Complete microbial genomes for public health in Australia and the Southwest Pacific

Baines, Sarah L.; Silva, Anders Gonçalves da; Carter, Glen P.; Jennison, Amy V.; Rathnayake, Irani; Graham, Rikki; Sintchenko, Vitali; Wang, Qinning; Rockett, Rebecca; Timms, Verlaine J.; Martínez, Elena; Ballard, Susan A; Tomita, Takehiro; Isles, Nicole; Horan, Kristy; Pitchers, William; Stinear, Timothy P.; Williamson, Deborah A; Howden, Benjamin P; Seemann, Torsten

doi:10.1099/mgen.0.000471

Cited by 13 publications

(16 citation statements)

References 40 publications

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“…Plasmid pMKUB1_2 was 21 117 bp with 22 CDSs and was similar to previously reported Mycobacterium chimaera plasmids with accession numbers CP045967 [ 28 ] and CP015276 [ 29 ]. The plasmid included a β-lactam target ( ldtB ), transmembrane proteins ( mmpL4/mmpS4 ), nicotine degradation gene ( nicB ) and TP053 resistance mutation (Rv24662) ( Fig.…”

Section: Resultssupporting

confidence: 78%

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

et al. 2021

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Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium , many of the less common but clinically relevant NTM species, including M. kubicae , still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.

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Section: Resultssupporting

confidence: 78%

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

et al. 2021

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“…The clinical and natural environment isolates harboured the same core and accessory stress genes as the isolates from food processing environments with three exceptions: i) one clinical isolate harboured a chromosomally encoded tet (M) tetracycline resistance gene, identified through search against the ResFinder database (59), ii) one clinical isolate belonging to CC7 harboured the emrC gene conferring QAC resistance (71), and iii) none of the isolates harboured internal deletion mutations in inlB . All unique combinations of the accessory gene subset for clinical and environmental isolates are presented in Fig.…”

Section: Resultsmentioning

confidence: 99%

PervasiveListeria monocytogenesare common in the Norwegian food system and associated with increased prevalence of stress survival and resistance determinants

Fagerlund

Wagner

Møretrø

et al. 2022

Preprint

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To investigate the diversity, distribution, persistence, and stress resistome of Listeria monocytogenes clones dominating in food processing environments in Norway, genome sequences from 769 L. monocytogenes isolates from food industry environments, foods, and raw materials (of which 512 were sequenced in the present study) were subjected to wgMLST, SNP, and comparative genomic analyses. The dataset comprised isolates from nine meat and six salmon processing facilities in Norway collected over a period of three decades. The most prevalent clonal complex (CC) was CC121, found in ten factories, followed by CC7, CC8, and CC9, found in seven factories each. Overall, 72% of the isolates were classified as persistent, showing 20 or fewer wgMLST allelic differences towards an isolate found in the same factory in a different calendar year. Moreover, over half of the isolates (56%) showed this level of genetic similarity towards an isolate collected from a different food processing facility. These were designated as pervasive strains, defined as clusters with the same level of genetic similarity as persistent strains but isolated from different factories. The prevalence of genetic determinants associated with increased survival in food processing environments, including heavy metal and biocide resistance determinants, stress response genes and inlA truncation mutations, showed a highly significant increase among pervasive isolates, but not among persistent isolates. Furthermore, these genes were significantly more prevalent among the isolates from food processing environments compared to in isolates from natural and rural environments (n=218) and clinical isolates (n=111) from Norway.

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“…Fifteen Samoan S. Typhi strains were also selected to undergo long-read sequencing to obtain a complete genome. Within each genotype of S. Typhi presently circulating in Samoa, the oldest and most recent isolates were selected for genome closure at the MDU PHL using established pipelines (58, 59). Long-read sequencing libraries were prepared using the Oxford Nanopore Technologies ligation sequencing kit (SQK-LSK109) and sequenced on the GridION system using R9.4.1 flow cells.…”

Section: Methodsmentioning

confidence: 99%

Persistence of rareSalmonellaTyphi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

Sikorski

Hazen

Desai

et al. 2022

Preprint

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For decades, the remote island nation of Samoa (pop. ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008-2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sub-lineages were identified and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other clade 3.5 isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically-cryptic plasmid, detected earliest in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as to fill a critical knowledge gap in S. Typhi genomic data from Oceania.IMPORTANCEIn this study we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rare S. Typhi population in Samoa that likely emerged around the early 1970s and evolved into sub-lineages that presently dominate. The dominance and persistence of these endemic genotypes in Samoa are not readily explained by any apparent genomic competitive advantage or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance of S. Typhi in Samoa for public health benefit.

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Complete microbial genomes for public health in Australia and the Southwest Pacific

Cited by 13 publications

References 40 publications

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

PervasiveListeria monocytogenesare common in the Norwegian food system and associated with increased prevalence of stress survival and resistance determinants

Persistence of rareSalmonellaTyphi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

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