Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer.

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive "One Health" approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

Comparative analysis of tuberculin and defined antigen skin tests for detection of bovine tuberculosis in buffaloes (Bubalus bubalis) in Haryana state, India.

BACKGROUND: Bovine tuberculosis (bTB) is a chronic disease that results from infection with any member of the Mycobacterium tuberculosis complex. Infected animals are typically diagnosed with tuberculin-based intradermal skin tests according to World Organization of Animal Health which are presently in use. However, tuberculin is not suitable for use in BCG-vaccinated animals due to a high rate of false-positive reactions. Peptide-based defined skin test (DST) antigens have been identified using antigens (ESAT-6, CFP-10 and Rv3615c) which are absent from BCG, but their performance in buffaloes remains unknown. To assess the comparative performance of DST with the tuberculin-based single intradermal test (SIT) and the single intradermal comparative cervical test (SICCT), we screened 543 female buffaloes from 49 organized dairy farms in two districts of Haryana state in India. RESULTS: We found that 37 (7%), 4 (1%) and 18 (3%) buffaloes were reactors with the SIT, SICCT and DST tests, respectively. Of the 37 SIT reactors, four were positive with SICCT and 12 were positive with the DST. The results show that none of the animals tested positive with all three tests, and 6 DST positive animals were SIT negative. Together, a total of 43 animals were reactors with SIT, DST, or both, and the two assays showed moderate agreement (Cohen's Kappa 0.41; 95% Confidence Interval (CI): 0.23, 0.59). In contrast, only slight agreement (Cohen's Kappa 0.18; 95% CI: 0.02, 0.34) was observed between SIT and SICCT. Using a Bayesian latent class model, we estimated test specificities of 96.5% (95% CI, 92-99%), 99.7% (95% CI: 98-100%) and 99.0% (95% CI: 97-100%) for SIT, SICCT and DST, respectively, but considerably lower sensitivities of 58% (95% CI: 35-87%), 9% (95% CI: 3-21%), and 34% (95% CI: 18-55%) albeit with broad and overlapping credible intervals. CONCLUSION: Taken together, our investigation suggests that DST has a test specificity comparable with SICCT, and sensitivity intermediate between SIT and SICCT for the identification of buffaloes suspected of tuberculosis. Our study highlights an urgent need for future well-powered trials with detailed necropsy, with immunological and microbiological profiling of reactor and non-reactor animals to better define the underlying factors for the large observed discrepancies in assay performance, particularly between SIT and SICCT.

Emergence of Mycobacterium orygis-Associated Tuberculosis in Wild Ruminants, India.

Tuberculosis caused by Mycobacterium orygis was detected in 2 spotted deer from a wildlife sanctuary in western India and an Indian bison from a national park in central India. Nationwide surveillance is urgently required to clarify the epidemiology of the Mycobacterium tuberculosis complex at the human-livestock-wildlife interface.

Strain and host-cell dependent role of type-1 fimbriae in the adherence phenotype of super-shed Escherichia coli O157:H7.

Super-shed (SS) Escherichia coli O157 (E. coli O157) demonstrate a strong, aggregative, locus of enterocyte effacement (LEE)-independent adherence phenotype on bovine recto-anal junction squamous epithelial (RSE) cells, and harbor polymorphisms in non-LEE-adherence-related loci, including in the type 1 fimbriae operon. To elucidate the role of type 1 fimbriae in strain- and host-specific adherence, we evaluated the entire Fim operon (FimB-H) and its adhesion (FimH) deletion mutants in four E. coli O157 strains, SS17, SS52, SS77 and EDL933, and evaluated the adherence phenotype in bovine RSE and human HEp-2 adherence assays. Consistent with the prevailing dogma that fimH expression is genetically switched off in E. coli O157, the ΔfimHSS52, ΔfimB-HSS52, ΔfimB-HSS17, and ΔfimHSS77 mutants remained unchanged in adherence phenotype to RSE cells. In contrast, the ΔfimHSS17 and ΔfimB-HSS77 mutants changed from a wild-type strong and aggregative, to a moderate and diffuse adherence phenotype, while both ΔfimHEDL933 and ΔfimB-HEDL933 mutants demonstrated enhanced binding to RSE cells (p < 0.05). Additionally, both ΔfimHSS17 and ΔfimHEDL933 were non-adherent to HEp-2 cells (p < 0.05). Complementation of the mutant strains with their respective wild-type genes restored parental phenotypes. Microscopy revealed that the SS17 and EDL933 strains indeed carry type 1 fimbriae-like structures shorter than those seen in uropathogenic E. coli. Taken together, these results provide compelling evidence for a strain and host cell type-dependent role of fimH and the fim operon in E. coli O157 adherence that needs to be further evaluated.

Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection.

The receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 spike (S) protein plays a central role in mediating the first step of virus infection to cause disease: virus binding to angiotensin-converting enzyme 2 (ACE2) receptors on human host cells. Therefore, S/RBD is an ideal target for blocking and neutralization therapies to prevent and treat coronavirus disease 2019 (COVID-19). Using a target-based selection approach, we developed oligonucleotide aptamers containing a conserved sequence motif that specifically targets S/RBD. Synthetic aptamers had high binding affinity for S/RBD-coated virus mimics (KD ≈7 nM) and also blocked interaction of S/RBD with ACE2 receptors (IC50 ≈5 nM). Importantly, aptamers were able to neutralize S protein-expressing viral particles and prevent host cell infection, suggesting a promising COVID-19 therapy strategy.

iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis.

BACKGROUND: One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking. RESULTS: We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline. CONCLUSIONS: The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli.

Cah is a calcium-binding autotransporter protein involved in autoaggregation and biofilm formation. Although cah is widespread in Shiga toxin-producing Escherichia coli (STEC), we detected mutations in cah at a frequency of 31.3% in this pathogen. In STEC O157:H7 supershedder strain SS17, a large deletion results in a smaller coding sequence, encoding a protein lacking the C-terminal 71 amino acids compared with Cah in STEC O157:H7 strain EDL933. We examined the function of Cah in biofilm formation and host colonization to better understand the selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro: it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain dependent since Cah-mediated biofilm formation was diminished when an EDL933 cah gene was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to spinach leaves and altered the adherence pattern of EDL933 to bovine recto-anal junction squamous epithelial (RSE) cells. In contrast, in trans expression of EDL933 cah in SS17 increased its attachment to leaf surfaces, and in DH5α, it enhanced its adherence to RSE cells. Hence, the ecological function of Cah appears to be modulated by environmental conditions and other bacterial strain-specific properties. Considering the prevalence of cah in STEC and its role in attachment and biofilm formation, cah mutations might be selected in ecological niches in which inactivation of Cah would result in an increased fitness in STEC during colonization of plants or animal hosts.IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) harbors genes encoding diverse adhesins, and many of these are known to play an important role in bacterial attachment and host colonization. We demonstrated here that the autotransporter protein Cah confers on E. coli DH5α cells a strong autoaggregative phenotype that is inversely correlated with its ability to form biofilms and plays a strain-specific role in plant and animal colonization by STEC. Although cah is widespread in the STEC population, we detected a mutation rate of 31.3% in cah, which is similar to that reported for rpoS and fimH The formation of cell aggregates due to increased bacterium-to-bacterium interactions may be disadvantageous to bacterial populations under conditions that favor a planktonic state in STEC. Therefore, a loss-of-function mutation in cah is likely a selective trait in STEC when autoaggregative properties become detrimental to bacterial cells and may contribute to the adaptability of STEC to fluctuating environments.

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite.

BACKGROUND: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform. RESULTS: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples. CONCLUSIONS: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids.

The genomes of a diverse set of Escherichia coli, including many Shiga toxin-producing strains of various serotypes were determined. A total of 39 plasmids were identified among these strains, and many carried virulence or putative virulence genes of Shiga toxin-producing E. coli strains, virulence genes for other pathogenic E. coli groups, and some had combinations of these genes. Among the novel plasmids identified were eight that carried resistance genes to aminoglycosides, carbapenems, penicillins, cephalosporins, chloramphenicol, dihydrofolate reductase inhibitors, sulfonamides, tetracyclines and resistance to heavy metals. Two of the plasmids carried six of these resistance genes and two novel IncHI2 plasmids were also identified. The results of this study showed that plasmids carrying diverse resistance and virulence genes of various pathogenic E. coli groups can be found in E. coli strains and serotypes regardless of the isolate's source and therefore, is consistent with the premise that these mobile elements carrying these traits may be broadly disseminated among E. coli.

Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218.

BACKGROUND: Escherichia coli is the most predominant Gram-negative bacterial pathogen associated with neonatal meningitis. Previous studies indicated that the prototypic neonatal meningitis E. coli (NMEC) strain RS218 (O18:K1:H7) harbors one large plasmid. Objectives of the present study were to analyze the complete nucleotide sequence of this large plasmid (pRS218) and its contribution to NMEC pathogenesis using in vitro and in vivo models of neonatal meningitis. RESULTS: The plasmid is 114,231 bp in size, belongs to the incompatibility group FIB/IIA (IncFIB/IIA), and contains a genetic load region that encodes several virulence and fitness traits such as enterotoxicity, iron acquisition and copper tolerance. The nucleotide sequence of pRS218 showed a 41- 46% similarity to other neonatal meningitis-causing E. coli (NMEC) plasmids and remarkable nucleotide sequence similarity (up to 100%) to large virulence plasmids of E. coli associated with acute cystitis. Some genes located on pRS218 were overly represented by NMEC strains compared to fecal E. coli isolated from healthy individuals. The plasmid-cured strain was significantly attenuated relative to the RS218 wild-type strain as determined in vitro by invasion potential to human cerebral microvascular endothelial cells and in vivo by mortalities, histopathological lesions in the brain tissue, and bacterial recovery from the cerebrospinal fluid of infected rat pups. CONCLUSIONS: The pRS218 is an IncFIB/IIA plasmid which shares a remarkable nucleotide sequence similarity to large plasmids of E. coli associated with cystitis. Both in vitro and in vivo experiments indicated that pRS218 plays an important role in NMEC pathogenesis.

An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows.

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more pairwise SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.

Molecular detection and characterization of the Mycobacterium tuberculosis complex subspecies responsible for bovine tuberculosis in Punjab, Pakistan.

Bovine tuberculosis (bTB), traditionally associated with Mycobacterium bovis, presents significant public health and economic challenges worldwide. This study investigated the causative agents of bTB in slaughtered cattle and buffalo in Lahore, Pakistan. Of the 3,581 animals screened, 34 were identified with gross TB-like lesions. The lesions were processed for culture, PCR, and Sanger sequencing to identify the causative agents of the disease. The results identified 10 Mycobacterium orygis and 8 Mycobacterium tuberculosis sensu stricto isolates. Whole-genome sequencing was performed on two M. orygis isolates, and the sequences were phylogenetically compared to 93 publicly available M. orygis sequences. The results also demonstrated that the JB21 and JB22 primers, which have been previously commonly applied to detect M. bovis in Pakistan, are unable to distinguish between M. tuberculosis complex subspecies. The identification of M. orygis and M. tuberculosis as causative agents of bTB in this slaughterhouse in Punjab may have important implications in identifying cases of zoonotic TB in humans and applying appropriate molecular tools to identify the prevalence of the disease. The data from this study align with recent findings suggesting M. orygis is the predominant cause of bTB in South Asia.IMPORTANCEThe study findings hold significant relevance to the Journal of Clinical Microbiology, as they directly impact the field. The first-time identification of Mycobacterium orygis and Mycobacterium tuberculosis as the predominant causative agents of bovine tuberculosis in Lahore, Pakistan underscores the urgent need for enhanced diagnostic methods. The study emphasizes the importance of improved assays for the accurate detection and differentiation of Mycobacterium subspecies. Additionally, the research addresses zoonotic risk assessment and public health implications, advocating for a multidisciplinary approach that integrates clinical microbiology with veterinary and human health sectors. These insights contribute to clinical microbiology knowledge, shaping effective strategies for disease prevention, surveillance, and control. The study's potential to advance the field makes it well suited for publication in the Microbiology Spectrum journal.

Temporal dynamics of the early immune response following Mycobacterium bovis infection of cattle.

Bovine tuberculosis is an infectious disease of global significance that remains endemic in many countries. Mycobacterium bovis infection in cattle is characterized by a cell-mediated immune response (CMI) that precedes humoral responses, however the timing and trajectories of CMI and antibody responses determined by newer generation assays remain undefined. Here we used defined-antigen interferon-gamma release assays (IGRA) and an eleven-antigen multiplex ELISA (Enferplex TB test) alongside traditional tuberculin-based IGRA and IDEXX M. bovis antibody tests to assess immune trajectories following experimental M. bovis infection of cattle. The results show CMI responses developed as early as two-weeks post-infection, with all infected cattle testing positive three weeks post-infection. Interestingly, 6 of 8 infected animals were serologically positive with the Enferplex TB assay as early as 4 weeks post-infection. As expected, application of the tuberculin skin test enhanced subsequent serological reactivity. Infrequent M. bovis faecal shedding was observed but was uncorrelated with observed immune trajectories. Together, the results show that early antibody responses to M. bovis infection are detectable in some individuals and highlight an urgent need to identify biomarkers that better predict infection outcomes, particularly for application in low-and-middle income countries where test-and-slaughter based control methods are largely unfeasible.

BCG vaccination reduces bovine tuberculosis transmission, improving prospects for elimination.

Bacillus Calmette-Guérin (BCG) is a routinely used vaccine for protecting children against Mycobacterium tuberculosis that comprises attenuated Mycobacterium bovis. BCG can also be used to protect livestock against M. bovis; however, its effectiveness has not been quantified for this use. We performed a natural transmission experiment to directly estimate the rate of transmission to and from vaccinated and unvaccinated calves over a 1-year exposure period. The results show a higher indirect efficacy of BCG to reduce transmission from vaccinated animals that subsequently become infected [74%; 95% credible interval (CrI): 46 to 98%] compared with direct protection against infection (58%; 95% CrI: 34 to 73%) and an estimated total efficacy of 89% (95% CrI: 74 to 96%). A mechanistic transmission model of bovine tuberculosis (bTB) spread within the Ethiopian dairy sector was developed and showed how the prospects for elimination may be enabled by routine BCG vaccination of cattle.

Assessing the feasibility of test-and-cull and test-and-segregation approaches for the control of high-prevalence bovine tuberculosis in Ethiopian intensive dairy farms.

Bovine tuberculosis (bTB) is endemic and has a substantial impact on the livestock sector in Ethiopia and other low and middle-income countries (LMICs). With a national emphasis on dairy farm intensification to boost milk production and spur economic growth, the incidence of bTB is anticipated to rise. However, Ethiopia, like other LMICs, lacks a comprehensive national bTB control strategy due to the economic and social infeasibility of traditional test-and-cull (TC) approaches. To inform the development of such a strategy, we evaluated the effectiveness and feasibility of TC and test-and-segregation (TSg) strategies for bTB control on Ethiopian dairy farms. A TC approach was used at Farm A [N = 62; comparative cervical test (CCT) > 4 mm, starting prevalence 11.3%] while TSg was implemented at Farm B (N = 45; CCT > 4 mm, prevalence 22.2%), with testing intervals of 2-4 months. Both strategies achieved a reduction in bTB prevalence to 0%, requiring seven rounds of TC over 18 months at Farm A, and five rounds of TSg over 12 months at Farm B's negative herd. The results show that adopting more sensitive thresholds [CCT > 0 mm or single cervical test (SCT) > 2 mm] during later rounds was pivotal in identifying and managing previously undetected infections, emphasizing the critical need for optimized diagnostic thresholds. Cost analysis revealed that TC was approximately twice as expensive as TSg, primarily due to testing, labor, and cow losses in TC, versus construction of new facilities and additional labor for TSg. This underscores the economic and logistical challenges of bTB management in resource-limited settings. Taken together, our study highlights an urgent need for the exploration of alternative approaches including TSg and or vaccination to mitigate within herd transmission and enable implementation of bTB control in regions where TC is not feasible.

Full-genome dissection of an epidemic of severe invasive disease caused by a hypervirulent, recently emerged clone of group A Streptococcus.

Group A Streptococcus (GAS) causes an exceptionally broad range of infections in humans, from relatively mild pharyngitis and skin infections to life-threatening necrotizing fasciitis and toxic shock syndrome. An epidemic of severe invasive human infections caused by type emm59 GAS, heretofore an exceedingly rare cause of disease, spread west to east across Canada over a 3-year period (2006 to 2008). By sequencing the genomes of 601 epidemic, historic, and other emm59 organisms, we discovered that a recently emerged, genetically distinct emm59 clone is responsible for the Canadian epidemic. Using near-real-time genome sequencing, we were able to show spread of the Canadian epidemic clone into the United States. The extensive genome data permitted us to identify patterns of geographic dissemination as well as links between emm59 subclonal lineages that cause infections. Mouse and nonhuman primate models of infection demonstrated that the emerged clone is unusually virulent. Transmission of epidemic emm59 strains may have occurred primarily by skin contact, as suggested by an experimental model of skin transmission. In addition, the emm59 strains had a significantly impaired ability to persist in human saliva and to colonize the oropharynx of mice, and seldom caused human pharyngitis. Our study contributes new information to the rapidly emerging field of molecular pathogenomics of bacterial epidemics and illustrates how full-genome data can be used to precisely illuminate the landscape of strain dissemination during a bacterial epidemic.

Is Pre-Exposure Prophylaxis a Cost-Effective Intervention to Avert Rabies Deaths among School-Aged Children in India? Comment on Royal et al. A Cost-Effectiveness Analysis of Pre-Exposure Prophylaxis to Avert Rabies Deaths in School-Aged Children in India. Vaccines 2023, 11, 88.

I read with interest the article "A Cost-Effectiveness Analysis of Pre-Exposure Prophylaxis to Avert Rabies Deaths in School-Aged Children in India" by Royal et al., recently published in Vaccines [...].

Complete genome of a 2014 isolate of peste des petits ruminants virus from Ethiopia.

This report describes the complete genome sequence of a peste des petits ruminants virus (PPRV) isolate from Ethiopia in 2014. The strain (PPRV/Ethiopia/Habru/2014), which showed a normal virulence and relatively low morbidity in the field, belongs to the North African subclade of Lineage IV.

Clinical features of human tuberculosis due to Mycobacterium orygis in Southern India.

Mycobacterium orygis is a member of the Mycobacterium tuberculosis complex (MTBC) and causes tuberculosis in a variety of animals, including humans in South Asia. Here, we describe the clinical features associated with 8 human cases of whole genome sequence (WGS) confirmed M. orygis from a tertiary care hospital in South India during 2018-2019. The patient ages ranged from 9 to 51 years, with 5 females and 3 males included. All the patients had extrapulmonary disease with 2 having concomitant pulmonary involvement. Clinical improvement was documented after a full course of anti-tuberculosis therapy in 6 cases for whom follow-up was available. Taken together, the results show that M. orygis causes human tuberculosis in India, with a predominant extrapulmonary disease. Standardized molecular assays of this emerging member of the MTBC are needed to provide further information on the frequency of M. orygis infection in India and other countries where it is found in livestock and domestic wildlife.

Is bovine density and ownership associated with human tuberculosis in India?

Zoonotic tuberculosis in humans is caused by infection with bacteria of the Mycobacterium tuberculosis complex acquired from animals, most commonly cattle. India has the highest burden of human tuberculosis in the world and any zoonotic risk posed by tuberculosis in bovines needs to be managed at the source of infection as a part of efforts to end human tuberculosis. Zoonotic tuberculosis in humans can be severe and is clinically indistinguishable from non-zoonotic tuberculosis. As a consequence, zoonotic tuberculosis remains under-recognised and the significance of its contribution to human tuberculosis is poorly understood. This study aimed to explore any association between bovine density, bovine ownership, and human tuberculosis reporting in India using self-reported tuberculosis data in households and officially reported tuberculosis cases while controlling for common confounders for human tuberculosis. We find an association between human tuberculosis reporting, bovine density and bovine ownership in India. Buffalo density was significantly associated with an increased risk of self-reported tuberculosis in households (odds ratio (OR) = 1.23 (95% credible interval (CI): 1.10-1.39) at household level; incidence rate ratio (IRR) = 1.17 (95% CI: 1.04-1.33) at district level), while cattle density (OR = 0.80, 95% CI: 0.71-0.89; IRR = 0.78, 95% CI: 0.70-0.87) and ownership of bovines in households (OR = 0.94, 95% CI: 0.9-0.99; IRR = 0.67, 95% CI: 0.57-0.79) had a protective association with tuberculosis reporting. It is unclear whether this relates to differences in tuberculosis transmission dynamics, or perhaps an association between bovines and other unexplored confounders for tuberculosis reporting in humans. Our study highlights a need for structured surveillance to estimate the prevalence of tuberculosis in cattle and buffaloes, characterisation of Mycobacterium tuberculosis complex species present in bovines and transmission analyses at the human-animal interface to better assess the burden and risk pathways of zoonotic tuberculosis in India.