Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus

Genetic profile and characterization of antimicrobial resistance in Acinetobacter baumannii post-COVID-19 pandemic: a study in a tertiary hospital in Recife, Brazil

AIMS

To investigate the genetic profile and characterize antimicrobial resistance, including the main β-lactam antibiotic resistance genes, in Acinetobacterbaumannii isolates from a tertiary hospital in Recife-PE, Brazil, in the post-COVID-19 pandemic period.

METHODS AND RESULTS

Acinetobacter baumannii isolates were collected between 2023 and 2024 from diverse clinical samples. Antimicrobial resistance testing followed standardized protocols, with β-lactamase-encoding genes detected via PCR and sequencing. Investigation into ISAba1 upstream of blaOXA-carbapenemase and blaADC genes was also conducted. Genetic diversity was assessed through ERIC-PCR. Among the 78 A. baumannii, widespread resistance to multiple antimicrobials was evident. Various acquired β-lactamase-encoding genes (blaOXA-23,-24,-58,-143, blaVIM, and blaNDM) were detected. Furthermore, this is the first report of blaVIM-2 in A. baumannii isolates harboring either the blaOXA-23-like or the blaOXA-143 gene in Brazil. Molecular typing revealed a high genetic heterogeneity among the isolates, and multi-clonal dissemination.

CONCLUSION

The accumulation of genetic resistance determinants underscores the necessity for stringent infection control measures and robust antimicrobial stewardship programs to curb multidrug-resistant strains.

Virulent Klebsiella pneumoniae ST11 clone carrying blaKPC and blaNDM from patients with and without COVID-19 in Brazil

AIMS

Investigated and compared the occurrence of virulence genes fimH, mrkD, irp2, entB, cps, rmpA, and wabG, resistance genes blaKPC and blaNDM, and the genetic variability and clonal relationship of 29 Klebsiella pneumoniae clinical isolates of patients with and without COVID-19, from a hospital in Brazil.

METHODS AND RESULTS

All isolates were resistant to beta-lactams. The genes were investigated by PCR, and for molecular typing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and MLST were used. The detection of blaNDM was greater (n = 23) when compared to that of blaKPC (n = 14). The virulence genes that most occurred were fimH, entB, cps, and wabG, which are responsible for adhesins, siderophore enterobactin, capsule, and lipopolysaccharides, respectively. Among the isolates, 21 distinct genetic profiles were found by ERIC-PCR, with multiclonal dissemination. Four isolates belonged to the ST11 clone.

CONCLUSIONS

The occurrence of the ST11 is worrying as it is a high-risk clone involved in the dissemination of virulent strains throughout the world.

Molecular Epidemiology of Ralstonia pseudosolanacearum Phylotype I Strains in the Southwest Indian Ocean Region and Their Relatedness to African Strains

The increasing requirement for developing tools enabling fine strain traceability responsible for epidemics is tightly linked with the need to understand factors shaping pathogen populations and their environmental interactions. Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is one of the most important plant diseases in tropical and subtropical regions. Sadly, little, outdated, or no information on its epidemiology is reported in the literature, although alarming outbreaks are regularly reported as disasters. A large set of phylotype I isolates (n = 2,608) was retrieved from diseased plants in fields across the Southwest Indian Ocean (SWIO) and Africa. This collection enabled further assessment of the epidemiological discriminating power of the previously published RS1-MLVA14 scheme. Thirteen markers were validated and characterized as not equally informative. Most had little infra-sequevar polymorphism, and their performance depended on the sequevar. Strong correlation was found with a previous multilocus sequence typing scheme. However, 2 to 3% of sequevars were not correctly assigned through endoglucanase gene sequence. Discriminant analysis of principal components (DAPC) revealed four groups with strong phylogenetic relatedness to sequevars 31, 33, and 18. Phylotype I-31 isolates were highly prevalent in the SWIO and Africa, but their dissemination pathways remain unclear. Tanzania and Mauritius showed the greatest diversity of RSSC strains, as the four DAPC groups were retrieved. Mauritius was the sole territory harboring a vast phylogenetic diversity and all DAPC groups. More research is still needed to understand the high prevalence of phylotype I-31 at such a large geographic scale.

nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples

Multilocus sequence typing (MLST) is one of the most commonly used methods for studying microbial lineage worldwide. However, the traditional MLST process using Sanger sequencing is time-consuming and expensive. We have designed a workflow that simultaneously sequenced seven full-length housekeeping genes of 96 meticillin-resistant Staphylococcus aureus isolates with dual-barcode multiplexing using just a single flow cell of an Oxford Nanopore Technologies MinION system, and then we performed bioinformatic analysis for strain typing. Fifty-one of the isolates comprising 34 sequence types had been characterized using Sanger sequencing. We demonstrate that the allele assignments obtained by our nanopore workflow (nanoMLST, available at https://github.com/jade-nhri/nanoMLST) were identical to those obtained by Sanger sequencing (359/359, with 100 % agreement rate). In addition, we estimate that our multiplex system is able to perform MLST for up to 1000 samples simultaneously; thus, providing a rapid and cost-effective solution for molecular typing.

Label-Free Immunoassay for Multiplex Detections of Foodborne Bacteria in Chicken Carcass Rinse with Surface Plasmon Resonance Imaging

The frequent outbreaks of foodborne pathogens have stimulated the demand of biosensors capable of rapid and multiplex detection of contaminated food. In this study, surface plasmon resonance imaging (SPRi) was used in simultaneous label-free detection of multiple foodborne pathogens, mainly Salmonella spp. and Shiga-toxin producing Escherichia coli (STEC), in commercial chicken carcass rinse. The antibodies were immobilized on the same SPRi sensor chip as a label-free immunoassay. Their immobilization concentrations were optimized to be ranging from 0.25 to 1.0 mg/mL, and independent of pH values. This label-free immunoassay achieved 10⁶ colony-forming unit (CFU)/mL limit of detection for Salmonella, which was further improved to 1.0 CFU/mL with overnight bacteria enrichment. The injected samples with different bacteria, Salmonella Enteritidis, STEC, and Listeria monocytogenes, have been identified by the same biochip. Moreover, the SPRi signals revealed complex interference effects among coexisting bacteria species in heterogeneous bacteria solutions. This SPRi-based immunoassay demonstrates the great potential in high-throughput screening of multiple pathogenic bacteria coexisting in chicken carcass rinse. The reliability of antibody immobilization and cross-reactions of different antibodies on the same biochip are the major challenges of practical application of SPRi.

Genetic Diversity and Virulence Factors of S. aureus Isolated from Food, Humans, and Animals

Staphylococcus aureus is a commensal bacterium in humans and animals able to adapt to multiple environments. The aim of this study was to compare the genetic diversity and virulence profiles of strains of S. aureus isolated from food (29 strains), humans (43 strains), and animals (8 strains). 80 lipase-producing strains belonging to a biobank of 360 isolates, identified phenotypically as S. aureus, were selected. Confirmation of the species was made by amplifying the spA gene and 80% (64/80) of the strains were confirmed within this species. The virulence profile of each of the isolates was determined by PCR. The seA gene coding for enterotoxin A was found in 53.1% of the strains, the saK gene, which codes for Staphylokinase, was amplified in 57.8% of the strains, and, finally, the hlB gene coding for β-Hemolysin was amplified in 17.2%. The profile of antimicrobial resistance was determined by the Kirby Bauer method showing that the strains from food presented greater resistance to erythromycin (40.7%) and ciprofloxacin (18.5%) while in strains isolated from humans were to erythromycin (48.4%) and clindamycin (21.2%). Also, in strains from animals, a high resistance to erythromycin was observed (75%). The frequency of MRSA was 12.5% due to the presence of the mec gene and resistance to cefoxitin. Of the total strains, 68.7% were typed by PCR-RFLP of the coa gene using the AluI enzyme; derived from this restriction, 17 profiles were generated. Profile 4 (490 bp, 300 bp) was the most frequent, containing a higher number of strains with a higher number of virulence factors and antimicrobial resistance, which is associated with greater adaptation to different environments. In this study, a wide genetic diversity of strains of S. aureus from different foods, humans, and animals was found. This demonstrates evolution, genetic versatility, and, therefore, the adaptation of this microorganism in different environments.

Antibiotic Susceptibility, Virulence Pattern, and Typing of Staphylococcus aureus Strains Isolated From Variety of Infections in India

Staphylococcus aureus is one of the major causes of nosocomial infections. This organism produces powerful toxins and cause superficial lesions, systemic infections, and several toxemic syndromes. A total of 109 S. aureus strains isolated from a variety of infections like ocular diseases, wound infection, and sputum were included in the study. Minimum inhibitory concentration (MIC) was determined against 8 antimicrobials. PCR determined the presence of 16S rRNA, nuc, mecA, czrC, qacA/B, pvl, and toxin genes in S. aureus isolates. Pulse-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), SCCmec, spa-, and agr-typing and serotyping determined the diversity among them. All isolates of S. aureus were resistant to two or more than two antibiotics and generated 32 resistance patterns. These isolates were positive for 16S rRNA and S. aureus-specific nuc gene, but showed variable results for mecA, czrC, and qacA/B and pvl genes. Of the 32 methicillin-resistant S. aureus (MRSA), 13 strains carried SCCmec type V, seven type IV, two type III, and nine carried unreported type UT6. Of the 109 strains, 98.2% were positive for hlg, 94.5% for hla, 86.2% for sei, 73.3% for efb, 70.6% for cna, 30.2% for sea, and 12.8% for sec genes. Serotypes VII and VI were prevalent among S. aureus strains. PFGE analysis grouped the 109 strains into 77 clusters. MLST classified the strains into 33 sequence types (ST) and eight clonal complexes (CCs) of which 12 were singletons, and two belong to new allelic profiles. Isolates showed 46 spa-types that included two new spa-types designated as t14911 and t14912. MRSA and methicillin-susceptible S. aureus (MSSA) isolates were diverse in terms of antibiotic resistance pattern, toxin genotypes, SCCmec types, serotypes and PFGE, MLST, and spa-types. However, few isolates from eye infection and wound infection belong to CC239, ST239, and spa-type t037/t657. The study thus suggests that S. aureus strains are multidrug resistant, virulent, and diverse irrespective of sources and place of isolation. These findings necessitate the continuous surveillance of multidrug-resistant and virulent S. aureus and monitoring of the transmission of infection.

Molecular typing of Staphylococcus aureus from different sources by RAPD-PCR analysis

Staphylococcus aureus is an opportunistic bacterium which is carried as a normal flora organism but has a major role in the epidemiology and pathogenesis of different staphylococcal infections in humans and animals. Fifty S. aureus isolated from banknotes, foods, human infections and bovine mastitis were subjected to DNA fingerprinting by randomly amplified polymorphic DNA (RAPD) analysis to examine their genotypic polymorphism and investigate the amount of genetic relatedness among these various isolates. At 100% RAPD profile similarity level, isolates were classified into four, five and seven groups of the same clone, according to the RAPDPCR with OLP6, OLP11 and OLP13 primers, respectively. Amplification of the isolates resulted in several polymorphic bands ranged from >50 to >1500 bp in size. Maximum number of bands was obtained by primer OLP13 which produced seven bands in bovine mastitis isolates. Most polymorphisms were observed in isolates of bovine mastitis and the lowest were associated with human infections isolates. There was no relationship between the RAPD patterns and the sources of isolates, except the three clusters which showed host specificity and only included the strains from the same sources. The results confirm the wide genotypic diversity of the studied S. aureus strains. RAPD-PCR technique can be a valuable tool for assessing the genetic relationship, detection of polymorphism in S. aureus and tracing the sources and management of S. aureus infections.

Coagulase gene polymorphisms of Staphylococcus aureus isolates from patients at Kosti Teaching Hospital, Sudan

Background

Staphylococcus aureus is a common cause of nosocomial infections. Epidemiological typing of S. aureus enables control of its spread. The objective of this study was to investigate coagulase gene polymorphisms of S. aureus isolated from patients at Kosti Hospital in Sudan.

Methods

In total, 110 S. aureus isolates were recovered from 110 patients who were enrolled in the study. S. aureus strains were isolated on blood agar and MacConkey agar and then identified by conventional tests. Resistance to methicillin was determined by detection of the mecA gene. Polymorphism in the coagulase gene (coa) was investigated using PCR followed by AluI RFLP analysis.

Results

Methicillin-resistant S. aureus accounted for 62/110 (56 %) of the isolates. PCR of the coa gene showed two different amplicons, one of 680 bp detected in 83/110 (75.5 %) of the isolates and one of 790 bp detected in 27/110 (24.5 %). When digested with the AluI enzyme, the 790 bp amplicon resulted in three restriction fragments of 500, 210 and 80 bp (coa1). Restriction of the 680 bp amplicon gave two patterns; the first (coa2) was found in 22/110 (20 %) of the isolates and showed four fragments of 210, 210, 180 and 80 bp, and the second (coa3) was found in 61/110 (55.5 %) and revealed three fragments of 390, 210 and 80 bp. Most of the coa3 isolates (75.4%) were methicillin-resistant.

Conclusion

Three polymorphic genotypes of S. aureus were identified in patients at Kosti Hospital. The coa3 genotype was the predominant one and was mostly detected in methicillin-resistant isolates.

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.

Antibiotic Based Phenotype and Hospital Admission Profile are the Most Likely Predictors of Genotyping Classification of MRSA

Background:

Methicillin-resistant Staphylococcus aureus (MRSA) infection is associated with increased morbidity, mortality, and financial burdens. Phenotyping methods are used to classify MRSA as either health care MRSA (HA-MRSA) or community-associated MRSA (CA-MRSA). Recent studies suggested the phenotyping methods are not always reliable, based on a lack of concordance with genotyping results.

Objective:

In this study, concordance of classification methods based on clinical characteristics or antibiotic susceptibility compared to the gold standard genotyping was assessed in the classification of MRSA.

Methods:

We compared the genotypes and phenotypes of MRSA in 133 samples taken from patients in Saudi Arabia. Statistical analyses included concordance, specificity and sensitivity, and logistic regression modeling.

Results:

There was fair a definite agreement between the health care risk and infection type methods (p < .001), but no statistically significant agreement between the susceptibility pattern and health care risk methods (p = 243), and between susceptibility pattern and infection type methods (p = .919). Reduced multiple regression modelling suggested the potential of a phenotyping-based method of antibiotic susceptibility pattern (OR = 15.47, p < .001) in conjunction with hospital admission profile(OR = 2.87, p = .008) to accurately identify MRSA as HA-MRSA and CA-MRSA.

Conclusion:

The use of a standardized phenotyping technique, using susceptibility pattern and hospital admission profiles to classify MRSA infections as either HA-MRSA or CA-MRSA, would facilitate diagnosis, infection control efforts, prevention, and assignment of appropriate therapies. The ability to use phenotyping in the classification of these strains would improve efforts to contend with this adept and evolving bacterial organism.

Identification of Major Sequence Types among Multidrug-Resistant Staphylococcus epidermidis Strains Isolated from Infected Eyes and Healthy Conjunctiva

We examined the presence of virulence and antibiotic resistance genes, SCCmec types and determined the genomic diversity among ocular S. epidermidis isolates (patients-23, healthy controls-29). PCR determined the presence of antibiotic resistance genes, virulence genes and SCCmec types among all isolates. MLST and PFGE determined the genomic relatedness among them. All isolates of S. epidermidis showed resistance to at least one class of antibiotics of which 48 isolates were multidrug resistant and carried ARGs. Thirty-five isolates were methicillin resistant and carried mecA gene. Majority of the isolates were resistant to fluoroquinolones and showed mutation in gyrA, parC, and parE genes, however, few isolates showed additional novel mutations in parC gene. Of the MRSE strains, 17 strains carried SCCmec type IV, four type V, two type II, and two UT4. Seven strains carried novel combination of ccr complex and SCCmercury element, not reported earlier. All the S. epidermidis strains harbored icaA and icaD genes, 47 carried ACME operon, and 50 contained IS256. A noteworthy finding was the presence of ST179 among 43% of infected eye isolates an observation rarely reported among S. epidermidis. PFGE and MLST analysis showed genomic diversity among them. Statistical analysis suggests that few healthy conjunctiva isolates had characteristics similar to infected eye isolates. S. epidermidis strains carrying mecA gene are multidrug resistant, virulent and diverse irrespective of sources of isolation. IS256 cannot be used as marker to differentiate isolates of infected eye from healthy conjunctiva.

Concordance of results of blood and tissue cultures from patients with pyogenic spondylitis: a retrospective cohort study

OBJECTIVES

To investigate the concordance of results of blood and tissue cultures in patients with pyogenic spondylitis.

METHODS

We searched for patients with pyogenic spondylitis in whom microorganisms were isolated from both blood and tissue cultures by retrospective review of medical records in three tertiary university-affiliated hospitals between January 2005 and December 2015. The species and antimicrobial susceptibility patterns of isolates from blood and tissue cultures were compared.

RESULTS

Among 141 patients with pyogenic spondylitis in whom microorganisms were isolated from both blood and tissue cultures, the species of blood and tissue isolates were identical in 135 patients (95.7%, 135/141). Excluding the four anaerobic isolates, we investigated antimicrobial susceptibility patterns of 131 isolates of the same species from blood and tissue cultures. Antibiotic susceptibility patterns were identical in 128 patients (97.7%, 128/131). The most common isolates were Staphylococcus aureus (86 patients; 85 concordant and one discordant), followed by streptococcus (24 patients; 22 concordant and two discordant), and Escherichia coli (eight patients; all concordant).

CONCLUSIONS

We suggest that a positive blood culture from patients with pyogenic spondylitis could preclude the need for additional tissue cultures, especially when S. aureus and streptococcus grew in blood cultures.

Bacteriophages and Their Immunological Applications against Infectious Threats

Bacteriophage therapy dates back almost a century, but the discovery of antibiotics led to a rapid decline in the interests and investments within this field of research. Recently, the novel threat of multidrug-resistant bacteria highlighted the alarming drop in research and development of new antibiotics: 16 molecules were discovered during 1983–87, 10 new therapeutics during the nineties, and only 5 between 2003 and 2007. Phages are therefore being reconsidered as alternative therapeutics. Phage display technique has proved to be extremely promising for the identification of effective antibodies directed against pathogens, as well as for vaccine development. At the same time, conventional phage therapy uses lytic bacteriophages for treatment of infections and recent clinical trials have shown great potential. Moreover, several other approaches have been developed in vitro and in vivo using phage-derived proteins as antibacterial agents. Finally, their use has also been widely considered for public health surveillance, as biosensor phages can be used to detect food and water contaminations and prevent bacterial epidemics. These novel approaches strongly promote the idea that phages and their proteins can be exploited as an effective weapon in the near future, especially in a world which is on the brink of a “postantibiotic era.”

Antimicrobial resistance profiles of Staphylococcus aureus clusters on small dairy farms in southern Brazil

ABSTRACT: In intensive dairy farming, persistent intramammary infection has been associated with specific Staphylococcus (S.) aureus strains, and these strains may be resistant to antimicrobials. The objective of this study was to evaluate the antimicrobial resistance phenotypes of S. aureus isolates and to assess the distribution and the persistence of clonal groups in small dairy herds of southern Brazil. Milk samples were collected from all lactating cows from 21 dairy farms over a two-year period, totaling 1,060 samples. S. aureus isolates were tested for susceptibility to thirteen antimicrobials using the disk diffusion method. The total DNA of the isolates was subjected to SmaI digestion followed by pulsed-field gel electrophoresis (PFGE). Banding patterns differing by ≤4 bands were considered members of a single PFGE cluster. The frequency of S. aureus isolation ranged from 3.45% to 70.59% among the 17 S. aureus-positive herds. Most S. aureus isolates (87.1%) were susceptible to all antimicrobials; resistance to penicillin (18.2%) was the most frequently observed. The 122 isolates subjected to macrorestriction analysis were classified into 30 PFGE-clusters. Among them, only 10 clusters were intermittent or persistent over the two-year period. The majority (93.6%) of isolates belonging to persistent and intermittent clusters were susceptible to all tested antimicrobials. S. aureus intramammary colonization in small dairy farms of southern Brazil is most frequently caused by sporadic PFGE clusters, although some persistent clusters can arise over time. Both sporadic and persistent isolates were highly susceptible to antimicrobials.

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones.

Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.

The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.

The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.

This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.

Genomics of Natural Populations of Staphylococcus aureus

Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. The first S. aureus genomes to be published, 15 years ago, provided the first view of genome structure and gene content. Since then, thousands of genomes from a wide array of strains from different sources have been sequenced. Comparison of these sequences has resulted in broad insights into population structure, bacterial evolution, clone emergence and expansion, and the molecular basis of niche adaptation. Furthermore, this information is now being applied clinically in outbreak investigations to inform infection control measures and to determine appropriate treatment regimens. In this review, we summarize some of the broad insights into S. aureus biology gained from the analysis of genomes and discuss future directions and opportunities in this dynamic field of research.

Pattern characterization of genes involved in non-specific immune response in Staphylococcus aureus isolates from intramammary infections

Staphylococcus aureus isolated from mammary gland are characterized by different genetic patterns. Ninety four isolates from 33 dairy herds were analyzed by the means of a microarray to investigate S. aureus virulence patterns and the distribution of genes believed to be involved in immune evasion. None of the 94 isolates considered were MRSA. However, 50% of the isolates belonged to complexes related to MRSA and to human diseases, while only about 25% of them can be considered as exclusively of bovine origin. The distribution of clonal complexes and the different gene patterns observed confirmed the presence of an influence of geographical localization. The assessment of the influence of genes related to immune evasion on quarter milk cell count showed as four of them showed to be significantly associated to an increase quarter milk SCC. These genes could be potential target for developing new vaccines against S. aureus.

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a new L. monocytogenes typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determined the breadth of the L. monocytogenes population based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67 L. monocytogenes isolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated five L. monocytogenes groups. Using all available NCBI RefSeq genomes (n = 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks.

Epidemiology of Methicillin-ResistantStaphylococcus aureusat a University Hospital in the Canary Islands

Objectives:

To describe the epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) at a university hospital in Tenerife, Canary Islands, during a 40-month period and to evaluate the effectiveness of the application of control measures.

Design:

Laboratory-based surveillance, medical charts and microbiological records review, and characterization of strains by pulsed-field gel electrophoresis (PFGE) were used to describe the epidemiology. Infection control practices were introduced as an intervention.

Setting:

A 650-bed, tertiary-care university hospital.

Subjects:

Patients with clinical and nasal isolates of MRSA and colonized staff members.

Results:

The rate of nosocomial MRSA infections was 32.5% for 1997, 17.9% for 1998, 14.5% for 1999, and 25.6% during the first 4 months of 2000. The major sites of isolation for nosocomial MRSA infection included surgical wounds (25%) and the lower respiratory tract (24%). Intensive care units and surgical specialties had more frequent MRSA cases. Characteristics associated with nosocomial MRSA isolates included prior use of intensive antibiotic therapy, prolonged hospital stays, major underlying illness, invasive procedures, and older age. PFGE type A (subtype A1) was the strain most frequently found and the only PFGE type involved in clusters.

Conclusions:

Surveillance cultures and contact droplet precautions were followed by decreased rates for 2 years. Nevertheless, the spread of PFGE subtype Al to many different areas of the hospital and the increase in incidence during the first third of 2000 indicates either that surveillance cultures were not used widely enough or that compliance with isolation measures was suboptimal.

Molecular Epidemiology of Methicillin–ResistantStaphylococcus Aureusin a Veterans Administration Medical Center

Objectives:

To determine whether patients who were colonized or infected with methicillin-resistantStaphylococcus aureus(MRSA) persistently carried the same strain and to identify the extent of strain variation within a population of patients.

Design:

Molecular typing by pulsed-field gel electrophoresis (PFGE) of stored MRSA isolates.

Setting:

A Veterans Administration Medical Center with 288 hospital, 45 intermediate-care, and 75 extended-care beds.

Isolates:

Between January 1991 and March 1993, 91 patients had MRSA identified in routine cultures. One hundred isolates from 57 patients (63%) were available for typing.

Results:

Before 1988, only occasional MRSA isolates were identified. By 1993, 50% ofS. aureusisolates from unique patients were resistant to methicillin. PFGE identified 7 MRSA strains, 3 of which were identified in specimens from 1 patient each. The most common strains were SD4 (20 patients), SD1 (12 patients), SD2 (12 patients), and SD5a (5 patients). Twenty patients had 2 or more isolates obtained at least 1 week apart (mean, 30.7 weeks; range, 1 to 102 weeks). Of these patients, 12 were colonized or infected with only one strain (mean time observed, 25.1 weeks; range, 1 to 82 weeks). Eight patients had at least 2 different strains (mean time observed, 39 weeks; range, 2 to 102 weeks).

Conclusion:

Numerous MRSA strains circulated in tiiis endemic setting; 40% of patients observed over time were colonized or infected witii more than one strain. Molecular typing was an essential tool for evaluating the epidemiology of MRSA in this setting.

Microbiological Quality Control for Laboratory Rodents and Lagomorphs

Mice (Mus musculus), rats (Rattus norvegicus), other rodent species, and domestic rabbits (Oryctolagus cuniculus) have been used in research for over 100 years. During the first half of the 20th century, microbiological quality control of lab animals was at best rudimentary as colonies were conventionally housed and little or no diagnostic testing was done. Hence, animal studies were often curtailed and confounded by infectious disease (Mobraaten and Sharp, 1999; Morse, 2007; Weisbroth, 1999). By the 1950s, it became apparent to veterinarians in the nascent field of comparative medicine that disease-free animals suitable for research could not be produced by standard veterinary disease control measures (e.g., improved sanitation and nutrition, antimicrobial treatments) in conventional facilities. Henry Foster, the veterinarian who founded Charles River Breeding Laboratories in 1948 and a pioneer in the large-scale production of laboratory rodents, stated in a seminar presented at the 30th anniversary of AALAS, “After a variety of frustrating health-related problems, it was decided that a major change in the company’s philosophy was required and an entirely different approach was essential”. Consequently, he and others developed innovative biosecurity systems to eliminate and exclude pathogens (Allen, 1999). In 1958, Foster reported on the Cesarean-originated barrier-sustained (COBS) process for the large-scale production of specific pathogen-free (SPF) laboratory rodents (Foster, 1958). To eliminate horizontally transmitted pathogens, a hysterectomy was performed on a near-term dam from a contaminated or conventionally housed colony. The gravid uterus was pulled through a disinfectant solution into a sterile flexible film isolator where the pups were removed from the uterus and suckled on axenic (i.e., germ-free) foster dams. After being mated to expand their number and associated with a cocktail of nonpathogenic bacteria to normalize their physiology and prime their immune system, rederived rodents were transferred to so-called barrier rooms for large-scale production. The room-level barrier to adventitious infection entailed disinfection of the room, equipment, and supplies, limiting access to trained and properly gowned personnel, and the application of new technologies such as high-efficiency particulate air-filtration of incoming air (Dubos and Schaedler, 1960; Foster, 1980; Schaedler and Orcutt, 1983; Trexler and Orcutt, 1999). The axenic and associated rodents mentioned in the COBS process are collectively classified as gnotobiotic to indicate that they have a completely known microflora. By contrast, barrier-reared rodent colonies are not gnotobiotic because they are housed in uncovered cages and thus acquire a complex microflora from the environment, supplies, personnel, and other sources. Instead, they are described as SPF to indicate that according to laboratory testing, they are free from infection with a defined list of infectious agents, commonly known as an ‘exclusion’ list.

Transmission and persistence of livestock-associated methicillin-resistant Staphylococcus aureus among veterinarians and their household members

After the first isolation of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in 2003, this MRSA variant quickly became the predominant MRSA obtained from humans as part of the Dutch national MRSA surveillance. Previous studies have suggested that human-to-human transmission of LA-MRSA, compared to that of other MRSA lineages, rarely occurs. However, these reports describe the transmission of LA-MRSA based on epidemiology and limited molecular characterization of isolates, making it difficult to assess whether transmission actually occurred. In this study, we used whole-genome maps (WGMs) to identify possible transmission of LA-MRSA between humans. For this, we used LA-MRSA isolates originating from a 2-year prospective longitudinal cohort study in which livestock veterinarians and their household members were repeatedly sampled for the presence of S. aureus. A considerable degree of genotypic variation among LA-MRSA strains was observed. However, there was very limited variability between the maps of the isolates originating from the same veterinarian, indicating that each of the veterinarians persistently carried or had reacquired the same LA-MRSA strain. Comparison of WGMs revealed that LA-MRSA transmission had likely occurred within virtually every veterinarian household. Yet only a single LA-MRSA strain per household appeared to be involved in transmission. The results corroborate our previous finding that LA-MRSA is genetically diverse. Furthermore, this study shows that transmission of LA-MRSA between humans occurs and that carriage of LA-MRSA can be persistent, thus posing a potential risk for spread of this highly resistant pathogen in the community.

Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition

Antibiotic resistance is a key medical concern, with antibiotic use likely being an important cause. However, here we describe an alternative route to clinically relevant antibiotic resistance that occurs solely due to competitive interactions among bacterial cells. We consistently observe that isolates of Methicillin-resistant Staphylococcus aureus diversify spontaneously into two distinct, sequentially arising strains. The first evolved strain outgrows the parent strain via secretion of surfactants and a toxic bacteriocin. The second is resistant to the bacteriocin. Importantly, this second strain is also resistant to intermediate levels of vancomycin. This so-called VISA (vancomycin-intermediate S. aureus) phenotype is seen in many hard-to-treat clinical isolates. This strain diversification also occurs during in vivo infection in a mouse model, which is consistent with the fact that both coevolved phenotypes resemble strains commonly found in clinic. Our study shows how competition between coevolving bacterial strains can generate antibiotic resistance and recapitulate key clinical phenotypes.

Prevalence of methicillin resistant Staphylococcus aureus among Egyptian patients after surgical interventions

BACKGROUND

Staphylococcus aureus (S. aureus) is isolated frequently from surgical site infections and other soft tissue infections. There are limited data examining the prevalence of methicillin resistant S. aureus (MRSA) among Egyptian patients after surgery. The current study determined the prevalence of MRSA isolated from surgical site and soft tissue infections at Minia University Hospital (MUH), determined their susceptibility to β-lactams and other antimicrobials, and examined their mecA gene expression.

METHODS

A total of 208 hospitalized patients attending the General Surgery Department at MUH were enrolled and all had skin and soft tissue infections (SSTIs) of different causes. These 208 patients (143 males and 65 females) were suffering from surgical site infection (SSI; n=82), diabetic foot (n=52), abscess (n=45), or burn (n=29) infections. Samples were cultured on different media for isolation and identification of S. aureus and the isolates were screened for antibiotic susceptibility. All MRSA isolates were tested by polymerase chain reaction to detect the mecA gene responsible for methicllin resistance.

RESULTS

241 Staphylococcal species represented the most common isolates (64.8%) among 371 collected isolates from the 208 patients. Out of the 241 staphylococcal isolates, 127 were S. aureus (61% of the total patients). The prevalence of S. aureus among SSI, diabetic foot, abscess, and burn patients were 59%, 75%, 56%, and 52%, whereas that of MRSA was 16%, 17%, 13%, and 10%, respectively. MRSA isolates (n=31; 15% of patients) showed multiple resistance to at least one member of the antimicrobial groups tested with an average resistance to 6.6±1.9 antimicrobial groups. Polymerase chain reaction data showed that only 29 isolates of the MRSA isolates (94%) were positive for mecA gene.

CONCLUSIONS

Staphylococcus aureus isolates are the major pathogens responsible for wound and surgical site infections at MUH and MRSA are a potential threat for wound patients in Egypt.

Propionibacterium-produced coproporphyrin III induces Staphylococcus aureus aggregation and biofilm formation

The majority of bacteria detected in the nostril microbiota of most healthy adults belong to three genera: Propionibacterium, Corynebacterium, and Staphylococcus. Among these staphylococci is the medically important bacterium Staphylococcus aureus. Almost nothing is known about interspecies interactions among bacteria in the nostrils. We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. Bioassay-guided fractionation implicated coproporphyrin III (CIII), the most abundant extracellular porphyrin produced by human-associated Propionibacterium spp., as a cause of S. aureus aggregation. This aggregation response depended on the CIII dose and occurred during early stationary-phase growth, and a low pH (~4 to 6) was necessary but was not sufficient for its induction. Additionally, CIII induced plasma-independent S. aureus biofilm development on an abiotic surface in multiple S. aureus strains. In strain UAMS-1, CIII stimulation of biofilm depended on sarA, a key biofilm regulator. This study is one of the first demonstrations of a small-molecule-mediated interaction among medically relevant members of the nostril microbiota and the first description of a role for CIII in bacterial interspecies interactions. Our results indicate that CIII may be an important mediator of S. aureus aggregation and/or biofilm formation in the nostril or other sites inhabited by Propionibacterium spp. and S. aureus. Importance: Very little is known about interspecies interactions among the bacteria that inhabit the adult nostril, including Staphylococcus aureus, a potential pathogen that colonizes about a quarter of adults. We demonstrated that coproporphyrin III (CIII), a diffusible small molecule excreted by nostril- and skin-associated Propionibacterium spp., induces S. aureus aggregation in a manner dependent on dose, growth phase, and pH. CIII also induces S. aureus to form a plasma-independent surface-attached biofilm. This report is the first description of a role for CIII in bacterial interspecies interactions at any human body site and a novel demonstration that nostril microbiota physiology is influenced by small-molecule-mediated interactions.

Characterization of multi-antibiotic-resistant Escherichia coli Isolated from beef cattle in Japan

The emergence of multiple-antibiotic-resistance bacteria is increasing, which is a particular concern on livestock farms. We previously isolated 1,347 antimicrobial-resistant (AMR) Escherichia coli strains from the feces of beef cattle on 14 Japanese farms. In the present study, the genetic backgrounds and phylogenetic relationships of 45 AMR isolates were characterized by the chromosome phylotype, AMR phenotype, AMR genotype, and plasmid type. These isolates were classified into five chromosome phylotypes, which were closely linked to the farms from which they were isolated, suggesting that each farm had its own E. coli phylotype. AMR phenotype and plasmid type analyses yielded 8 and 14 types, all of which were associated with the chromosomal phylotype and, thus, to the original farms. AMR genotype analysis revealed more variety, with 16 types, indicating both inter- and intra-farm diversity. Different phylotype isolates from the same farm shared highly similar plasmid types, which indicated that plasmids with AMR genes could be transferred between phylotypes, thereby generating multi-antibiotic-resistant microorganisms. This ecological study demonstrated that the chromosome phylotype was strongly correlated with the farm from which they were isolated, while the AMR phenotype, genotype, and plasmid type were generally correlated with the chromosome phylotype and farm source.

Antibiotic resistance and molecular analysis of Staphylococcus aureus isolated from cow's milk and dairy products in northeast Brazil

This work aimed to assess the clonal distribution among 94 strains of Staphylococcus aureus isolated from cow's milk, raw cheese, and a milking machine in 12 dairy farms in northeast Brazil, by analyzing different typing methods and detecting resistance and toxigenic profiles. For the first time, isolates of this region were assessed simultaneously by the polymorphism of the 3'-end coa gene and 16S-23S rDNA, pulsed-field gel electrophoresis, antibiotic resistance phenotyping, and toxigenic arsenal. Although pulsed-field gel electrophoresis patterns showed a wider variation (discriminatory index 0.83) than the PCR-based methods, the internal transcribed spacer-PCR proved to be a useful and inexpensive procedure for conducting epidemiological surveys of S. aureus on a regional scale. Each dairy farm had its own resistance profile, and in two herds, 63% of the strains were multiresistant, probably due to the indiscriminate use of antibiotics in bovine mastitis treatment. No methicillin-resistant S. aureus strains were detected in this study; however, 93.6% of S. aureus strains harbored variable profiles of staphylococcal enterotoxin genes seg, seh, sei, and sej. Transcriptional analysis revealed that 53.3% of staphylococcal enterotoxin genes actually transcribed, pointing out the food poisoning risk of these dairy products to consumers in the region. Based on the detection of the most prevalent clones in a herd or region, appropriate antibiotic therapy and specific immunization can be used for the treatment and control of staphylococcal mastitis.

Population structure analyses of Staphylococcus aureus at Tygerberg Hospital, South Africa, reveals a diverse population, a high prevalence of Panton-Valentine leukocidin genes, and unique local methicillin-resistant S. aureus clones

Studies reporting on the population structure of Staphylococcus aureus in South Africa have focused only on methicillin-resistant S. aureus (MRSA). This study describes the population structure of S. aureus, including methicillin-susceptible S. aureus (MSSA) isolated from patients at Tygerberg Academic Hospital, Western Cape province. Pulsed-field gel electrophoresis (PFGE), detection of Panton-Valentine leukocidin (PVL), spa typing, multilocus sequence typing (MLST), agr typing and SCCmec typing were used to characterize strains. Of 367 non-repetitive S. aureus isolates collected over a period of 1 year, 56 (15.3%) were MRSA. Skin and soft tissue infections were the most frequent source (54.8%), followed by bone and joint (15.3%) and respiratory tract infections (7.7%). For strain typing, PFGE was the most discriminative method, and resulted in 31 pulsotypes (n = 345, 94.0%), as compared with 16 spa clonal complexes (CCs) (n = 344, 93.4%). Four MLST CCs were identified after eBURST of sequence types (STs) of selected isolates. One hundred and sixty isolates (MSSA, n = 155, 42.2%) were PVL-positive, and agr types I-IV and SCCmec types I-V were identified. Our S. aureus population consisted of genotypically diverse strains, with PVL being a common characteristic of MSSA. MSSA and MRSA isolates clustered in different clones. However, the dominant MRSA clone (ST612) also contained an MSSA isolate, and had a unique genotype. Common global epidemic MRSA clones, such as ST239-MRSA-III and ST36-MRSA-II, were identified. A local clone, ST612-MRSA-IV, was found to be the dominant MRSA clone.

Relationship between nasal colonization and ventilator-associated pneumonia and the role of the environment in transmission of Staphylococcus aureus in intensive care units

BACKGROUND

This study assessed the relationship between nasal colonization and ventilator-associated pneumonia (VAP) by Staphylococcus aureus, as well the role of the environment in the transmission of this organism.

METHODS

We performed a cohort study of patients with VAP caused by methicillin-resistant S aureus (MRSA) or methicillin-sensitive S aureus during 2 years in an adult intensive care unit (ICU). All patients had nasal swab specimens obtained at admission and during the ICU stay. Clinical samples also were collected for analysis, as were samples from the hands of health care professionals and the environment, and were typed using pulsed-field gel electrophoresis.

RESULTS

S aureus VAP represented 12.5% of the cases, and statistical analysis identified colonization as a risk factor for the development of this infection. MRSA was isolated from the environment and hands, indicating the existence of a secondary reservoir. Molecular typing revealed a polyclonal profile; however, clone J was the most frequent (45.5%) among isolates of MRSA tested, with a greater profile of resistance than the other isolates. There was strong evidence suggesting transmission of MRSA to patients from the environment.

CONCLUSION

Nasal colonization for S aureus is a risk factor for development of VAP.

International multicenter evaluation of the DiversiLab bacterial typing system for Escherichia coli and Klebsiella spp

Successful multidrug-resistant clones are increasing in prevalence globally, which makes the ability to identify these clones urgent. However, adequate, easy-to-perform, and reproducible typing methods are lacking. We investigated whether DiversiLab (DL), an automated repetitive-sequence-based PCR bacterial typing system (bioMérieux), is suitable for comparing isolates analyzed at different geographic centers. A total of 39 Escherichia coli and 39 Klebsiella species isolates previously typed by the coordinating center were analyzed. Pulsed-field gel electrophoresis (PFGE) confirmed the presence of one cluster of 6 isolates, three clusters of 3 isolates, and three clusters of 2 isolates for each set of isolates. DL analysis was performed in 11 centers in six different countries using the same protocol. The DL profiles of 425 E. coli and 422 Klebsiella spp. were obtained. The DL system showed a lower discriminatory power for E. coli than did PFGE. The local DL data showed a low concordance, as indicated by the adjusted Rand and Wallace coefficients (0.132 to 0.740 and 0.070 to 1.0 [E. coli] and 0.091 to 0.864 and 0.056 to 1.0 [Klebsiella spp.], respectively). The central analysis showed a significantly improved concordance (0.473 to 1.0 and 0.290 to 1.0 [E. coli] and 0.513 to 0.965 and 0.425 to 1.0 [Klebsiella spp.], respectively). The misclassifications of profiles for individual isolates were mainly due to inconsistent amplification, which was most likely due to variations in the quality and amounts of the isolated DNA used for amplification. Despite local variations, the DL system has the potential to indicate the occurrence of clonal outbreaks in an international setting, provided there is strict adherence to standardized, reproducible DNA isolation methods and analysis protocols, all supported by a central database for profile comparisons.

Molecular typing of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) isolated from animals and retail meat in North Dakota, United States

The objective of this study was to determine the prevalence and molecular typing of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) in food-producing animals and retail meat in Fargo, North Dakota. A two-step enrichment followed by culture methods were used to isolate S. aureus from 167 nasal swabs from animals, 145 samples of retail raw meat, and 46 samples of deli meat. Positive isolates were subjected to multiplex polymerase chain reaction in order to identify the genes 16S rRNA, mecA, and Panton-Valentine Leukocidin. Pulsed-field gel electrophoresis and multilocus sequence typing were used for molecular typing of S. aureus strains. Antimicrobial susceptibility testing was carried out using the broth microdilution method. The overall prevalence of S. aureus was 37.2% (n=133), with 34.7% (n=58) of the animals positive for the organism, and the highest prevalence observed in pigs (50.0%) and sheep (40.6%) (p<0.05); 47.6% (n=69) of raw meat samples were positive, with the highest prevalence in chicken (67.6%) and pork (49.3%) (p<0.05); and 13.0% (n=6) of deli meat was positive. Five pork samples (7.0%) were positive for MRSA, of which three were ST398 and two were ST5. All exhibited penicillin resistance and four were multidrug resistant (MDR). The Panton-Valentine Leukocidin gene was not detected in any sample by multiplex polymerase chain reaction. The most common clones in sheep were ST398 and ST133, in pigs and pork both ST398 and ST9, and in chicken ST5. Most susceptible S. aureus strains were ST5 isolated from chicken. The MDR isolates were found in pigs, pork, and sheep. The presence of MRSA, MDR, and the subtype ST398 in the meat production chain and the genetic similarity between strains of porcine origin (meat and animals) suggest the possible contamination of meat during slaughtering and its potential transmission to humans.

Population genetics and the evolution of virulence in Staphylococcus aureus

Staphylococcus aureus is one of the most important human pathogens, causing life-threatening infection in the community and hospital setting. The population genetics of S. aureus and the evolution of virulence is the focus of this review. We describe the various techniques in determining S. aureus population structure and discuss the insights gained from whole genome sequencing of various S. aureus strains. The emergence of community-acquired, methicillin-resistant S. aureus provides a framework for the discussion on evolution of virulence, and the role of horizontal gene transfer in the development of virulence and antibiotic resistance is explored. The knowledge generated from population genetics has the potential to inform strategies to assist in the prevention or treatment of this highly successful human pathogen.

Temporal changes in pulsed-field gel electrophoresis banding in vancomycin-resistant Enterococcus faecium and implications for outbreak investigations

BACKGROUND

Patients are often screened with surveillance cultures to discern transmissions vs transformation of an isolate to vancomycin-resistant Enterococcus faecium. To determine the amount of time between which isolates could be considered genetically similar by pulsed-field gel electrophoresis, isolate change over time within single patients was studied.

METHODS

A minimum of 4 isolates per patient, separated by at least 2 months, were collected from previously frozen stores. Visual comparison of banding patterns was conducted, and percent relatedness was calculated.

RESULTS

Twenty-eight isolates from 6 patients were studied. No isolate differed by more than 3 bands before 150 days, and the average percent difference per band was 3.7%. The isolates diverged genetically as a linear function of number of bands over time (good model fit intrapatient r(2) = 0.42; poor model fit interpatient r(2) = 0.0062).

CONCLUSION

Trajectory of genetic variation appears to be isolate/patient specific; however, commonalities exist and tested isolates were relatively stable out to 150 days.

Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era

Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.

Aromatic Compound-Dependent Staphylococcus aureus Is Safe in a Nasal Colonization Leukopenic Murine Model

Staphylococcus aureus nasal carriage is a risk factor for individuals suffering from trauma, surgical procedures, invasive devices, and/or decreased immunity. Recently, we demonstrated that artificial nasal colonization with an attenuated S. aureus mutant reduced by bacterial interference with the colonization of pathogenic strains of S. aureus. This could be an optional tool to diminish the rate of S. aureus infections in hospitalized patients. The aim of this study was to construct a safe ΔaroA mutant of S. aureus and to discriminate it from nasal colonizing and osteomyelitis S. aureus isolates by SmaI pulsed-field gel electrophoresis (PFGE) typing. The ΔaroA mutant, named RD17, exhibited an LD(50) (3.2 × 10(6) colony-forming unit (CFU)) significantly higher than that of the parental strain (2.2 × 10(3) CFU). The colony number of the RD17 mutants recovered from nares of leukopenic mice was similar to that observed in the animals of the control group. Therefore, the ΔaroA mutant was demonstrated to be safe due to maintaining low growth levels in the nares regardless of immune status of the animals. PFGE typing allowed the unequivocal identification of the S. aureus and differentiation of aroA mutants in nasal colonizing and osteomyelitis isolates. This information could be important to discriminate endogenous infections from laboratory strains of S. aureus.

Carriage frequency, phenotypic and genotypic characteristics of Staphylococcus aureus isolated from dialysis and kidney tranplant patients at a hosptial in northern paraná

The objective of the present study was to determine the frequency of Staphylococcus aureus nasal carriage among dialysis and kidney transplant patients, to identify the antimicrobial resistance profile of these strains and to verify their genetic profiles with the RW3A primer. The study included 159 individuals, comprising 111 dialysis and 48 kidney transplant patients. Of the 48 transplant patients, 75% were positive for S. aureus, whereas 49% of the 111 dialysis patients were carriers. Two samples yielded conflicting results for oxacillin sensitivity between the disk diffusion and minimum inhibitory concentration (MIC) assays: both were sensitive by the disk diffusion assay and resistant by MIC (4 μg/ml). In the antibiogram by disk diffusion, ten samples were resistant to cefoxitin, among which eight were also resistant to oxacillin. The resistance of the ten samples to cefoxitin by the disk diffusion assay was confirmed by MIC. Of the ten oxacillin-resistant samples, eight harbored the mecA gene. All samples were sensitive to vancomycin, and most were resistant to penicillin and demonstrated high rates of resistance to the other antimicrobials tested. The samples from dialysis patients exhibited a more homogenous genetic profile. Among the samples with a high percent similarity, no correlation with sensitivity or resistance to oxacillin was observed. According to the results of this study, the implementation of prevention and control measures, such as increased restrictions on prescriptions for antimicrobial drugs and nasal decontamination prior to high-risk procedures, is recommended.

The use of spa and phage typing for characterization of clinical isolates of methicillin-resistant Staphylococcus aureus in the University Clinical Center in Gdańsk, Poland

The emergence of spa types and spa–clonal complexes (CC) among clinical methicillin-resistant Staphylococcus aureus isolates collected from the University Clinical Center in Gdańsk between 2008 and 2009 were investigated. Phage typing was used as the initial screening in the study. The basic set of phages and the additional set of phages were used. Most of the isolates (56 %) belonged to the phage group III. With the additional set of phages, eight types were found, with predominant one MR8 (50 %). Sixteen distinct spa types were observed. The most frequent were t003 (22 %), t151 (16 %), and t008 (12 %). The spa types were clustered into two spa-CC and eight singletons. The predominant CC010 (50 %) consisted of six types, with the most common t003 (36.7 %) and t151(26.7 %), and in 80 % was identified as staphylococcal chromosomal casette mec (SCCmec) type II. The second cluster has no founder (12 %) with only two spa types: t037 belonging to SCCmec type III and t029. In the most frequent singleton, spa type t008 alone was clustered in 12 % of the isolates. All singletons correspond to SCCmec type IV. The CC010 was distributed in most of the hospital wards, corresponded to Multilocus sequence typing type ST5/ST225 and was constantly present throughout the observed period. The isolates of CC010 generally belonged to the phage group III, and most of them (53.3 %) were resistant to erythromycin, clindamycin, and ciprofloxacin. The concordance between spa-clone and phage type was very high, but the same phage type MR8 was observed within different spa types of the predominant clone.

Selected antimicrobial essential oils eradicate Pseudomonas spp. and Staphylococcus aureus biofilms

Biofilms are difficult to eliminate with standard antimicrobial treatments due to their high antibiotic resistance relative to free-living cells. Here, we show that selected antimicrobial essential oils can eradicate bacteria within biofilms with higher efficiency than certain important antibiotics, making them interesting candidates for the treatment of biofilms.