Macrococcus caseolyticus, the most studied species of the Macrococcus genus, is associated with the development of aroma and flavor in fermented foods and is, thus, used as starter cultures in fermentations. However, certain important issues regarding food safety must be taken into account when employing these microorganisms in fermentations. Recent studies have reported the presence of genes associated with resistance to methicillin and other antibiotics in M. caseolyticus. This can be harmful to human health as these genes can be transferred to other bacteria present in the food, mainly staphylococcal species. This work, therefore, aims to highlight the importance of a more critical view on the presence of macrococci in foods and the possible indirect risks to human health.

Comparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats

Food poisoning due to the consumption of Staphylococcus aureus contaminated food is a major health problem worldwide. In this study, we sequenced the genomes of ten plasmid-bearing S. aureus strains isolated from retail beef, chicken, turkey, and pork. The chromosomes of the strains varied in size from 2,654,842 to 2,807,514 bp, and a total of 25 plasmids were identified ranging from 1.4 to 118 kb. Comparative genomic analysis revealed similarities between strains isolated from the same retail meat source, indicating an origin-specific genomic composition. Genes known to modulate attachment, invasion, and toxin production were identified in the 10 genomes. Strains from retail chicken resembled human clinical isolates with respect to virulence factors and genomic islands, and retail turkey and pork isolates shared similarity with S. aureus from livestock. Most chromosomes contained antimicrobial resistance, heavy metal resistance, and stress response genes, and several plasmids contained genes involved in antimicrobial resistance and virulence. In conclusion, the genomes of S. aureus strains isolated from retail meats showed an origin-specific composition and contained virulence and antimicrobial resistance genes similar to those present in human clinical isolates.

Human mecC-Carrying MRSA: Clinical Implications and Risk Factors

A new methicillin resistance gene, named mecC, was first described in 2011 in both humans and animals. Since then, this gene has been detected in different production and free-living animals and as an agent causing infections in some humans. The possible impact that these isolates can have in clinical settings remains unknown. The current available information about mecC-carrying methicillin resistant S. aureus (MRSA) isolates obtained from human samples was analyzed in order to establish its possible clinical implications as well as to determine the infection types associated with this resistance mechanism, the characteristics of these mecC-carrying isolates, their possible relation with animals and the presence of other risk factors. Until now, most human mecC-MRSA infections have been reported in Europe and mecC-MRSA isolates have been identified belonging to a small number of clonal complexes. Although the prevalence of mecC-MRSA human infections is very low and isolates usually contain few resistance (except for beta-lactams) and virulence genes, first isolates harboring important virulence genes or that are resistant to non-beta lactams have already been described. Moreover, severe and even fatal human infection cases have been detected. mecC-carrying MRSA should be taken into consideration in hospital, veterinary and food safety laboratories and in prevention strategies in order to avoid possible emerging health problems.

Prevalence of Panton-Valentine leukocidin in methicillin-resistant Staphylococcus aureus clinical isolates at a university hospital in Northern Cyprus: a pilot study

Objective

Panton-Valentine leukocidin (PVL)-positive methicillin-resistant Staphylococcus aureus (MRSA) is a healthcare problem worldwide. There are no reports on the virulence characteristics of MRSA in Northern Cyprus (NC). This study aimed to determine the presence of pvl among MRSA isolates from patients admitted to a university hospital in NC using molecular methods. Fifty S. aureus strains were included in this study. BD Phoenix automated identification system was used for bacterial identification and antibiotic susceptibility testing. Methicillin resistance was confirmed by disc diffusion assay. Presence of nuc and mecA genes was tested by multiplex PCR. Detection of pvl gene was performed by single-target PCR.

Results

Out of 50 S. aureus isolates identified as MRSA by BD Phoenix system, 3 were susceptible to cefoxitin with disc diffusion assay and were confirmed as methicillin-sensitive S. aureus (MSSA). All isolates (n = 50, 100%) tested positive for the presence nuc gene and 68% (n = 34/50) were mecA positive. pvl was detected in 27.7% (n = 13/47) of the MRSA isolates. Among PVL-positive MRSA isolates, 69.2% (9/13) were inpatients. PVL-MRSA was more common in isolates from deep tracheal aspirate (30.8%, 4/13) and abscess/wound (23.1%, 3/13). This represents the first study of PVL presence among MRSA in hospital setting in NC.

Methicillin-Resistant Macrococcus bohemicus Encoding a Divergent SCCmecB Element

A methicillin-resistant Macrococcus isolate from canine otitis, H889678/16/1, was whole-genome sequenced using HiSeq technology to identify the species, antimicrobial resistance determinates and their genomic context. H889678/16/1 belonged to the newly described species Macrococcus bohemicus. It encoded mecB within a novel SCCmec element most similar to that of Macrococcus canis KM45013^T. This SCCmec_H889678/16/1 element also encoded blaZ_m and fusC, but no other resistance determinates were found in the H889678/16/1 genome. The ccrA and ccrB recombinase genes within SCCmec_H889678/16/1 were distinct from those previously described in staphylococci and macrococci and therefore designated here as ccrAm3 and ccrBm3. Our study represents, to the best of our knowledge, the first description of mecB being encoded by M. bohemicus and of methicillin resistance in this species. Furthermore, the SCCmec described here is highly dissimilar to other such elements and encodes novel ccr genes. Our report demonstrates a wider distribution of mecB among Macrococcus species and expands the genomic context in which mecB may be found. The potential for dissemination of mec genes from Macrococcus to related but more pathogenic Staphylococcus species highlights the need to understand the epidemiology of these genes in macrococci.

Macrococcus canis contains recombinogenic methicillin resistance elements and the mecB plasmid found in Staphylococcus aureus

OBJECTIVES

To analyse the genetic context of mecB in two Macrococcus canis strains from dogs, compare the mecB-containing elements with those found in other Macrococcus and Staphylococcus species, and identify possible mobilizable mecB subunits.

METHODS

Whole genomes of the M. canis strains Epi0076A and KM0218 were sequenced using next-generation sequencing technologies. Multiple PCRs and restriction analysis confirmed structures of mecB-containing elements, circularization and recombination of mecB subunits.

RESULTS

Both M. canis strains contained novel composite pseudo (Ψ) staphylococcal cassette chromosome mec (SCCmec) elements. Integration site sequences for SCC flanked and subdivided composite ΨSCCmecEpi0076A (69569 bp) into ΨSCC1Epi0076A-ΨSCCmecEpi0076A-ΨSCC2Epi0076A and composite ΨSCCmecKM0218 (24554 bp) into ΨSCCKM0218-ΨSCCmecKM0218. Putative γ-haemolysin genes (hlgB and hlgC) were found at the 3' end of both composite elements. ΨSCCmecKM0218 contained a complete mecB gene complex (mecIm-mecR1m-mecB-blaZm) downstream of a new IS21-family member (ISMaca1). ΨSCCmecEpi0076A carried a blaZm-deleted mecB gene complex similar to that reported in 'Macrococcus goetzii' CCM4927T. A second mecB gene was found on the 81325 bp MDR plasmid pKM0218 in KM0218. This plasmid contained a complete Tn6045-associated mecB gene complex distinct from that of ΨSCCmecKM0218. pKM0218 was almost identical to the mecB-containing plasmid recently reported in Staphylococcus aureus (overall 99.96% nucleotide identity). Mobilization of mecB within an unconventional circularizable structure was observed in Epi0076A as well as chromosomal plasmid insertion via recombination of mecB operons in KM0218.

CONCLUSIONS

Our findings provide evidence of both the continuing evolution of mecB-containing elements in macrococci and M. canis as a potential source of the mecB-containing plasmid found in staphylococci.

Borderline resistance to oxacillin in Staphylococcus aureus after treatment with sub-lethal sodium hypochlorite concentrations

Surface disinfectants are regularly used in prophylactic and infection control measures. Concern has been raised whether residues of sub-inhibitory disinfectant concentrations may constitute a selective pressure and could contribute to the development of strains which are tolerant and/or resistant to biocides including antibiotics. The current study investigated whether Staphylococcus (S.) aureus ATCC® 29213™ and ATCC® 6538™ would change their growth characteristics and antimicrobial susceptibility profiles after prolonged treatment with sub-inhibitory concentrations of sodium hypochlorite (NaOCl). NaOCl is a fast-acting disinfectant with a broad-spectrum activity, inexpensive and widely used in healthcare and the food production industry. Minimum inhibitory concentration (MIC) for NaOCl was determined by broth macrodilution according to the guidelines for disinfectant efficacy testing provided by the German Veterinary Medical Society. Serial passages after 24 h and 72 h, respectively, in defined sub-inhibitory concentrations of NaOCl resulted in a number of phenotypic variants. Two of these variants, derived from S. aureus ATCC® 29213™, showed elevated MICs of oxacillin and were considered as in vitro-generated borderline oxacillin-resistant S. aureus (BORSA). Transmission electron microscopy revealed a significantly thickened cell wall in these isolates, a phenomenon that has also been described for Listeria monocytogenes after low-level exposure to NaOCl. Whole genome sequencing revealed an early stop codon in the gene coding for the GdpP protein and thereby abolishing the function of this gene. GdpP represents a phosphodiesterase that regulates gene expression, and loss of function of the GdpP protein has been described in association with borderline oxacillin resistance. Our findings suggest that a mutation in the GdpP protein gene and morphological changes of the cell wall were induced by repeated exposure to sub-lethal NaOCl concentrations, and most likely accounted for a BORSA phenotype in two variants derived from S. aureus ATCC® 29213™.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC

BACKGROUND

Methicillin resistance in staphylococci is conferred by an alternative PBP (PBP2a/2') with low affinity for most β-lactam antibiotics. PBP2a is encoded by mecA, which is carried on a mobile genetic element known as SCCmec. A variant of mecA, mecC, was described in 2011 and has been found in Staphylococcus aureus from humans and a wide range of animal species as well as a small number of other staphylococcal species from animals.

OBJECTIVES

We characterized a novel mecC allotype, mecC3, encoded by an environmental isolate of Staphylococcus caeli cultured from air sampling of a commercial rabbit holding.

METHODS

The S. caeli isolate 82BT was collected in Italy in 2013 and genome sequenced using MiSeq technology. This allowed the assembly and comparative genomic study of the novel SCCmec region encoding mecC3.

RESULTS

The study isolate encodes a novel mecA allotype, mecC3, with 92% nucleotide identity to mecC. mecC3 is encoded within a novel SCCmec element distinct from those previously associated with mecC, including a ccrAB pairing (ccrA5B3) not previously linked to mecC.

CONCLUSIONS

This is the first description of the novel mecC allotype mecC3, the first isolation of a mecC-positive Staphylococcus in Italy and the first report of mecC in S. caeli. Furthermore, the SCCmec element described here is highly dissimilar to the archetypal SCCmec XI encoding mecC in S. aureus and to elements encoding mecC in other staphylococci. Our report highlights the diversity of mecC allotypes and the diverse staphylococcal species, ecological settings and genomic context in which mecC may be found.

Genome Sequence of a Highly Virulent pvl-positive Vancomycin intermediate- resistant Staphylococcus aureus Sequence Type 30

Background:

Staphylococcus aureus isolates expressing the Panton-Valentine Leukocidin (PVL) have been related to a wide range of diseases. Recently, pvl-positive community-associated methicillin-resistant S. aureus belonging to USA1100 (ST30/CC30/SCCmec IV) lineage has emerged in Brazilian hospitals.

Objective:

The aim of this work was to sequence the genome of a pvl-positive USA1100 Vancomycin- Intermediate-Resistant S. aureus (VISA) isolate from Rio de Janeiro, Brazil.

Methods:

The 13420 genome was sequenced using the HiSeq 2500 platform. The draft genome, plasmids annotation, and genome analysis were performed using RAST. Comparison of the relative pvl gene expression of six S. aureus isolates was performed by qRT-PCR.

Results:

The isolate presented the ϕPVL phage codifying for the H2b PVL protein isoform, and another prophage carrying a PVL variant named lukF and lukS-PV.2. The 13420 genome presented a high number of virulence determinants, such as genes codifying for serine-protease proteins, enterotoxins (egc), the immune evasion cluster (IEC), adhesion proteins, spermine/spermidine acetyltransferase gene (blt), superantigen-like proteins, as well as the ica operon. Point mutations at vraS, tcaA, and tcaB genes were detected. Moreover, the PVL mRNA relative expression of the 13420 isolate was five times higher than mRNA PVL levels of the USA300/ST8 reference strain.

Conclusion:

We described for the first time the genome sequence of a VISA isolate harboring two pvl-associated genes and other virulence factors that may improve the USA1100/ST30 lineage fitness and impact its pathogenicity and spreading at Brazilian hospitals.

Characterization of Staphylococci and Streptococci Isolated from Milk of Bovides with Mastitis in Egypt

The aim of this study was to characterize staphylococci and streptococci in milk from Egyptian bovides. In total, 50 milk samples were collected from localities in the Nile Delta region of Egypt. Isolates were cultivated, identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and antibiotic susceptibility testing was performed by the broth microdilution method. PCR amplifications were carried out, targeting resistance-associated genes. Thirty-eight Staphylococcus isolates and six Streptococcus isolates could be cultivated. Staphylococcus aureus isolates revealed a high resistance rate to penicillin, ampicillin, clindamycin, and erythromycin. The mecA gene defining methicillin-resistant Staphylococcus aureus, erm(C) and aac-aphD genes was found in 87.5% of each. Coagulase-negative staphylococci showed a high prevalence of mecA, blaZ and tetK genes. Other resistance-associated genes were found. All Streptococcus dysgalactiae isolates carried blaZ, erm(A), erm(B), erm(C) and lnuA genes, while Streptococcus suis harbored erm(C), aphA-3, tetL and tetM genes, additionally. In Streptococcus gallolyticus, most of these genes were found. The Streptococcus agalactiae isolate harbored blaZ, erm(B), erm(C), lnuA, tetK, tetL and tetM genes. Streptococcus agalactiae isolate was analyzed by DNA microarray analysis. It was determined as sequence type 14, belonging to clonal complex 19 and represented capsule type VI. Pilus and cell wall protein genes, pavA, cadD and emrB/qacA genes were identified by microarray analysis.

Novel strategies for rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes.

AREAS COVERED

We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence.

EXPERT OPINION

Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.

Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.

The Novel Macrolide Resistance Genes mef(D), msr(F), and msr(H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus

Chromosomal resistance islands containing the methicillin resistance gene mecD (McRI _mecD ) have been reported in Macrococcus caseolyticus Here, we identified novel macrolide resistance genes in Macrococcus canis on similar elements, called McRI _msr These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (rpsI), delimited by characteristic attachment (att) sites, and carried a related site-specific integrase gene (int) at the 5' end. They carried novel macrolide resistance genes belonging to the msr family of ABC subfamily F (ABC-F)-type ribosomal protection protein [msr(F) and msr(H)] and the macrolide efflux mef family [mef(D)]. Highly related mef(D)-msr(F) fragments were found on diverse McRI _msr elements in M. canis, M. caseolyticus, and Staphylococcus aureus Another McRI _msr -like element identified in an M. canis strain lacked the classical att site at the 3' end and carried the msr(H) gene but no neighboring mef gene. The expression of the novel resistance genes in S. aureus resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the mef(D)-msr(F) operon, the msr(F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI _msr and the mef(D)-msr(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI _msr in different Macrococcus species and S. aureus indicates that these islands have a potential for dissemination of antibiotic resistance within the Staphylococcaceae family.

What's new in mechanisms of antibiotic resistance in bacteria of clinical origin?

The discovery, commercialization and administration of antibiotics revolutionized the world of medicine in the middle of the last century, generating a significant change in the therapeutic paradigm of the infectious diseases. Nevertheless, this great breakthrough was soon threatened due to the enormous adaptive ability that bacteria have, through which they are able to develop or acquire different mechanisms that allow them to survive the exposure to antibiotics. We are faced with a complex, multifactorial and inevitable but potentially manageable threat. To fight against it, a global and multidisciplinary approach is necessary, based on the support, guidance and training of the next generation of professionals. Nevertheless, the information published regarding the resistance mechanisms to antibiotics are abundant, varied and, unfortunately, not always well structured. The objective of this review is to structure the, in our opinion, most relevant and novel information regarding the mechanisms of resistance to antibiotics that has been published from January 2014 to September 2019, analysing their possible clinical and epidemiological impact.

The Porcine Nasal Microbiota with Particular Attention to Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Germany-A Culturomic Approach

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) remains a serious public health threat. Porcine nasal cavities are predominant habitats of LA-MRSA. Hence, components of their microbiota might be of interest as putative antagonistically acting competitors. Here, an extensive culturomics approach has been applied including 27 healthy pigs from seven different farms; five were treated with antibiotics prior to sampling. Overall, 314 different species with standing in nomenclature and 51 isolates representing novel bacterial taxa were detected. Staphylococcus aureus was isolated from pigs on all seven farms sampled, comprising ten different spa types with t899 (n = 15, 29.4%) and t337 (n = 10, 19.6%) being most frequently isolated. Twenty-six MRSA (mostly t899) were detected on five out of the seven farms. Positive correlations between MRSA colonization and age and colonization with Streptococcus hyovaginalis, and a negative correlation between colonization with MRSA and Citrobacter spp. were found (p < 0.05). Of 209 non-S. aureus members of the Staphylococcaceae family, 25 isolates (12.0%) from three out of the seven farms exhibited methicillin resistance, including two Macrococcus goetzii isolates carrying the mecB gene. Among 125 Enterobacterales, none tested positive for extended-spectrum beta-lactamase (ESBL) and carbapenemase production. The high frequency of methicillin-resistant staphylococci supports the need for enhanced efforts within the “One Health” concept to manage the antibiotic resistance crisis in the human and veterinary medicine sector.

Molecular Epidemiology of Staphylococcus aureus Lineages in Wild Animals in Europe: A Review

Staphylococcus aureus is an opportunist pathogen that is responsible for numerous types of infections. S. aureus is known for its ability to easily acquire antibiotic resistance determinants. Methicillin-resistant S. aureus (MRSA) is a leading cause of infections both in humans and animals and is usually associated with a multidrug-resistant profile. MRSA dissemination is increasing due to its capability of establishing new reservoirs and has been found in humans, animals and the environment. Despite the fact that the information on the incidence of MRSA in the environment and, in particular, in wild animals, is scarce, some studies have reported the presence of these strains among wildlife with no direct contact with antibiotics. This shows a possible transmission between species and, consequently, a public health concern. The aim of this review is to better understand the distribution, prevalence and molecular lineages of MRSA in European free-living animals.

Coagulase-negative staphylococci carrying cfr and PVL genes, and MRSA/MSSA-CC398 in the swine farm environment

This work aimed at characterizing four Staphylococcus aureus and 68 coagulase-negative staphylococci (CoNS), recovered from the air and liquid manure tank of two swine farms with intensive- and semi-extensive-production types, for their antimicrobial resistance pheno-/genotypes and their virulence gene content. Molecular typing was performed by spa typing, MLST, agr typing, and SCCmec typing, where applicable. Conjugation experiments were performed to assess the transferability of the linezolid resistance gene cfr, and its genetic environment was determined by Whole-Genome-Sequencing. The four S. aureus (intensive-production farm, IP-farm) were typed as t011-agrI-CC398-ST398, were scn-negative and two of them were methicillin-resistant (MRSA) with the mecA gene (SCCmec-V). Multidrug resistance was seen in 87 % of the CoNS. Statistically significant differences among the antimicrobial resistance rates of CoNS from the two farms were observed for cefoxitin, aminoglycosides, tetracycline, ciprofloxacin and trimethoprim-sulfamethoxazole. Eight methicillin-resistant CoNS, which were recovered from the IP-farm, carried the mecA gene. One S. simulans isolate was PVL-positive and three S. cohnii eta-positive. One S. equorum and one S. arlettae showed linezolid resistance and carried the cfr gene (IP-farm), which was non-transferable by conjugation into S. aureus. The cfr genetic context in both isolates was identical, with the lsa(B) gene located upstream of cfr. The environment of swine farms might contribute to the dissemination of CoNS that show multidrug resistance and harbor important virulence factors.