Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing

Genomic Evidence for Direct Transmission of mecC-MRSA between a Horse and Its Veterinarian

Methicillin-resistant Staphylococcus aureus bearing the mecC gene (mecC-MRSA) has been reported from animals and humans in recent years. This study describes the first mecC-MRSA isolates of human and equine origin in Hungary (two isolates from horses and one from a veterinarian, who treated one of the infected horses, but was asymptomatic). MRSA isolates were identified by cultivation and PCR detection of the species-specific spa gene and mecA/mecC methicillin resistance genes. The isolates were characterized by antibiotic susceptibility testing, MLST, spa, SCCmec typing, PFGE and whole genome sequencing (WGS). All three isolates belonged to the ST130-t843-SCCmec XI genotype, and carried the mecC and blaZ genes. Apart from beta-lactam drugs, they were sensitive to all tested antibiotics. The isolates of the infected horse and its veterinarian had the same PFGE pulsotype and showed only slight differences with WGS. Hence, this is the first description of direct transmission of a mecC-carrying MRSA between a horse and its veterinarian. The emergence of mecC in the country highlights the importance of the appropriate diagnostics in MRSA identification.

Estimated Roles of the Carrier and the Bacterial Strain When Methicillin-Resistant Staphylococcus aureus Decolonization Fails: a Case-Control Study

Methicillin-resistant Staphylococcus aureus (MRSA) is a common bacterial pathogen that frequently colonizes healthy individuals, with potential to cause invasive infection. In Denmark, to keep the prevalence low, MRSA carriers are recommended to undergo decolonization treatments, but achieving decolonization is challenging. Knowledge about the factors contributing to decolonization is scarce. We aimed to identify bacterial genome and clinical factors influencing MRSA decolonization. We identified all new MRSA patients above 2 years of age within the Hvidovre catchment area, Copenhagen, Denmark, in 2017 and 2018. Carriers were defined as chronic carriers (cases) if they were MRSA positive after two or more treatments and as nonchronic carriers (controls) if they were MRSA free after the first or second treatment. Using whole-genome sequencing (WGS), we constructed a pangenome of bacterial strains. With the incorporation of bacterial genome and clinical patient data, machine learning and multivariate analyses were performed to determine the factors associated with decolonization. A total of 477 MRSA carriers were included. An age of ≥13 years was significantly associated with nonchronic carriage. We identified 278 bacterial genetic features that were statistically significantly associated with chronic carriage (P < 0.05 by Fisher's exact test). Chronic MRSA carriage was predicted with 68% accuracy using a combination of bacterial genome data and patient clinical data. Decolonization success is multifactorial. Apart from the 68% predicted accuracy found in this study, we estimate that the remaining 32% is a result of host factors and microbiome composition. IMPORTANCE Carriage of methicillin-resistant Staphylococcus aureus (MRSA) and other multiresistant bacteria is a prerequisite for infection and transmission. Successful decolonization treatment removes these risks. We aimed to identify bacterial genome and host clinical factors that influence MRSA decolonization to estimate the roles of the carrier and the bacterial strain, respectively, when decolonization fails. The long-term goal, beyond this study, is to optimize decolonization success, minimize MRSA transmission, and, ultimately, improve the quality of life of MRSA carriers.

Prevalence of Livestock-Associated MRSA ST398 in a Swine Slaughterhouse in Guangzhou, China

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an important zoonotic microorganism that is increasingly causing public health concern worldwide. The objective of this study was to determine the transmission and occurrence of MRSA in a slaughterhouse environment and evaluate its antimicrobial resistance and genetic characterization. In this study, we conducted a comprehensive epidemiological survey of S. aureus by spa typing and whole-genome sequencing (WGS) of samples obtained from the pork production chain, the environment, and community residents. To clarify the evolutionary relationships of MRSA sequence type (ST) 398 in this study and global isolates, 197 published whole-genome sequences data of MRSA ST398 strains were downloaded from the GenBank database and included in the phylogenetic analysis. A total of 585 porcine samples (snout and carcass swabs), 78 human nasal samples, and 136 environmental samples were collected. The MRSA isolates were detected at higher frequencies in samples from swine (15.0%) than carcasses (10.0%), slaughterhouse workers (8.0%), community residents (0%), and environment samples (5.9%). The spa typing results showed that t571 accounted for a higher proportion than other spa types. Closely related isolates from the samples of swine, slaughterhouse workers, carcasses, carrier vehicle, and surrounding fishpond water indicate that MRSA ST398 strains may spread among swine, humans, and the environment. MRSA ST398-t571 isolates were genetically different from global strains, except for two Korean isolates, which showed genetic closeness with it. In addition, a MRSA ST398 isolate recovered from an infected patient in Europe differed by only 31 SNPs from the airborne dust-associated strain isolated in this study, thereby suggesting potential transmission among different countries. Antimicrobial susceptibility testing results demonstrated that 99.0% (96/97) of MRSA and 95.1% (231/243) of methicillin-sensitive S. aureus (MSSA) showed multidrug-resistant (MDR) phenotypes. According to WGS analysis, the poxtA-carrying segment (IS431mec-optrA-IS1216-fexB-IS431mec) was reported in MRSA ST398 isolates for the first time. The coexistence of cfr and optrA in a plasmid was first detected in MRSA ST398. The potential transmission of MRSA among humans, animals, and the environment is a cause for concern. The emergence and transmission of LA-MRSA ST398 with high levels of resistance profiles highlight the urgent need for LA-MRSA surveillance.

A randomized, placebo-controlled, double-blinded trial of MRSA throat carriage treatment, with either standard decolonization alone or in combination with oral clindamycin

Background

Staphylococcus aureus is a frequent colonizer of the human skin and mucous membranes but can also cause a variety of serious infections. Antimicrobial resistance is an increasing worldwide challenge and is mainly driven by an overuse of antimicrobials. To avoid the spread of methicillin-resistant Staphylococcus aureus (MRSA) in Denmark, the Danish Health Authority recommends decolonization treatment of MRSA carriers and their household contacts. Standard decolonization treatment includes chlorhexidine body wash and mupirocin nasal ointment, especially throat carriage is difficult to treat. The broad-spectrum antibiotic, clindamycin, is often added to the decolonization treatment, but there is currently low scientific evidence for this treatment.

Aim

To investigate whether the addition of clindamycin to the standard decolonization treatment increases decolonization success in MRSA throat carriers.

Methods

A randomized, placebo-controlled, double-blinded trial, including patients ≥ 18 years, who tested MRSA positive in the throat after completing one standard decolonization treatment. All carriers included in the trial receive standard decolonization treatment and are randomized to treatment with either placebo or clindamycin capsules for 10 days. We plan to include 40 participants in each of the two treatment arms.

Discussion

Due to the lack of consistent scientific evidence of clindamycin’s effect in MRSA decolonization and the worldwide urgent need to reduce the use of antibiotics, we judged that a 30% increase in the decolonization success rate in carriers treated with clindamycin is appropriate to justify prescribing clindamycin as part of the decolonization treatment of asymptomatic MRSA carriers.

Trial registration

EudraCT number 2019-002631-29

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-022-06443-1.

Characterization of Pseudomonas syringae Isolated from Systemic Infection of Zucchini in Australia

Zucchini plants with symptoms including twisted petioles, necrotic leaves, crown rot, and internal fruit rot were found in Bundaberg, Australia, at a commercial field for the first time during late autumn 2016, resulting in direct yield losses of 70 to 80%. Three Pseudomonas syringae strains isolated from symptomatic leaf (KL004-k1), crown (77-4C), and fruit (KFR003-1) were characterized and their pathogenicity evaluated on pumpkin, rockmelon, squash, and zucchini. Biochemical assays showed typical results for P. syringae. The three isolates differed, however, in that two produced fluorescent pigment (KFR003-1 and 77-4C) whereas the third, KL004-k1, was nonfluorescent. Multilocus sequence analysis classified the isolates to phylogroup 2b. The single-nucleotide polymorphism analysis of core genome from the Australian and closely related international isolates of P. syringae showed two separate clusters. The Australian isolates were clustered based on fluorescent phenotype. Pathogenicity tests demonstrated that all three isolates moved systemically within the inoculated plants and induced necrotic leaf symptoms in zucchini plants. Their identities were confirmed with specific PCR assays for P. syringae and phylogroup 2. Pathogenicity experiments also showed that the Eva variety of zucchini was more susceptible than the Rosa variety for all three isolates. Isolate KL004-k1 was more virulent than 77-4C on pumpkin, rockmelon, squash, and zucchini. This study expands the knowledge of P. syringae isolates that infect cucurbits and provides useful information for growers about the relative susceptibility of a range of cucurbit species.

Characterisation and Molecular Analysis of an Unusual Chimeric Methicillin Resistant Staphylococcus Aureus Strain and its Bacteriophages

In the context of microarray-based epidemiological typing of the clonal organism Staphylococcus aureus/MRSA, a strain was identified that did not belong to known clonal complexes. The molecular analysis by microarray-based typing yielded signals suggesting that it was a mosaic or hybrid strain of two lineages. To verify this result, the isolate was sequenced with both, short-read Illumina and long-read Nanopore technologies and analysed in detail. This supported the hypothesis that the genome of this strain, ST6610-MRSA-IVg comprised of segments originating from two different clonal complexes (CC). While the backbone of the strain’s genome, i.e., roughly 2 megabases, belongs to CC8, a continuous insert of 894 kb (approx. 30% of the genome) originated from CC140. Beside core genomic markers in the normal succession and orientation, this insert also included the mecA gene, coding for PbP2a and causing methicillin resistance, localised on an SCCmec IVg element. This particular SCCmec type was also previously observed in CC140 MRSA from African countries. A second conspicuous observation was the presence of the trimethoprim resistance gene dfrG within on a prophage that occupied an attachment site normally used by Panton-Valentine Leucocidin phages. This observation could indicate a role of large-scale chromosomal recombination in the evolution of S. aureus as well as a role of phages in the dissemination of antibiotic resistance genes.

Whole Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection

BACKGROUND

Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (EHR) to identify undetected outbreaks and the responsible transmission routes, respectively.

METHODS

We performed WGS surveillance of healthcare-associated bacterial pathogens from November 2016 to November 2018. EHR ML was used to identify the transmission routes for WGS-detected outbreaks, which were investigated by an IP expert. Potential infections prevented were estimated and compared to traditional IP practice during the same period.

RESULTS

Of 3,165 isolates, there were 2,752 unique patient isolates in 99 clusters involving 297 (10.8%) patient isolates were identified by WGS; clusters ranged from 2-14 patients. At least one transmission route was detected for 65.7% of clusters. During the same time, traditional IP investigation prompted WGS for 15 suspected outbreaks involving 133 patients, for which transmission events were identified for 5 (3.8%). If EDS-HAT had been running in real-time, 25-63 transmissions could have been prevented. EDS-HAT was found to be cost-saving and more effective than traditional IP practice, with overall savings of $192,408 - $692,532.

CONCLUSION

EDS-HAT detected multiple outbreaks not identified using traditional IP methods, correctly identified the transmission routes for most outbreaks, and would save the hospital substantial costs. Traditional IP practice misidentified outbreaks for which transmission did not occur. WGS surveillance combined with EHR ML has the potential to save costs and enhance patient safety.

Evaluation of virulence potential of methicillin-sensitive and methicillin-resistant Staphylococcus aureus isolates from a German refugee cohort

BACKGROUND

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) seem to be highly transmissible, often infect otherwise healthy humans and frequently occur in hospital outbreaks.

METHODS

Refugees, living in accommodations in Germany were screened for nasal carriage of S. aureus. The isolates were investigated regarding resistance and virulence, phenotypically and by whole genome data analysis.

RESULTS

5.6% (9/161) of the refugees are carriers of S. aureus. 2.5% (4/161) are MRSA carriers. Among the refugees, spa-types t021, t084, t304, t991 and t4983 were detected, as well as the new spa-types t18794 and t18795. t304 and t991 are assumed to be local spa-types from the middle east. The isolates are less resistant and marginal biofilm formers. Each isolate has a remarkable set of virulence genes, although genes, encoding for proteins strongly associated with invasive S. aureus infections, like Panton-Valentine leucocidin, were not detected.

CONCLUSION

The detection of strains from the middle east, supports the assumption that strains co-travel with the refugees and persist despite a transition of the host's living conditions. Whole genome data analysis does not permit to finally evaluate a germ's virulence. Nevertheless, an impression of the virulence potential of the strains, regarding skills in colonization, resistance, immune evasion, and host cell damaging can be pictured.

Reducing the Risk of Transmission of Critical Antimicrobial Resistance Determinants From Contaminated Pork Products to Humans in South-East Asia

Antimicrobial resistance (AMR) is a critical challenge worldwide as it impacts public health, especially via contamination in the food chain and in healthcare-associated infections. In relation to farming, the systems used, waste management on farms, and the production line process are all determinants reflecting the risk of AMR emergence and rate of contamination of foodstuffs. This review focuses on South East Asia (SEA), which contains diverse regions covering 11 countries, each having different levels of development, customs, laws, and regulations. Routinely, here as elsewhere antimicrobials are still used for three indications: therapy, prevention, and growth promotion, and these are the fundamental drivers of AMR development and persistence. The accuracy of detection of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) depends on the laboratory standards applicable in the various institutes and countries, and this affects the consistency of regional data. Enterobacteriaceae such as Escherichia coli and Klebsiella pneumoniae are the standard proxy species used for indicating AMR-associated nosocomial infections and healthcare-associated infections. Pig feces and wastewater have been suspected as one of the hotspots for spread and circulation of ARB and ARG. As part of AMR surveillance in a One Health approach, clonal typing is used to identify bacterial clonal transmission from the production process to consumers and patients - although to date there have been few published definitive studies about this in SEA. Various alternatives to antibiotics are available to reduce antibiotic use on farms. Certain of these alternatives together with improved disease prevention methods are essential tools to reduce antimicrobial usage in swine farms and to support global policy. This review highlights evidence for potential transfer of resistant bacteria from food animals to humans, and awareness and understanding of AMR through a description of the occurrence of AMR in pig farm food chains under SEA management systems. The latter includes a description of standard pig farming practices, detection of AMR and clonal analysis of bacteria, and AMR in the food chain and associated environments. Finally, the possibility of using alternatives to antibiotics and improving policies for future strategies in combating AMR in a SEA context are outlined.

Evaluation of the Hologic Panther Fusion MRSA Assay for the detection of MRSA in ESwab specimens obtained from nose, throat, and perineum

Enrichment culture (EC) remains gold standard for detecting MRSA colonisation, but molecular methods shorten turnaround time. The CE-marked automated Hologic Panther Fusion MRSA Assay (HPFM) is validated for nasal swabs. We compared HPFM with EC following an in-house PCR for detection of MRSA in nasal, pharyngeal, and perineal ESwabs. The same ESwabs were analysed using HPFM and inoculated in selective Tryptic Soy Broth (TSB) for overnight incubation. TSBs were screened by a PCR targeting nuc, femA, mecA, and mecC. Only samples with PCR results compatible with MRSA presence were inoculated onto 5% blood agar and chromogenic MRSA plates. HPFM detected MRSA in 103 of 132 EC positive samples indicating a sensitivity of 78.0% across sample types. When paired TSBs of 29 EC positive/HPFM negative samples were re-analysed by HPFM, MRSA was detected in 17/29 TSBs indicating that enrichment will increase the sensitivity of HPFM. HPFM analyses of cultured isolates from the remaining 12 EC positive/HPFM negative samples failed to detect orfX. HPFM reported the presence of MRSA in 22 samples where EC failed to identify MRSA. Fifteen of these ESwabs had been kept and direct culture without enrichment identified MRSA in seven samples. HPFM was useful for all sample sites. Compared to EC, the sensitivity of HPFM was limited because of lack of analytical sensitivity and failure to detect all MRSA variants. Failure of some MRSA-containing samples to enrich in cefoxitin-containing TSB indicates an unappreciated limitation of EC, which may lead to underestimation of the specificity of molecular assays.

Increasing Incidences and Clonal Diversity of Methicillin-Resistant Staphylococcus aureus in the Nordic Countries - Results From the Nordic MRSA Surveillance

Methicillin-resistant Staphylococcus aureus (MRSA) is notifiable in Denmark, Finland, Iceland, Norway and Sweden. The prevalence of MRSA in this region has been low for many years, but all five countries experience increasing numbers of new cases. The aim of the study was to describe the molecular epidemiology in the Nordic countries 2009-2016. Numbers of new cases of MRSA from 1997 to 2016 were compared, and a database containing information on spa-type and place of residence or acquisition, for all new MRSA isolates from 2009 to 2016 was established. A website was developed to visualize the geographic distribution of the spa-types. The incidence of new MRSA cases increased in all Nordic countries with Denmark having 61.8 new cases per 100,000 inhabitants in 2016 as the highest. The number of new cases 2009 to 2016 was 60,984. spa-typing revealed a high genetic diversity, with a total of 2,344 different spa-types identified. The majority of these spa-types (N = 2,017) were found in 1-10 cases. The most common spa-types t127/CC1, t223/CC22, and t304/CC6:8 increased significantly in all Nordic countries during the study period, except for Iceland, while spa-type t002/CC5 decreased in the same four countries. The trends of other common spa-types were different in each of the Nordic countries. The Nordic countries were shown to share similar trends but also to have country-specific characteristics in their MRSA populations. A continued increasing numbers of MRSA will challenge the surveillance economically. A more selected molecular surveillance will probably have to be employed in the future.

spa diversity of methicillin-resistant and -susceptible Staphylococcus aureus in clinical strains from Malaysia: a high prevalence of invasive European spa-type t032

Background

Staphylococcus aureus is one of the important pathogens causing nosocomial infection. spa typing allows identification of S. aureus clones in hospital isolates and is useful for epidemiological studies and nosocomial infection control. This study aims to investigate the spa types in Malaysian S. aureus isolates obtained from various clinical specimens.

Method

A total of 89 methicillin-resistant S. aureus (MRSA) [pus (n = 55), blood (n = 27), respiratory (n = 5), eye (n = 2)] isolates and 109 methicillin-susceptible S. aureus (MSSA) [pus (n = 79), blood (n = 24), respiratory (n = 3), eye (n = 2) and urine (n = 1)] isolates were subjected to spa typing with sequences analysed using BioNumerics version 7.

Results

The spa sequence was successfully amplified from 77.8% of the strains (154/198) and 47 known spa types were detected. The distribution of known spa types in MRSA (36.2%, 17/47) was less diverse than in MSSA (70.2%, 33/47). The most predominant spa types were t032 (50%) in MRSA, and t127 (19%) and t091 (16.7%) in MSSA, respectively. spa type t091 in MSSA was significantly associated with skin and soft tissue infections (p = 0.0199).

Conclusion

The previously uncommon spa type t032 was detected in the Malaysian MRSA strains, which also corresponded to the most common spa type in Europe and Australia, and has replaced the dominant spa type t037 which was reported in Malaysia in 2010.

Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting

Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.

Genomic analysis revealed a novel genotype of methicillin-susceptible Staphylococcus aureus isolated from a fatal sepsis case in dengue patient

Staphylococcus aureus (S. aureus) is an opportunistic pathogen capable of causing serious health implications in susceptible individuals once it invades the host’s protective barriers. Methicillin-susceptible S. aureus (MSSA) often receives lesser attention although it has been frequently associated with serious infections in human. We aim to investigate the genomic features of a highly virulent yet pan susceptible MSSA strain (coded as HS-MSSA) which caused concurrent bacteraemia in a dengue patient, ultimately resulted in sepsis death of the patient. Whole genome sequence analysis was performed. The draft genome of HS-MSSA is approximately 2.78 Mb (GC content = 32.7%) comprising of 2637 predicted coding sequences. In silico genotyping of the HS-MSSA strain revealed a novel combined genotype (t091/ST2990). The HS-MSSA carries a SaPIn1-like pathogenicity island that harbours the staphylococcal enterotoxin and enterotoxin-like genes (sec3 and selL). The strain-specific β-lactamase (blaZ)-bearing plasmid region was identified in HS-MSSA. Core genome phylogeny showed that the HS-MSSA strain shared a common ancestry with the European MRSA clone. We report herein the genomic features of an MSSA lineage with novel genotype previously not reported elsewhere.

Prevalence of MRSA nasal carriage among pregnant women in Copenhagen

Background

Methicillin resistant Staphylococcus aureus (MRSA) frequently causes outbreaks in neonatal intensive care units (NICUs). It is believed that MRSA predominantly enters the NICU with MRSA colonized parents. In Denmark, 27 MRSA NICU outbreaks have been registered between 2008 and 2019.

Aim

The aim of this study was to determine the prevalence of MRSA nasal carriage in pregnant women in Copenhagen and to clarify if MRSA screening during pregnancy could add to the prevention of NICU outbreaks.

Methods

All pregnant women 18 years or older were offered MRSA nasal screening at their first midwife visit between 13 and 20 weeks of gestation.

Results

1778 pregnant women were included, two (0.11%) carried MRSA in the nose.

Conclusion

Infants of the two MRSA positive women were not admitted to a NICU and therefore the screening had no impact on NICU outbreaks. The low prevalence of MRSA found in this study does not justify MRSA screening of all pregnant women in Denmark.

Comparative Microbiological and Whole-Genome Analysis of Staphylococcus aureus Populations in the Oro-Nasal Cavities, Skin and Diabetic Foot Ulcers of Patients With Type 2 Diabetes Reveals a Possible Oro-Nasal Reservoir for Ulcer Infection

Patients with type 2 diabetes are at higher risk for periodontal disease and diabetic foot ulcer infections (DFUIs), the latter of which are predominantly caused by staphylococcal bacteria. Staphylococci have also been detected in the mouth, nose and gums (the oro-nasal cavity) of patients with periodontal disease and can move between the mouth and nose. The present study investigated if the oro-nasal cavity and/or periodontal pockets (PPs) in diseased gum tissue can provide a microbial reservoir for DFUIs. Eighteen patients with type 2 diabetes and at least three natural teeth (13 patients with ulcers and 5 patients without ulcers) underwent non-invasive microbiological sampling of PP, oro-nasal, skin and ulcer sites. Staphylococci were recovered using selective chromogenic agar, definitively identified and subjected to DNA microarray profiling, whole-genome sequencing and core-genome multilocus sequence typing (cgMLST). Staphylococcus aureus and Staphylococcus epidermidis were recovered from both the oro-nasal and ulcer sites of 6/13 and 5/13 patients with ulcers, respectively. Molecular typing based on the staphylococcal protein A (spa) gene and DNA microarray profiling indicated that for each patient investigated, S. aureus strains from oro-nasal and ulcer sites were identical. Comparative cgMLST confirmed that isolates from multiple anatomical sites of each individual investigated grouped into closely related, patient-distinct clusters (Clusters 1-7). Isolates belonging to the same cluster exhibited an average of 2.9 allelic differences (range 0-11). In contrast, reference genomes downloaded from GenBank selected as representatives of each sequence type identified in the present study exhibited an average of 227 allelic differences from the most closely related isolate within each cluster.

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

This review assessed the molecular characterization of the methicillin-resistant Staphylococcus aureus (MRSA)-ST80 clone with an emphasis on its proportion of total MRSA strains isolated, PVL production, spa-typing, antibiotic resistance, and virulence. A systematic review of the literature was conducted on MRSA-ST80 clone published between 1 January 2000 and 31 August 2019. Citations were chosen for a review of the full text if we found evidence that MRSA-ST80 clone was reported in the study. For each isolate, the country of isolation, the sampling period, the source of isolation (the type of infection, nasal swabs, or extra-human), the total number of MRSA strains isolated, number of MRSA-ST80 strains, antibiotic resistance patterns, PVL production, virulence genes, and spa type were recorded. The data from 103 articles were abstracted into an Excel database. Analysis of the data showed that the overall proportion of MRSA-ST80 has been decreasing in many countries in recent years. The majority of MRSA-ST80 were PVL positive with spa-type t044. Only six reports of MRSA-ST80 in extra-human niches were found. This review summarizes the rise of MRSA-ST80 and the evidence that suggests that it could be in decline in many countries.

Comparative Microbiological and Whole-Genome Analysis of Staphylococcus aureus Populations in the Oro-Nasal Cavities, Skin and Diabetic Foot Ulcers of Patients With Type 2 Diabetes Reveals a Possible Oro-Nasal Reservoir for Ulcer Infection

Patients with type 2 diabetes are at higher risk for periodontal disease and diabetic foot ulcer infections (DFUIs), the latter of which are predominantly caused by staphylococcal bacteria. Staphylococci have also been detected in the mouth, nose and gums (the oro-nasal cavity) of patients with periodontal disease and can move between the mouth and nose. The present study investigated if the oro-nasal cavity and/or periodontal pockets (PPs) in diseased gum tissue can provide a microbial reservoir for DFUIs. Eighteen patients with type 2 diabetes and at least three natural teeth (13 patients with ulcers and 5 patients without ulcers) underwent non-invasive microbiological sampling of PP, oro-nasal, skin and ulcer sites. Staphylococci were recovered using selective chromogenic agar, definitively identified and subjected to DNA microarray profiling, whole-genome sequencing and core-genome multilocus sequence typing (cgMLST). Staphylococcus aureus and Staphylococcus epidermidis were recovered from both the oro-nasal and ulcer sites of 6/13 and 5/13 patients with ulcers, respectively. Molecular typing based on the staphylococcal protein A (spa) gene and DNA microarray profiling indicated that for each patient investigated, S. aureus strains from oro-nasal and ulcer sites were identical. Comparative cgMLST confirmed that isolates from multiple anatomical sites of each individual investigated grouped into closely related, patient-distinct clusters (Clusters 1-7). Isolates belonging to the same cluster exhibited an average of 2.9 allelic differences (range 0-11). In contrast, reference genomes downloaded from GenBank selected as representatives of each sequence type identified in the present study exhibited an average of 227 allelic differences from the most closely related isolate within each cluster.

Status and potential of bacterial genomics for public health practice: a scoping review

Background

Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective.

Methods

In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed.

Results

Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data.

Conclusions

For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.

Electronic supplementary material

The online version of this article (10.1186/s13012-019-0930-2) contains supplementary material, which is available to authorized users.

Genomic analysis of Staphylococcus aureus along a pork production chain and in the community, Shandong Province, China

Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) is an increasingly important public health concern worldwide; however, data on LA-MRSA from Asian countries is scarce. As such, a comprehensive molecular epidemiological survey of S. aureus along a pork production chain and in the community was undertaken in Shandong Province, China. spa typing and whole-genome sequencing were used to survey the occurrence and potential transmission of S. aureus in various sectors, including 899 porcine samples (snout or skin swabs, carcass swabs and pork portions), 845 human nasal samples and 239 environmental samples from commercial farms, a slaughterhouse, a pork wholesale market and the surrounding community. MRSA was detected in higher frequencies in samples from two commercial pig farms (pigs, 49%; farm workers, 64%; environmental samples, 16%) than in samples from the slaughterhouse (fatteners, 8.2%; carcasses, 1.1%; operation workers, 0%; environmental samples, 3.8%), the pork wholesale market (pork, 14%; sellers, 0%) and individuals in the community (6.8%). There were significant differences in population structures, antimicrobial susceptibility profiles, and the presence of resistance and virulence genes between human- and pig-associated isolates. The phylogenetic analysis confirmed the dissemination of LA-MRSA between various segments along the pork production chain. However, MRSA of the same sequence type was not found to be disseminated between the commercial farms and the surrounding communities. Furthermore, one MRSA ST398 was observed, and a novel CC9 variant ST3597 was detected within the chain. The high MRSA carriage rates and the emergence of a new MRSA CC9 variant identified in this study highlight the need for MRSA surveillance.

Eradicating MRSA carriage: the impact of throat carriage and Panton-Valentine leukocidin genes on success rates

In Denmark, eradication treatment is recommended for methicillin-resistant Staphylococcus aureus (MRSA) carriers. Here, we analyze factors associated with eradication outcome. MRSA carriers referred to the MRSA Knowledge Center at Hvidovre Hospital in 2013 were included. Carriers were sampled from nose, throat, and perineum. Eradication regimen was 5 days of mupirocin nasal ointment and chlorhexidine whole-body wash. Oral antibiotics were sometimes added. Factors associated with eradication after the first eradication attempt were analyzed by logistic regression and expressed as odds ratio (OR) with 95% confidence interval (95% CI). Of 164 individuals, 143 completed 1- and 6-month follow-up after 1st treatment. Eradication was achieved in 63 (38.4%) patients after one treatment and 101 (61.6%) individuals became MRSA free after up to 4 eradication treatments. Throat carriage was associated with a higher failure rate (OR 0.29 (0.10-0.80)), while the presence of Panton-Valentine leukocidin (PVL) genes (37%) was associated with higher success rate (OR 3.52 (1.44-8.57)). Other factors analyzed were not significantly associated with eradication outcome. None of the 26 patients lost to follow-up developed later MRSA infections. This study estimates the efficacy of treatment of MRSA carriage with an eradication rate of 38.4% after the first treatment and a total eradication rate of 61.6% after several treatments. Throat carriers had a lower eradication success rate. Adding oral antibiotics to the first treatment did not increase success. The finding of a significant higher success rate when having a PVL-positive clone should be further investigated.

A Sporadic Four-Year Hospital Outbreak of a ST97-IVa MRSA With Half of the Patients First Identified in the Community

This study describes a sporadically occurring 4-year outbreak of methicillin-resistant Staphylococcus aureus (MRSA) originating from a surgical ward. Whole-genome sequencing (WGS) identified the outbreak clone as spa type t267, sequence type ST97, and SCCmec IVa. Prompted by the finding of four patients within 6 months in the same ward with this unusual MRSA type, an outbreak was suspected. Subsequent MRSA screening in the ward in February 2017 identified three-additional patients and two health care workers (HCWs) with t267/ST97-IVa. WGS linked these 9 isolates to 16 previous isolates in our WGS database and the outbreak thus included 23 patients and two HCWs. Twenty-one patients had a connection to the surgery ward during the period 2013-2017, but half of them had MRSA diagnosed in the community long after discharge. The community debut of several patients MRSA infections weeks to months after hospital discharge made the identification of a hospital source difficult and it was the SNP relatedness of the isolates that led us to identify the common denominator of hospitalization. An index patient was not identified, but our hypothesis is that HCWs with unrecognized long-term MRSA colonization could have caused sporadic nosocomial transmission due to intermittent breaches in infection prevention and control practice.

Multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and intermediate resistance to azithromycin, Denmark, 2017

We describe a multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and azithromycin intermediate resistance in a heterosexual man in Denmark, 2017. Whole genome sequencing of the strain GK124 identified MSLT ST1903, NG-MAST ST1614 and all relevant resistance determinants including similar penA resistance mutations previously described in ceftriaxone-resistant gonococcal strains. Although treatment with ceftriaxone 0.5 g plus azithromycin 2 g was successful, increased awareness of spread of gonococcal strains threatening the recommended dual therapy is crucial.

Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulent S. aureus lineages [clonal complexes (CCs): CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based on de novo assembly (reference-free approach), single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers. We examined the phylogeographic diversity of the French dominant hospital-acquired CC8-MRSA (methicillin-resistant S. aureus) Lyon clone through WGS analysis which did not demonstrate evidence of large-scale geographic clustering. We analyzed sporadic cases along with two outbreaks of a CC1-MSSA (methicillin-susceptible S. aureus) clone containing the Panton–Valentine leukocidin (PVL) and results showed that two sporadic cases were closely related. We investigated an outbreak of PVL-positive CC30-MSSA in a school environment and were able to reconstruct the transmission history between eight families. We explored different outbreaks among newborns due to the CC5-MRSA Geraldine clone and we found evidence of an unsuspected link between two otherwise distinct outbreaks. Here, WGS provides the resolving power to disprove transmission events indicated by conventional methods (same sequence type, spa type, toxin profile, and antibiotic resistance profile) and, most importantly, WGS can reveal unsuspected transmission events. Therefore, WGS allows to better describe and understand outbreaks and (inter-)national dissemination of S. aureus lineages. Our findings underscore the importance of adding WGS for (inter-)national surveillance of infections caused by virulent clones of S. aureus but also substantiate the fact that technological optimization at the bioinformatics level is still urgently needed for routine use. However, the greatest limitation of WGS analysis is the completeness and the correctness of the reference database being used and the conversion of floods of data into actionable results. The WGS bioinformatics pipeline (EpiSeq^TM) we used here can easily generate a uniform database and associated metadata for epidemiological applications.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016

The data on antimicrobial resistance in zoonotic and indicator bacteria in 2016, submitted by 28 EU Member States (MSs), were jointly analysed by the EFSA and ECDC. Resistance in bacterial isolates of zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as in meticillin-resistant Staphylococcus aureus from animals and food were addressed. 'Microbiological' resistance was assessed using epidemiological cut-off (ECOFF) values; for some countries, qualitative data on isolates from humans were interpreted in a way that corresponds closely to ECOFF-defined 'microbiological' resistance. In Salmonella from humans, the occurrence of resistance to ampicillin, sulfonamides and tetracyclines was high, whereas resistance to third-generation cephalosporins was low. In Salmonella and E. coli isolates from broilers, fattening turkeys and their meat, resistance to ampicillin, (fluoro)quinolones, tetracyclines and sulfonamides was frequently high, whereas resistance to third-generation cephalosporins was rare. The occurrence of ESBL-/AmpC producers was low in Salmonella and E. coli from poultry and in Salmonella from humans. The prevalence of ESBL-/AmpC-producing E. coli, assessed in poultry and its meat for the first time, showed marked variations among MSs. Fourteen presumptive carbapenemase-producing E. coli were detected from broilers and its meat in two MSs. Resistance to colistin was observed at low levels in Salmonella and E. coli from poultry and meat thereof and in Salmonella from humans. In Campylobacter from humans, broilers and broiler meat, resistance to ciprofloxacin and tetracyclines was high to extremely high, whereas resistance to erythromycin was low to moderate. Combined resistance to critically important antimicrobials in isolates from both humans and animals was generally uncommon, but very high to extremely high multidrug resistance levels were observed in certain Salmonella serovars. Specific serovars of Salmonella (notably Kentucky) from both humans and animals exhibited high-level resistance to ciprofloxacin, in addition to findings of ESBL.

Use of a Regression Model to Study Host-Genomic Determinants of Phage Susceptibility in MRSA

Staphylococcus aureus is a major agent of nosocomial infections. Especially in methicillin-resistant strains, conventional treatment options are limited and expensive, which has fueled a growing interest in phage therapy approaches. We have tested the susceptibility of 207 clinical S. aureus strains to 12 (nine monovalent) different therapeutic phage preparations and subsequently employed linear regression models to estimate the influence of individual host gene families on resistance to phages. Specifically, we used a two-step regression model setup with a preselection step based on gene family enrichment. We show that our models are robust and capture the data’s underlying signal by comparing their performance to that of models build on randomized data. In doing so, we have identified 167 gene families that govern phage resistance in our strain set and performed functional analysis on them. This revealed genes of possible prophage or mobile genetic element origin, along with genes involved in restriction-modification and transcription regulators, though the majority were genes of unknown function. This study is a step in the direction of understanding the intricate host-phage relationship in this important pathogen with the outlook to targeted phage therapy applications.

Development of a rapid MALDI-TOF MS based epidemiological screening method using MRSA as a model organism

In this study we present a method using whole cell MALDI-TOF MS and VITEK MS RUO/SARAMIS as a rapid epidemiological screening tool. MRSA was used as a model organism for setting up the screening strategy. A collection of well-characterised MRSA strains representing the 19 most common Pulsed-Field Gel Electrophoresis (PFGE)-types in the region of South-West Sweden for the past 20 years was analysed with MALDI-TOF MS. A total of 111 MRSA strains were used for creating 19 PFGE-specific Superspectra using VITEK MS RUO/SARAMIS. Prior to performing the final analysis, the 19 Superspectra were combined into ten groups displaying similar peak patterns, hereafter named “MALDI-types”. Two-hundred fifty-five MRSA strains were analysed to test the constructed Superspectra/MALDI-type database. Matches to the Superspectra above a threshold of 65% (corresponding to the number of matched peaks in the Superspectrum) were considered as positive assignment of a strain to a MALDI-type. The median peak matching value for correct assignment of a strain to a MALDI-type was 78% (range 65.3–100%). In total, 172 strains (67.4%) were assigned to the correct MALDI-type and only 5.5% of the strains were incorrectly assigned to another MALDI-type than the expected based on the PFGE-type of the strain. We envision this methodology as a cost-efficient step to be used as a first screening strategy in the typing scheme of MRSA isolates, to exclude epidemiological relatedness of isolates or to identify the need for further typing.

Staphylococcal aureus Enterotoxin C and Enterotoxin-Like L Associated with Post-partum Mastitis

Denmark is a low prevalence country with regard to methicillin resistant Staphylococcus aureus (MRSA). In 2008 and 2014, two neonatal wards in the Copenhagen area experienced outbreaks with a typical community acquired MRSA belonging to the same spa type and sequence type (t015:ST45) and both were PVL and ACME negative. In outbreak 1, the isolates harbored SCCmec IVa and in outbreak 2 SCCmec V. The clinical presentation differed between the two outbreaks, as none of five MRSA positive mothers in outbreak 1 had mastitis vs. five of six MRSA positive mothers in outbreak 2 (p < 0.02). To investigate if whole-genome sequencing could identify virulence genes associated with mastitis, t015:ST45 isolates from Denmark (N = 101) were whole-genome sequenced. Sequence analysis confirmed two separate outbreaks with no sign of sustained spread into the community. Analysis of the accessory genome between isolates from the two outbreaks revealed a S. aureus pathogenicity island containing enterotoxin C and enterotoxin-like L only in isolates from outbreak 2. Enterotoxin C and enterotoxin-like L carrying S. aureus are associated with bovine mastitis and our findings indicate that these may also be important virulence factors for human mastitis.

Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus: Blurring of the traditional definitions

The evolution of meticillin-resistant Staphylococcus aureus (MRSA) from meticillin-susceptible S. aureus has been a result of the accumulation of genetic elements under selection pressure from antibiotics. The traditional classification of MRSA into healthcare-associated MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA) is no longer relevant as there is significant overlap of identical clones between these groups, with an increasing recognition of human infection caused by livestock-associated MRSA (LA-MRSA). Genomic studies have enabled us to model the epidemiology of MRSA along these lines. In this review, we discuss the clinical relevance of genomic studies, particularly whole-genome sequencing, in the investigation of outbreaks. We also discuss the blurring of each of the three epidemiological groups (HA-MRSA, CA-MRSA and LA-MRSA), demonstrating the limited relevance of this classification.

Can MLVA Differentiate among Endemic-Like MRSA Isolates with Identical Spa-Type in a Low-Prevalence Region?

The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Norway is low, but an endemic-like MRSA clone with Staphylococcal protein A (spa)-type t304 has been established especially in nursing homes in the Oslo region causing several large outbreaks. The challenge was that spa-typing and the gold standard Pulsed-Field Gel Electrophoresis (PFGE) were inadequate in discriminating isolates in outbreak investigations. Additional higher resolution genotyping methods were needed. The aims of this study were a) to evaluate whether Multiple-Locus Variable number of tandem repeat Analysis (MLVA) could differentiate within the PFGE clusters between epidemiologically related and unrelated endemic-like ST8-MRSA-IV-t304-PVL-neg (MRSA-t304) isolates and b) investigate the evolution of the endemic-like MRSA-t304 clone over a 15-year time period. All MRSA-t304 isolates detected in the region from 1998 through April 2013 were included. In total, 194 of 197 isolates were available for PFGE and MLVA analyses. PFGE results on isolates from 1998-2010 have been published previously. Two PFGE clusters subdivided into eight MLVA types were detected. One major outbreak clone (PFGE cluster C2/ MLVA type MT5045) appeared from 2004 to 2011 causing long-lasting and large outbreaks in seven nursing homes and one hospital. Five new MLVA types (N = 9 isolates) differing in only one VNTR compared to the outbreak clone C2/MT5045 were detected, but only one (C2/MT5044) was seen after 2011. We suggest that MLVA can replace PFGE analysis, but MLVA may not be the optimal method in this setting as it did not discriminate between all epidemiologically unrelated isolates. The results may indicate that all eight outbreaks in different locations within the PFGE C2 cluster may be branches of one large regional outbreak. The major outbreak strain C2/MT5045 may now, however, be under control, extinguished or has moved geographically.

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England and was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.