Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome

Molecular detection and typing of pathogenic Leptospira species from livestock and small mammals in Uganda

Leptospira are bacteria that cause leptospirosis in both humans and animals. Human Leptospira infections in Uganda are suspected to arise from animal-human interactions. From a nationwide survey to determine Leptospira prevalence and circulating sequence types in Uganda, we tested 2030 livestock kidney samples, and 117 small mammals (rodents and shrews) using real-time PCR targeting the lipL32 gene. Pathogenic Leptospira species were detected in 45 livestock samples but not in the small mammals. The prevalence was 6.12% in sheep, 4.25% in cattle, 2.08% in goats, and 0.46% in pigs. Sequence typing revealed that Leptospira borgpetersenii, Leptospira kirschneri, and Leptospira interrogans are widespread across Uganda, with 13 novel sequence types identified. These findings enhance the East African MLST database and support the hypothesis that domesticated animals may be a source of human leptospirosis in Uganda, highlighting the need for increased awareness among those in close contact with livestock.

Evolutionary insights into the emergence of virulent Leptospira spirochetes

Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the mammalian complement system and the adaptations to avoid activation of the innate immune cells by the highly-virulent Leptospira species (also called P1+ species), unlike other species belonging to the phylogenetically related P1- and P2 groups, as well as saprophytes. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.

Evolutionary insights into the emergence of virulent Leptospira spirochetes

Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the human complement system and the adaptations to avoid activation of the innate immune cells. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.

Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus

Hydrocephalus, the leading indication for childhood neurosurgery worldwide, is particularly prevalent in low- and middle-income countries. Hydrocephalus preceded by an infection, or postinfectious hydrocephalus, accounts for up to 60% of hydrocephalus in these areas. Since many children with hydrocephalus suffer poor long-term outcomes despite surgical intervention, prevention of hydrocephalus remains paramount. Our previous studies implicated a novel bacterial pathogen, Paenibacillus thiaminolyticus, as a causal agent of neonatal sepsis and postinfectious hydrocephalus in Uganda. Here, we report the isolation of three P. thiaminolyticus strains, Mbale, Mbale2, and Mbale3, from patients with postinfectious hydrocephalus. We constructed complete genome assemblies of the clinical isolates as well as the nonpathogenic P. thiaminolyticus reference strain and performed comparative genomic and proteomic analyses to identify potential virulence factors. All three isolates carry a unique beta-lactamase gene, and two of the three isolates exhibit resistance in culture to the beta-lactam antibiotics penicillin and ampicillin. In addition, a cluster of genes carried on a mobile genetic element that encodes a putative type IV pilus operon is present in all three clinical isolates but absent in the reference strain. CRISPR-mediated deletion of the gene cluster substantially reduced the virulence of the Mbale strain in mice. Comparative proteogenomic analysis identified various additional potential virulence factors likely acquired on mobile genetic elements in the virulent strains. These results provide insight into the emergence of virulence in P. thiaminolyticus and suggest avenues for the diagnosis and treatment of this novel bacterial pathogen. IMPORTANCE Postinfectious hydrocephalus, a devastating sequela of neonatal infection, is associated with increased childhood mortality and morbidity. A novel bacterial pathogen, Paenibacillus thiaminolyticus, is highly associated with postinfectious hydrocephalus in an African cohort. Whole-genome sequencing, RNA sequencing, and proteomics of clinical isolates and a reference strain in combination with CRISPR editing identified type IV pili as a critical virulence factor for P. thiaminolyticus infection. Acquisition of a type IV pilus-encoding mobile genetic element critically contributed to converting a nonpathogenic strain of P. thiaminolyticus into a pathogen capable of causing devastating diseases. Given the widespread presence of type IV pilus in pathogens, the presence of the type IV pilus operon could serve as a diagnostic and therapeutic target in P. thiaminolyticus and related bacteria.

Prevalence of anti-leptospiral IgM and detection of pathogenic Leptospira species DNA in neonates presenting with clinical sepsis in Southwestern Uganda

BACKGROUND

Leptospirosis is an emerging neglected zoonotic disease that presents with nonspecific signs/symptoms and it can be mistaken for other diseases. Owing to limited diagnostic capacity and unawareness, the data on human leptospirosis particularly in neonates are scarce in many sub-Saharan countries. It has been underreported hindering preventive and control measures in place. The study aimed at determining prevalence of leptospirosis as a cause of febrile illness in neonates using IgM ELISA and a quantitative real-time PCR (qPCR).

METHODS

This was a descriptive cross-sectional study that included 103 neonatal sepsis cases whose parents/legal guardians gave informed consent. The data on demographic and clinical characteristics were collected using structured data collection form. EDTA whole blood sample was collected from the neonates by trained study nurses. From the samples, IgM ELISA was done using automated analyzers, DNA extracted and qPCR was performed using primers for LipL32, specific for the pathogenic leptospires.

RESULTS

The prevalence of anti-leptospiral IgM among the neonates as determined by ELISA was 4.3%, where all of them presented with lethargy and poor feeding. No pathogenic Leptospira species DNA was amplified by qPCR.

CONCLUSIONS

Evidence of leptospirosis was demonstrated in neonatal sepsis cases in this study. The findings suggest considerations of leptospirosis in the differential diagnosis of neonates with sepsis. More data are needed on the real epidemiology, clinical features, and burden of leptospirosis in neonates. There is need to include intermediate pathogenic species of Leptospira in the diagnostic qPCR assays.

The Problem of Microbial Dark Matter in Neonatal Sepsis

Neonatal sepsis (NS) kills 750,000 infants every year. Effectively treating NS requires timely diagnosis and antimicrobial therapy matched to the causative pathogens, but most blood cultures for suspected NS do not recover a causative pathogen. We refer to these suspected but unidentified pathogens as microbial dark matter. Given these low culture recovery rates, many non–culture-based technologies are being explored to diagnose NS, including PCR, 16S amplicon sequencing, and whole metagenomic sequencing. However, few of these newer technologies are scalable or sustainable globally. To reduce worldwide deaths from NS, one possibility may be performing population-wide pathogen discovery. Because pathogen transmission patterns can vary across space and time, computational models can be built to predict the pathogens responsible for NS by region and season. This approach could help to optimally treat patients, decreasing deaths from NS and increasing antimicrobial stewardship until effective diagnostics that are scalable become available globally.

Changes in Ugandan Climate Rainfall at the Village and Forest Level

In 2013, the US National Oceanographic and Atmospheric Administration (NOAA) refined the historical rainfall estimates over the African Continent and produced the African Rainfall Climate version 2.0 (ARC2) estimator. ARC2 offers a nearly complete record of daily rainfall estimates since 1983 at 0.1° × 0.1° resolution. Despite short-term anomalies, we identify an overall decrease in average rainfall of about 12% during the past 34 years in Uganda. Spatiotemporally, these decreases are greatest in agricultural regions of central and western Uganda, but similar rainfall decreases are also reflected in the gorilla habitat within the Bwindi Forest in Southwest Uganda. The findings carry significant implications for agriculture production, food security, wildlife habitat, and economic impact at the community and societal level.

Economic burden of neonatal sepsis in sub-Saharan Africa

Background and significance

The third Sustainable Development Goal for child health, which aims to end preventable deaths of newborns and children less than 5 years of age by 2030, cannot be met without substantial reduction of infection-specific neonatal mortality in the developing world. Neonatal infections are estimated to account for 26% of annual neonatal deaths, with mortality rates highest in sub-Saharan Africa (SSA). Reliable and comprehensive estimates of the incidence and aetiology surrounding neonatal sepsis in SSA remain incompletely available. We estimate the economic burden of neonatal sepsis in SSA.

Methods

Data available through global health agencies and in the medical literature were used to determine population demographics in SSA, as well as to determine the incidence, disease burden, mortality and resulting disabilities associated with neonatal sepsis. The disability-adjusted life years (DALY) associated with successful treatment or prevention of neonatal sepsis in SSA for 1 year were calculated. The value of a statistical life (VSL) methodology was estimated to evaluate the economic burden of untreated neonatal sepsis in SSA.

Results

We conservatively estimate that 5.29–8.73 million DALYs are lost annually in SSA due to neonatal sepsis. Corresponding VSL estimates predict an annual economic burden ranging from $10 billion to $469 billion.

Conclusions

Our results highlight and quantify the scope of the public health and economic burden posed by neonatal sepsis in SSA. We quantify the substantial potential impact of more successful treatment and prevention strategies, and we highlight the need for greater investment in strategies to characterise, diagnose, prevent and manage neonatal sepsis and its long-term sequelae in SSA.