Lessons Learnt From Using the Machine Learning Random Forest Algorithm to Predict Virulence in Streptococcus pyogenes

Group A Streptococcus is a globally significant human pathogen. The extensive variability of the GAS genome, virulence phenotypes and clinical outcomes, render it an excellent candidate for the application of genotype-phenotype association studies in the era of whole-genome sequencing. We have catalogued the distribution and diversity of the transcription regulators of GAS, and employed phylogenetics, concordance metrics and machine learning (ML) to test for associations. In this review, we communicate the lessons learnt in the context of the recent bacteria genotype-phenotype association studies of others that have utilised both genome-wide association studies (GWAS) and ML. We envisage a promising future for the application GWAS in bacteria genotype-phenotype association studies and foresee the increasing use of ML. However, progress in this field is hindered by several outstanding bottlenecks. These include the shortcomings that are observed when GWAS techniques that have been fine-tuned on human genomes, are applied to bacterial genomes. Furthermore, there is a deficit of easy-to-use end-to-end workflows, and a lag in the collection of detailed phenotype and clinical genomic metadata. We propose a novel quality control protocol for the collection of high-quality GAS virulence phenotype coupled to clinical outcome data. Finally, we incorporate this protocol into a workflow for testing genotype-phenotype associations using ML and ‘linked’ patient-microbe genome sets that better represent the infection event.

The Persistence of Neutralising Antibodies up to 11 months after SARS-CoV-2 Infection in the Southern Region of New Zealand

SummaryDuring the first wave of SARS-CoV-2 infection in New Zealand a cohort of 78 PCR-confirmed COVID-19 cases was recruited in the Southern District Health Board region. Here we report on this unique cohort nearly 1-year after infection. There was no known community transmission in the region over the study period due to New Zealand’s elimination status at the time, nor had any participants received a COVID-19 vaccine. In the absence of re-exposure, antibody reactivity to the viral spike protein, as well as neutralising antibodies to both the ancestral strain and the delta variant remained relatively stable between 8 and 11 months post-infection. This suggests long-lived antibody responses can be generated from a single natural infection event. However, given the risks of serious disease associated with SARS-CoV-2 infection, vaccination is still strongly recommended.

Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia

We describe the case of a 23-year-old immunocompromised male patient with clinically diagnosed X-linked agammaglobulinemia who was admitted to the hospital on the 14th April 2020 due to coronavirus disease of 2019 (COVID-19). Despite COVID-19 test negativizations, the patient was hospitalized most of the time and finally admitted to the intensive care unit where he died from multiorgan failure and shock. Over 149 days, 26 respiratory samples were collected, subjected to viral genome sequencing, and all assigned to the same lineage, supporting a single viral infection event. The accumulation of mutations throughout the course of the infection was accelerated and suggested the presence of compartmentalized viral subpopulations that evolved independently in the upper and lower respiratory airways. These results support that long-term viral shedding in immunocompromised patients is one possible mechanism for the emergence of variants of concern and provide evidence towards the infection control guidelines in these patients.

Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia

We describe the case of a 23-year-old immunocompromised male patient with clinically diagnosed X-linked agammaglobulinemia who was admitted to the hospital on the 14th April 2020 due to coronavirus disease of 2019 (COVID-19). Despite COVID-19 test negativizations, the patient was hospitalized most of the time and finally admitted to the intensive care unit where he died from multiorgan failure and shock. Over 149 days, 26 respiratory samples were collected, subjected to viral genome sequencing, and all assigned to the same lineage, supporting a single viral infection event. The accumulation of mutations throughout the course of the infection was accelerated and suggested the presence of compartmentalized viral subpopulations that evolved independently in the upper and lower respiratory airways. These results support that long-term viral shedding in immunocompromised patients is one possible mechanism for the emergence of variants of concern and provide evidence towards the infection control guidelines in these patients.

The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients

BackgroundInfection and rejection are the two most common complications after lung transplantation (LT) and are associated with increased morbidity and mortality. The differential diagnosis of infection and rejection is sometimes difficult due to similar clinical manifestations. However, few studies have investigated the airway microbiota between lung transplant recipients (LTRs) with infection and rejection. ResultsA total of 181 sputum samples (event-free, n=47; infection, n=103; rejection, n=31) were collected from 59 LTRs. A distinct airway microbiota was observed among clinically stable (or event-free) recipients and those with infection or acute rejection after LT. Alpha and beta diversity were significantly different between event-free and rejection recipients and between infection and rejection recipients. Ten differential genera were identified by linear discriminant analysis effect size (LEfSe), with Corynebacterium, unclassified Enterococcaceae and unclassified Lactobacillales enriched in recipients with infection, and Rothia, Granulicatella, Neisseria, Actinomyces, Leptotrichia, Lactobacillus and unclassified Aerococcaceae more abundant in LTRs with acute rejection. Random forest analyses indicated that the combination of the 10 microbiota constituents and procalcitonin (PCT) and T-lymphocyte levels showed AUCs of 0.894, 0.955 and 0.913 to differentiate between event-free and infection, event-free and rejection, and infection and rejection recipients, respectively. ConclusionsOur study is the first to compare the airway microbiota between LTRs with infection and acute rejection. The airway microbiota, especially combined with PCT and T-lymphocyte levels, showed satisfactory predictive efficiency in discriminating among clinically stable recipients and those with infection and acute rejection, suggesting that the airway microbiota was an indicator to differentiate between infection and acute rejection after LT.

Three SARS-CoV-2 reinfection cases by the new Variant of Concern (VOC) P.1/501Y.V3

The SARS-CoV-2 lineage B.1.1.28 has been evolving in Brazil since February 2020 giving origin to multiple local clades including the new Variant of Concern (VOC) designated P.1 or 501Y.V3. The recent emergence of sub-lineages with convergent mutations in the spike (S) protein raises concern about the potential impact on viral infectivity and immune escape. We describe here the first three confirmed SARS-CoV-2 reinfections cases with the new VOC P.1 in residents of the Amazonas state, Brazil. Three female patients, 29, 40, and 50-year-old, were RT-PCR confirmed for SARS-CoV-2 on two occasions, with at least 92 days apart. Next-generation sequencing and phylogenetic analysis were conducted to precisely access the SARS-CoV-2 lineages of each infection event. SARS-CoV-2 genomic analysis confirmed three cases of reinfections caused by the VOC P.1 in patients that were primo-infected by distinct viral lineages 3–9 months earlier. Case 1 (29-year-old) was positive on March 24, 2020 (lineage B.1.195) and then on December 30, 2020 (lineage P.1); case 2 (50-year-old) was positive on October 19, 2020 (lineage B.1.1.33) and on January 19, 2021 (lineage P.1); case 3 (40-year-old) was positive on April 22, 2020 (lineage B.1.195) and on January 29, 2021 (lineage P.1). The three patients displayed low mean Ct values (< 22) at nasopharyngeal samples and reported less severe illness during reinfection. The present study provides the first evidence of the new VOC P.1 causing multiple reinfections during the second epidemic peak in the Amazonas state. Our findings suggest that reinfected individuals may have been infectious. Although immune responses induced by natural infections do not necessarily prevent subsequent infections by the VOC P.1, they may still protect from severe disease.

Validation of the Strawberry Advisory System in the Mid-Atlantic Region

Anthracnose fruit rot (AFR) and Botrytis fruit rot (BFR) are primary diseases affecting strawberry, which typically drive fungicide applications throughout the growing season. The Strawberry Advisory System (StAS), a disease forecasting tool, was originally developed in Florida to better time fungicide sprays by monitoring AFR and BFR infection risk based on leaf wetness and temperature input in real-time. Thirteen field trials were conducted in Maryland and Virginia between 2017 and 2019 to evaluate the StAS performance in the Mid-Atlantic region. As a result, 55%, 18%, and 31% fewer sprays were recorded on average in the model-based StAS treatment compared with the grower standard treatment in 2017, 2018, and 2019, respectively. Marketable yield, as well as AFR and BFR incidence were largely comparable between the two treatments. However, poor disease control occurred during the StAS treatment in four trials in 2017, presumably due to a missed fungicide spray during a high-risk infection event and attributable to heavy rainfall that led to impassable fields. The implementation of the StAS may be further challenged by the employment of floating row covers that are essential for growing strawberries in plasticulture systems in open-fields in the Mid-Atlantic region. Preliminary results indicated that row covers can alter canopy-level microclimatic conditions, possibly increasing the risk for disease occurrence. Overall, the StAS can be a valuable tool for Mid-Atlantic growers to control AFR and BFR, but sprays may need to be promptly applied when consecutive or heavy rainfalls are predicted, especially for highly susceptible cultivars. Complications in disease forecasting and management arising from the use of row covers need to be further addressed in this region due to its highly diverse climate.

Clustering cases of Chlamydia psittaci pneumonia in COVID-19 screening ward staff

Four medical staff cases of Chlamydia psittaci pneumonia in a COVID-19 screening ward, as well as the experience in dealing with such a nosocomial infection event, were described. It reminds that atypical pneumonia except for COVID-19 should also be considered when clustering cases occurred even during a COVID-19 pneumonia pandemic.

Sex-based differences in clearance of chronic Plasmodium falciparum infection

Multiple studies have reported a male bias in incidence and/or prevalence of malaria infection in males compared to females. To test the hypothesis that sex-based differences in host-parasite interactions affect the epidemiology of malaria, we intensively followed Plasmodium falciparum infections in a cohort in a malaria endemic area of eastern Uganda and estimated both force of infection (FOI) and rate of clearance using amplicon deep-sequencing. We found no evidence of differences in behavioral risk factors, incidence of malaria, or FOI by sex. In contrast, females cleared asymptomatic infections at a faster rate than males (hazard ratio [HR]=1.82, 95% CI 1.20 to 2.75 by clone and HR = 2.07, 95% CI 1.24 to 3.47 by infection event) in multivariate models adjusted for age, timing of infection onset, and parasite density. These findings implicate biological sex-based differences as an important factor in the host response to this globally important pathogen.