NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource.

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains - many of medical, scientific and veterinary importance - available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection's second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.

No widespread dissemination of Chlamydia trachomatis diagnostic-escape variants and the impact of Neisseria gonorrhoeae positivity on the Aptima Combo 2 assay.

OBJECTIVES: A Finnish Chlamydia trachomatis (CT) new variant was detected in 2019 that escaped detection in the Hologic Aptima Combo 2 (AC2) assay due to a C1515T mutation in the CT 23S rRNA target region. Reflex testing of CT-negative/CT-equivocal specimens as well as those positive for Neisseria gonorrhoeae (NG) with the Hologic Aptima CT (ACT) assay was recommended to identify any CT variants. METHODS: From June to October 2019, specimens with discrepant AC2/ACT CT results were submitted to Public Health England and screened for detectable CT DNA using an inhouse real-time (RT)-PCR. When enough DNA was present, partial CT 23S rRNA gene sequencing was performed. Analysis of available relative light units and interpretative data was performed. RESULTS: A total of 317 discordant AC2/ACT specimens were collected from 315 patients. Three hundred were tested on the RT-PCR; 53.3% (n=160) were negative and 46.7% (n=140) were positive. Due to low DNA load in most specimens, sequencing was successful for only 36 specimens. The CT 23S rRNA wild-type sequence was present in 32 specimens, and two variants with C1514T or G1523A mutation were detected in four specimens from three patients. Of the discordant specimens with NG interpretation, 36.6% of NG-negative/CT-negative AC2 specimens had detectable CT DNA on the inhouse RT-PCR vs 53.3% of NG-positive/CT-negative specimens. CONCLUSIONS: No widespread dissemination of AC2 diagnostic-escape CT variants has occurred in England. We however identified the impact of NG positivity on the discordant AC2/ACT specimens; a proportion appeared due to NG positivity and the associated NG signal, rather than any diagnostic-escape variants or low DNA load. Several patients with gonorrhoea may therefore receive false-negative AC2 CT results. Single diagnostic targets and multiplex diagnostic assays have their limitations such as providing selection pressure for escape mutants and potentially reduced sensitivity, respectively. These limitations must be considered when establishing diagnostic pathways.

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies.

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.

Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511.

Kocuria rosea is a Gram-positive coccus found in the environment and within normal human skin microbiota, and more recently, it has been potentially implicated as an opportunistic pathogen. Here, we describe the genome sequences of five strains of K. rosea (NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511).

Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases.

Raoultella terrigena is a bacterial species associated with soil and aquatic environments; however, sporadic cases of opportunistic disease in humans have been reported. Here, we report the first two complete genome sequences from clinical strains isolated from human sources that have been deposited in the National Collection of Type Cultures (NCTC).

Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839.

Haemophilus haemolyticus is a Gram-negative bacterium that is a commensal of the respiratory tract in humans. Here, we report the complete genome sequence available for Haemophilus haemolyticus strain NCTC 10839, which was originally isolated from the nasopharynx of a child.

The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One.

The sixth global cholera pandemic lasted from 1899 to 1923. However, despite widespread fear of the disease and of its negative effects on troop morale, very few soldiers in the British Expeditionary Forces contracted cholera between 1914 and 1918. Here, we have revived and sequenced the genome of NCTC 30, a 102-year-old Vibrio cholerae isolate, which we believe is the oldest publicly available live V. cholerae strain in existence. NCTC 30 was isolated in 1916 from a British soldier convalescent in Egypt. We found that this strain does not encode cholera toxin, thought to be necessary to cause cholera, and is not part of V. cholerae lineages responsible for the pandemic disease. We also show that NCTC 30, which predates the introduction of penicillin-based antibiotics, harbours a functional ß-lactamase antibiotic resistance gene. Our data corroborate and provide molecular explanations for previous phenotypic studies of NCTC 30 and provide a new high-quality genome sequence for historical, non-pandemic V. cholerae.

Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939.

Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.

Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a gastrointestinal pathogen of increasing notoriety, often associated with diarrheal disease. P. shigelloides is waterborne, and infection is often linked to the consumption of seafood. Here, we describe the first complete genome for P. shigelloides type strain NCTC10360.

Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.

Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional opportunistic human pathogen which is associated with dog bite wounds. Here we report the first complete genomic sequence of the N. weaveri NCTC13585 (CCUG30381) strain, which was originally isolated from a patient with a canine bite wound.

Elemental analyses and determination of lead content in kohl (stone) by laser-induced breakdown spectroscopy.

Elemental analyses of kohl (stone) samples collected from three different parts of the world were performed using laser-induced breakdown spectroscopy (LIBS). The analyses indicated that lead (Pb), copper (Cu), silver (Ag), iron (Fe), calcium (Ca), aluminum (Al), silicon (Si), and sodium (Na) were present in all the kohl samples. In addition to these elements, the sample from Madina, Kingdom of Saudi Arabia (KSA), contained the elements tin (Sn), zirconium (Zr), and antimony (Sb). The sample from Mount Toor, Egypt, also contained Sn. Also, quantitative analysis for lead was carried out by the standard addition method using the LIBS technique. The result showed the presence of 14.12 ± 0.28% by weight of Pb in the sample from Madina, which compares well with the measurement done using atomic absorption spectroscopy (AAS) (13.31 ± 0.46%). The standard addition method used three calibration curves drawn for three emission lines of the LIBS spectra of Pb. The limits of detection (LoD) for these calibration curves varied from 0.27% to 1.16% by weight. The lead contents of the samples from Mount Toor and the local market of Bangladesh were also measured by the AAS technique, and the results were 14.61 ± 0.48% and 8.98 ± 0.35% by weight, respectively. The reason for determining only the lead content in kohl, which may be used as an eye cosmetic, is the adverse effect that lead has on health.

Relationship between postoperative cardiac troponin I levels and outcome of cardiac surgery.

BACKGROUND: Cardiac surgery may be associated with significant perioperative and postoperative morbidity and mortality. Underlying pathology, surgical technique, and postoperative complications may all influence outcome. These factors may be reflected as a rise in postoperative troponin levels. Interpretation of troponin levels in this setting may therefore be complex. This study assessed the prognostic significance of such measurements, taking into account potential confounding variables. METHODS AND RESULTS: One-thousand three hundred sixty-five patients undergoing cardiac surgery underwent measurement of cardiac troponin I (cTnI) at 2 and 24 hours after surgery. The relationship of these measurements to subsequent mortality was established. After taking into account all other variables, cTnI levels measured at 24 hours were independently predictive of mortality at 30 days (odds ratio [OR] 1.14 per 10 microg/L, 95% confidence interval [CI] 1.05 to 1.24, P=0.002), 1 year (OR 1.10 per 10 microg/L, 95% CI 1.03 to 1.18, P=0.006), and 3 years (OR 1.07 per 10 microg/L, 95% CI 1.00 to 1.15, P=0.04). Cardiac TnI levels in the highest quartile at 24 hours were associated with a particularly poor outcome. CONCLUSIONS: cTnI levels measured 24 hours after cardiac surgery predict short-, medium-, and long-term mortality and remain independently predictive when adjusted for all other potentially confounding variables, including operation complexity.