Potential impact of whole genome sequencing in diagnostic and public health microbiology.

<p>Clinical samples processed by diagnostic microbiology laboratories commonly pass through up to four stages, characterised by a stepwise decrease in the number of samples analysed at each successive stage and an inverse association with turn-around time (TAT), labour, and costs (shown in dark blue). Detection, identification, and susceptibility testing in virology are achieved using serological or molecular methods, whereas bacteriology generally relies on phenotypic methods. Epidemiological typing is only done for a handful of organisms using molecular and sometimes phenotypic methods. The most compelling immediate applications for WGS are molecular epidemiology for the purposes of surveillance and outbreak investigation (e.g. for MRSA) and drug susceptibility testing for organisms that are either slow growers or difficult to culture (e.g. MTBC and HIV). This is likely to lead to more samples being typed than is currently the case (depicted in purple), all while drastically reducing turnaround times, provided that WGS is performed in a regional or local laboratory rather than a reference centre. Assuming that this information enables cost-effective clinical interventions, the number of pathogens sequenced is likely to increase over time. Approaches to detection and identification of pathogens and the majority of susceptibility testing are likely to remain largely unchanged in the near future.</p

Overview of pathogen WGS data interpretation and use.

<p>After an enrichment step for pathogen DNA via culture or direct molecular enrichment/amplification (e.g. by RT-PCR for HIV) from the clinical sample, WGS could be performed in regional sequencing hubs. Fully automated analysis software would extract information of immediate clinical importance (i.e. an epidemiological analysis, susceptibility testing, and/or the precise identity of the pathogen). The results would be presented such that no knowledge of genomics would be required. Only in cases of new and emerging types of concern, where the genotype-phenotype relationship was unclear, or for quality control (QC) purposes would samples be sent for analysis by reference laboratories. Reference laboratories could routinely make anonymised sequence data available in the first part of an international online encyclopaedia to spur basic as well as translational research via a user-friendly interface to analyse whole genomes. Moreover, they could perform routine <i>in silico</i> surveillance of all genomes in their respective countries to relate treatment outcomes to particular genotypes or mutations. Clinically relevant surveillance results such as the discovery of novel pathogens or new markers for drug-resistance could be shared with appropriate international bodies and ultimately deposited in the encyclopaedia <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002824#ppat.1002824-National1" target="_blank">[101]</a>. A forum could provide an opportunity for the scientific community to contribute and discuss findings with clinical implications. Novel markers would require review by an expert panel and, if approved, be incorporated into the read-only diagnostic database containing a catalogue of known resistance markers, which would then be used clinically by the automated WGS interpretation software.</p

Characteristics of the eight MRSA isolates found in the survey of conference participants.

1<p>Susceptibilities tested: linezolid, rifampicin, kanamycin, norfloxacin, erythromycin, clindamycin, fusidic acid, tetracycline, trimethoprim/sulfamethoxazole and mupirocin.</p>2<p>Genome screened for <i>tetM</i> M21136, <i>tetK</i> NC_017331_REGION: 69118.70497, <i>msrSA</i> AB013298_487.1953, <i>mphC</i> NC_017351 REGION: 53170.54069, <i>ileS</i> AJJR01000036 REGION: 742.3816, <i>fusC</i> HE980450 REGION: 10019.10657, <i>ermA</i> NC_002745 _N315, <i>dfrG</i> AB205645 REGION: 1013.1510, AB568461 <i>Staphylococcus aureus aacA</i>-<i>aphD</i> gene for bifunctional AAC/APH, <i>gyrA</i> CP000046_COL, <i>rpoB</i> X64172 REGION: 1222.4770, <i>tetL</i> JN970906 REGION: 8454.9830, <i>ermC</i> NC007792 REGION: 7865.8599 <i>ermT</i> NC017673 REGION: 1795197.1795946.</p

Characteristics of the three <i>S</i>. <i>haemolyticus</i> isolates found in the survey of conference participants.

1<p>Susceptibilities tested: linezolid, rifampicin, kanamycin, norfloxacin, erythromycin, clindamycin, fusidic acid, tetracycline, trimethoprim/sulfamethoxazole and mupirocin.</p

A summary of the results from previous MRSA carriage surveys undertaken at veterinary or animal health conferences.

<p>ACVIM, The American College of Veterinary Internal Medicine; AAEP, American Association of Equine practitioners; ACVS, American College of Veterinary Surgeons.</p

Image_6_Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.PDF

<p>Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas.</p><p>Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973–1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia’s east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations.</p><p>Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.</p

Image_5_Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.PDF

<p>Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas.</p><p>Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973–1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia’s east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations.</p><p>Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.</p

Table_4_Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.XLSX

<p>Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas.</p><p>Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973–1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia’s east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations.</p><p>Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.</p

Table_5_Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.XLSX

<p>Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas.</p><p>Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973–1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia’s east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations.</p><p>Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.</p

Image_3_Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.PDF

<p>Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas.</p><p>Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973–1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia’s east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations.</p><p>Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.</p