Strains Worldwide Research Articles (Page 5)

Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt duplication) of the G gene have been reported in recent years. Since the initial reports, viruses with these characteristics have been reported in several countries. We analyzed all complete HMPV G gene ectodomain sequences available at GenBank to determine if viruses with 111-nt or 180-nt duplication have become the leading HMPV strains worldwide, and to describe their temporal and geographic distribution. We identified 1462 sequences that fulfilled study criteria (764 HMPV A and 698 HMPV B) reported from 37 countries. The most frequent HMPV A genotype was A2b2 (n = 366), and the most frequent B genotype was B2 (n = 374). A total of 84 sequences contained the 111-nt duplication, and 90 sequences contained the 180-nt duplication. Since 2016, viruses with a partial duplication comprise the most frequent HMPV A sequences globally and have displaced other HMPV A viruses in Asia, Europe, and South America; no sequences of viruses with partial duplication have been reported in North America or Africa so far. Continued surveillance of HMPV is required to identify the emergence and spread of epidemiologically relevant variants.

2019-nCoV Omicron (B.1.1.529) variant, which has brought new challenges to the prevention and control of COVID-19 pandemic, has the characteristics of stronger transmissibility and more rapid transmission and more significant immune evasion. It took only two months to become a predominant strain worldwide after its identification in South Africa in November 2021. Local epidemics caused by Omicron variant have been reported in several provinces in China. However, the epidemiological characteristics of highly mutated Omicron variant remain unclear. This article summarizes the progress in the research of functional mutations, transmissibility, virulence, immune evasion and cross-reactive immune responses of Omicron variant, to provide references for the effective prevention and control of COVID-19 pandemic caused by Omicron variant.

Population of the world run into several health-related emergencies among mankind and humans as it creates a challenge for the evolution of novel drug discoveries. One such can be the emergence of multidrug-resistant (MDR) strains in both hospital and community settings, which have been due to an inappropriate use and inadequate control of antibiotics that has led to the foremost human health concerns with a high impact on the global economy. So far, there has been application of two strategies for the development of anti-infective agents either by classical antibiotics that have been derived for their synthetic analogs with increased efficacy or screening natural compounds along with the synthetic compound libraries for the antimicrobial activities. However, need for newer treatment options for infectious diseases has led research to develop new generation of antimicrobial activity to further lessen the spread of antibiotic resistance. Currently, the principles aim to find novel mode of actions or products to target the specific sites and virulence factors in pathogens by a series of better understanding of physiology and molecular aspects of the microbial resistance, mechanism of infection process, and gene-pathogenicity relationship. The design various novel strategies tends to provide us a path for the development of various antimicrobial therapies that intends to have a broader and wider antimicrobial spectrum that helps to combat MDR strains worldwide. The development of antimicrobial peptides, metabolites derived from plants, microbes, phage-based antimicrobial agents, use of metal nanoparticles, and role of CRISPR have led to an exceptional strategies in designing and developing the next-generation antimicrobials. These novel strategies might help to combat the seriousness of the infection rates and control the health crisis system.

Hepatitis B virus genotype C (HBV/C) is one of the most prevalent HBV strains worldwide, especially in the Western Pacific and the South-East Asia. However, the origin and evolutionary timescale of HBV/C remains largely unresolved. We analyzed the evolutionary rate and molecular clock phylogeny of 101 full-genome HBV/C sequences sampled globally using a Bayesian Markov Chain Monte Carlo (MCMC) approach. We inferred the spatiotemporal dynamics of the HBV/C worldwide by the Bayesian Stochastic Search Variable Selection (BSSVS). We found that the estimated mean evolution rate of the HBV/C genotype full-genome was 4.32 × 10-5 subs/site/year (95% highest posterior density 3.02 × 10-6 - 8.97 × 10-5). Phylogeographic reconstruction was able to identify a single location for the origin of the global HBV/C in Australia around A.D. 715. The subgenotype C4 diverged earliest and mainly circulated in Australia, C1 mainly in Southeast Asia, C2 mainly in East Asia and C3 in Remote Oceania. The effective number of HBV infection presented a rapid exponential increase between the 1760s and 1860s followed by a maintained high level until now. Our study, for the first time, provides an estimated timescale for the HBV/C epidemic, and brings new insight to the dispersal of HBV/C in humans globally. Based on the continuous presence of a highly effective viral population, this study provides further evidence of the challenge from a population-based molecular level to eliminate HBV by 2030, and calls for a concerted effort from policy makers, health providers, and society in the globalized world.

SARS-CoV-2 is an RNA coronavirus responsible for Acute Respiratory Syndrome (COVID-19). In January 2021, the re-occurrence of COVID-19 infection was at its peak, considered the second wave of epidemics. In the initial stage, it was considered a double mutant strain due to two significant mutations observed in their Spike protein (E484Q and L452R). Although it was first detected in India later on, it was spread to several countries worldwide, causing high fatality due to this strain. In the present study, we investigated the spreading of B.1.617 strain worldwide through 822 genome sequences submitted in GISAID on 21 April 2021. All genome sequences were analyzed for variations in genome sequences based on their effects due to changes in nucleotides. At Allele frequency 0.05, there were a total of 47 variations in ORF1ab, 22 in Spike protein gene, 6 variations in N gene, 5 in ORF8 and M gene, four mutations in Orf7a, and one nucleotide substitution observed for ORF3a, ORF6 and ORF7b gene. The clustering for similar mutations mentioned B.1.617 sub-lineages. The outcome of this study established relative occurrence and spread worldwide. The study’s finding represented that “double mutant” strain is not only spread through traveling but it is also observed to evolve naturally with different mutations observed in B.1.617 lineage. The information extracted from the study helps to understand viral evolution and genome variations of B.1.617 lineage. The results support the need of separating B.1.617 into sub-lineages.

Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection

Colistin is one of the few antibiotics that exhibit bactericidal effect on carbapenemase-producing Klebsiella pneumoniae strains. In recent years, however, colistin resistance is increasingly being reported among clinical carbapenem-resistant K. pneumoniae strains worldwide, posing serious challenge to treatment of infections caused by these organisms. In this study, we investigated one colistin-susceptible (YJH4) and one colistin-resistant (YJH15) K. pneumoniae strain, which were collected from a patient before and after colistin treatment, respectively. We characterized the effects of mgrB inactivation-induced colistin resistance on the physiological fitness and virulence in ST11 carbapenem-resistant K. pneumoniae both in vitro and in vivo. The colistin-resistant strain YJH15 was found to exhibit increased fitness and biofilm formation potential in vitro, and increased survival rate in the presence of normal human serum. Interestingly, YJH15 exhibited reduced virulence in the mouse infection model but enhanced virulence in Galleria mellonella infection model when compared to the colistin-susceptible parental strain YJH4. Infection with YJH15 was also found to result in lower expression level of inflammatory cytokine IL-1β in blood and significantly decreased bacterial loads in heart, liver, spleen, lung, kidney and blood. These results demonstrated that mgrB inactivation-induced colistin resistance has significant effects on multiple fitness and virulence-associated traits in K. pneumoniae.

The SARS‐CoV‐2 Delta (B.1.617.2) strain is a variant of concern (VOC) that has become the dominant strain worldwide in 2021. Its transmission capacity is approximately twice that of the original strain, with a shorter incubation period and higher viral load during infection. Importantly, the breakthrough infections of the Delta variant have continued to emerge in the first‐generation vaccine recipients. There is thus an urgent need to develop a novel vaccine with SARS‐CoV‐2 variants as the major target. Here, receptor binding domain (RBD)‐conjugated nanoparticle vaccines targeting the Delta variant, as well as the early and Beta/Gamma strains, are developed. Under both a single‐dose and a prime‐boost strategy, these RBD‐conjugated nanoparticle vaccines induce the abundant neutralizing antibodies (NAbs) and significantly protect hACE2 mice from infection by the authentic SARS‐CoV‐2 Delta strain, as well as the early and Beta strains. Furthermore, the elicitation of the robust production of broader cross‐protective NAbs against almost all the notable SARS‐CoV‐2 variants including the Omicron variant in rhesus macaques by the third re‐boost with trivalent vaccines is found. These results suggest that RBD‐based monovalent or multivalent nanoparticle vaccines provide a promising second‐generation vaccine strategy for SARS‐CoV‐2 variants.

The ongoing pandemic of COVID-19 is causing more health, economic and social issues worldwide. As of July 5, 2021, the world registered more than 184 million cases across 222 countries; more than 4 million have died from the deadly infection. The SARSCoV-2 continues spreading globally; new variants emerge randomly due to errors in the virus' gRNAs replication process. The present paper treats the new delta variant of concern, also known as B.1.617.2 lineage. The study highlights transmissibility, vaccine effectiveness, pathogenicity, and the likelihood of hospital admission related to delta variant infection based on a literature review of 10 indexed databases. The findings indicate high transmissibility of the B.1.617.2 lineage, approving it to be the dominant strain worldwide. Also, reduced vaccine effectiveness is confirmed. However, approved vaccines for emergency use remain valuable against COVID-19's delta variant. Finally, the risk of hospitalization seems to be twice in the case of delta variant infection. A combined approach of vaccination and nonpharmaceutical interventions is the leading way to contain the ongoing pandemic of COVID-19. Keywords: SARS-CoV-2; delta variant; literature review.

The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved by whole genome sequencing. Unfortunately the number of publicly available genomes remains low as most sequencing methods rely on virus isolation. Therefore, we developed a robust, cost-effective and widely applicable method that allows to generate (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches. A set of pan-CaPVs long-range PCRs spanning the entire genome was designed to generate PCR amplicons that can be sequenced on commonly used high-throughput sequencing platforms: MiSeq (Illumina), RSII (PacBio) and MinION (Oxford Nanopore Technologies). The robustness of the LR-PCR strategy was evaluated for all 3 members of CaPV directly from a variety of samples, including clinical samples (N = 7), vaccine batches (N = 6), and virus isolates (N = 2). The sequencing method described here allows to reconstruct (nearly) complete CaPV genomes in less than a week and will aid researchers studying closely-related CaPV strains worldwide.

Human papillomaviruses (HPV) are one of the most prevalent causes of cervical, anal, and oral cancer, and it is believed that nearly all sexually active males and females have been infected with HPV at some point in their lives. The purpose of this study is to highlight epidemiological characteristics of the age and genotypical incidence of HPV infection among females in Canton Sarajevo during a 10-year period. This cross-sectional study was conducted in the period between January 2012 and December 2021 at the medical institutions "Zavod za Ginekologiju, Perinatologiju i Neplodnost "Mehmedbašić" among females who were admitted for a routine gynaecological exam in Canton Sarajevo in Bosnia and Herzegovina. In total, 1517 patients who reported typical sexarche at 18.35±1.92, having one 721 (47.5%) sexual partner, regular use of contraceptive methods 820 (54.5%) with male condom 513 (62.6%) being the dominant choice of contraception and having gynacological hereditary oncological positive history 141 (9.3%), were included in the study from which 653 (43.05%) patients had positive HPV test and 864 (56.95%) had negative HPV results. HPV positive patients, 386 (59.1%) were infected either with one type of virus only, while 267 (40.9%) patients were infected with multiple virus strains where we have identified 166 virus strain combinations. Analysis showed that the patients infected by only one virus strain were one of next specific HPV viruses: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68. HPV-16 was the predominately strain 16 (22.5%) identified among all the patients. Mean age of HPV positive patients was 33.38±7.85, ranging from 18 to 61 years. This study highlights the significance of the most frequent HPV high-risk strains (HPV-16, -18, -31.-33,-45,-52, and -58) among the Bosnia and Herzegovina population as one of the most common cancer-causing strains worldwide.

Abstract Farm products are considered important vehicles for the transmission of Listeria monocytogenes (L. monocytogenes). The typing of L. monocytogenes from farm products contributes to the surveillance and source tracing of the pathogen. In this study, 77 L. monocytogenes strains from seven farm product categories in Shanghai were analyzed by serological typing, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and whole-genome nucleotide polymorphism (wgSNP). The results showed that the 77 isolates were classified into four serovars (1/2a, 1/2c, 1/2b, and 4b), and of these, 1/2a (n=47) was the most prevalent. Seventeen sequence types (STs) were generated by MLST with two novel STs (ST1402 and ST1403), and 20 of 77 L. monocytogenes isolates had high genetic identity with previously documented outbreak isolates according to the minimum spanning tree from the MLST results. Moreover, 34 PFGE patterns (PF1–PF34) were differentiated, and based on a similarity value higher than 80% by the unweighted pair group method dendrogram, the discriminatory index was relatively low (equal to 0.775). Furthermore, 14 isolates were chosen and further analyzed by wgSNP based on the previous typing results, which demonstrated that wgSNP and MLST yielded mostly consistent typing results but higher resolution than PFGE. In conclusion, 77 L. monocytogenes isolates from farm products collected in nine districts in Shanghai were highly genetically diverse, and 20 of these isolates had high relatedness with previously documented outbreak strains worldwide. The results indicate a possible cross-contamination risk of L. monocytogenes and a potential public health concern resulting from farm products during the supply chain in Shanghai, China.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is the dominant circulating strain worldwide. To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic, the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019 (COVID-19) cases in the mainland of China during the first half of 2022 were analyzed. Sequences submitted from January to July 2022, with a collection date before June 30, 2022, were incorporated. The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed. 4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions (PLADs), and the median submission interval was within 1 month after collection. In 3,851 Omicron sequences with good quality, 1 recombinant (XU) and 4 subvariants under monitoring (BA.4, BA.5, BA.2.12.1, and BA.2.13) were recorded, and 3 of them (BA.4, BA.5, and BA.2.12.1) caused local transmissions in the mainland of China later than that recorded in the surveillance. Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5. The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data (GISAID). The imported cases from Hong Kong Special Administrative Region, China, accounted for 32.30% of Omicron cases sampled, and 98.71% of them were BA.2. The Omicron variant showed the intra-Omicron evolution in the first half of 2022, and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.

The Delta variant is now the predominant circulating SARS-CoV-2 strain worldwide. Severity of illness in persons infected with the SARS-CoV-2 Delta variant compared with the Beta variant is not known. To directly compare clinical outcomes in persons infected with the SARS-CoV-2 Delta variant vs those infected with the Beta variant in Qatar. This retrospective cohort study used data from the national COVID-19 database in Qatar, which includes information on all individuals who were ever tested for SARS-CoV-2 using a reverse transcriptase-polymerase chain reaction test and all individuals who received any SARS-CoV-2 vaccine in Qatar. Among persons with confirmed SARS-CoV-2 infection between March 22 and July 7, 2021, those infected with the Delta variant were identified and were propensity score matched with control individuals infected with the Beta variant. The variants were ascertained by variant genotyping of the positive samples. SARS-CoV-2 infection with the Delta or Beta variant. The main outcomes were admission to the hospital, admission to the intensive care unit, use of supplemental oxygen, use of high-flow oxygen, receipt of mechanical ventilation, or death among those infected with the Delta or Beta variant overall and stratified by vaccination status. Among 1427 persons infected with the Delta variant (252 [55.9%] male; median age, 34 years [IQR, 17-43 years]) and 5353 persons infected with the Beta variant (233 [51.7%] male; median age, 34 years [IQR, 17-45 years]), 451 propensity score-matched pairs were identified. Persons infected with the Delta variant were more likely to be hospitalized (27.3% [95% CI, 23.2%-31.6%] vs 20.0% [95% CI, 16.4-24.0]; P = .01) or to have mild-moderate or severe-critical disease outcomes (27.9% [95% CI, 23.8%-32.3%] vs 20.2% [95% CI, 16.6%-24.2%]; P = .01) compared with persons infected with the Beta variant. Infection with the Delta variant was independently associated with higher odds of experiencing any adverse outcome (adjusted odds ratio [aOR], 2.53; 95% CI, 1.72-3.72). Compared with being unvaccinated, being vaccinated with a second dose more than 3 months before infection was associated with lower odds of any adverse outcome among persons infected with the Delta variant (aOR, 0.11; 95% CI, 0.04-0.26) and among those infected with the Beta variant (aOR, 0.22; 95% CI, 0.05-0.98). Protection was similar among those who received a second vaccine dose less than 3 months before infection, but having received only a single dose was not associated with a lower odds of any severe outcome among those infected with the Delta variant (aOR, 1.12; 95% CI, 0.41-3.06) or those infected with the Beta variant (aOR, 0.74; 95% CI, 0.20-2.72). In this cohort study of persons with COVID-19 in Qatar, infection with the SARS-CoV-2 Delta variant was associated with more severe disease than was infection with the Beta variant. Being unvaccinated was associated with greater odds of severe-critical disease.

BackgroundA gonococcal vaccine is urgently needed due to increasing gonorrhea incidence and emerging multidrug-resistant gonococcal strains worldwide. Men who have sex with men (MSM) have among the highest incidences of gonorrhea and may be a key target population for vaccination when available.MethodsAn individual-based, anatomical site-specific mathematical model was used to simulate Neisseria gonorrhoeae transmission in a population of 10 000 MSM. The impact of vaccination on gonorrhea prevalence was assessed.ResultsWith a gonococcal vaccine of 100% or 50% protective efficacy, gonorrhea prevalence could be reduced by 94% or 62%, respectively, within 2 years if 30% of MSM are vaccinated on presentation for sexually transmitted infection (STI) testing. Elimination of gonorrhea is possible within 8 years with vaccines of ≥ 50% efficacy lasting 2 years, providing a booster vaccination is available every 3 years on average. A vaccine’s impact may be reduced if it is not effective at all anatomical sites.ConclusionsOur study indicates that with a vaccine of modest efficacy and an immunization strategy that targets MSM presenting for STI screening, the prevalence of gonorrhea in this population could be rapidly and substantially reduced.

The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report the structure, function, and antigenicity of its full-length spike (S) trimer as well as those of the Gamma and Kappa variants, and compare their characteristics with the G614, Alpha, and Beta variants. Delta S can fuse membranes more efficiently at low levels of cellular receptor angiotensin converting enzyme 2 (ACE2), and its pseudotyped viruses infect target cells substantially faster than the other five variants, possibly accounting for its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the amino-terminal domain of the S protein but only makes produces changes in the receptor binding domain (RBD), making the RBD a better target for therapeutic antibodies.

SARS-CoV-2 Delta variant has the characteristics of stronger infectivity, higher viral load, and shorter incubation period, posing new challenges to the prevention and control of COVID-19 pandemic. SARS-CoV-2 Delta variant was first discovered in India, then quickly spread in many countries and has gradually become one of the main epidemic strains worldwide. Local epidemics caused by SARS-CoV-2 Delta variant also occurred in several provinces in China. This article summarizes the progress in research of etiological characteristics, transmission characteristics or possible mechanism and epidemiological characteristics of SARS-CoV-2 Delta variant, and the protective effects of vaccines and control measures against SARS-CoV-2 Delta variant in order to provide references for the effective prevention and control of COVID-19 epidemic caused by SARS-CoV-2 Delta variant.

BackgroundFounder events have been observed among numerous plants and animal species living on oceanic islands due to the geographic separation of these islands and the small amount of original life they harbor. However, there has been little research on the ecological characteristics of pathogenic microorganisms on islands. Trichophyton rubrum ranks the most common isolated dermatophyte causing dermatophytosis in clinic and has become an epidemic strain worldwide in recent decades.ObjectiveTo study the phylogenetic characteristics and the distribution pattern of genetic polymorphism of T. rubrum in China, which further provide theoretical basis for the prevention and control of T. rubrum.MethodsIn the present study, we sequenced and analyzed the genetic characteristics of 204 T. rubrum isolates from Hainan Island and other sites in China. Phylogenetic analysis and genetic polymorphisms were studied based on a total of 41,409 high-quality whole-genome SNPs.ResultsThe majority of the isolates from Hainan Island clustered together. Mixed T. rubrum population differentiation was observed among the strains of different geographical origins. In addition, the genetic diversity (π) of the Hainan isolates was low and showed no significant difference from that of isolates from other sites.ConclusionThis study is the first to discuss general ecological and evolutionary principles related to pathogenic fungi. Our findings reveal a founder effect during the origination of T. rubrum on Hainan Island and provide guidance regarding prevention and treatment strategies.

Influenza is an acute viral respiratory disease that is currently causing severe financial and resource strains worldwide. With the COVID-19 pandemic exceeding 153 million cases worldwide, there is a need for a low-cost and contactless surveillance system to detect symptomatic individuals. The objective of this study was to develop FluNet, a novel, proof-of-concept, low-cost and contactless device for the detection of high-risk individuals. The system conducts face detection in the LWIR with a precision rating of 0.98, a recall of 0.91, an F-score of 0.96, and a mean intersection over union of 0.74 while sequentially taking the temperature trend of faces with a thermal accuracy of ± 1 K. In parallel, determining if someone is coughing by using a custom lightweight deep convolutional neural network with a precision rating of 0.95, a recall of 0.92, an F-score of 0.94 and an AUC of 0.98. We concluded this study by testing the accuracy of the direction of arrival estimation for the cough detection revealing an error of ± 4.78°. If a subject is symptomatic, a photo is taken with a specified region of interest using a visible light camera. Two datasets have been constructed, one for face detection in the LWIR consisting of 250 images of 20 participants’ faces at various rotations and coverings, including face masks. The other for the real-time detection of coughs comprised of 40,482 cough / not cough sounds. These findings could be helpful for future low-cost edge computing applications for influenza-like monitoring.

BackgroundHuman tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains.MethodsTo avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment.ResultsA significant Odds Ratio (OR range: 1.8–8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB with 4.3.1, 4.3.3, and 4.5 and Asian African 2 and Europe/Russia B0/W148 modern Beijing sublineages was found. We also observed a significant association of Lineage 3 strains with multidrug resistance (OR 3.8; 95% CI [1.1–13.6]), as well as between modern Beijing sublineages and antibiotic resistance (OR 4.3; 3.8–8.6). In this work, it was found that intralineage diversity can drive differences in the immune response that triggers the PTB/EPTB phenotype.