Our study was limited to

Our study was limited to enrollment at sites in New York City. Nevertheless, our subjects revealed a broad spectrum in demographics, particularly race and country of origin. This is not surprising, as TB in the US, and particularly in New York City, is a disease predominantly diagnosed in foreign-born individuals who typically are infected during childhood with the Mtb strains prevalent in their country of origin (New York City Department of Health and Mental Hygiene, 2013; CDC, 2013). Our subjects originated from various countries of North, Central and South America, Africa and Asia. We therefore believe that our results are neither restricted to one part of the world nor to one particular Mtb strain. Another relevant limitation was the small sample size. Yet, we were able to demonstrate statistically significant differences between TB cases and controls, as well as highly reproducible data when comparing the discovery to the verification protein expression patterns, both supporting the robustness of our data. Further studies using larger sample sizes from both HIV− and HIV+ subjects from various regions are warranted to validate the robustness of our panel compositions as well as identify any potential regional variations. The following is the supplementary data related to this article.
Conflicts of Interest
Introduction Recent CDC estimates indicate that one in five pathogens from hospital-acquired infections in the U.S. are multidrug-resistant (Kallen et al., 2010; Sievert et al., 2013), dramatically limiting therapeutic options to AP24534 manufacturer that may be more toxic, less effective, or more expensive (Centers for Disease Control and Prevention, 2013). In such cases, patients often have longer hospital stays, delayed recuperation, long-term disability, and increased mortality. Deciphering the mechanisms that govern the emergence of multidrug-resistant pathogens is critical to the development of new approaches to control bacterial infections. Many mechanisms of antibiotic resistance have been established, including horizontal gene transfer; genomic mutation; and intrinsic bacterial mechanisms that pre-date antibiotics (Allen et al., 2010; Andersson and Hughes, 2010; Cox and Wright, 2013; D\'Costa et al., 2011; Davies and Davies, 2010). Significant advances have been made regarding the generation of antibiotic resistant variants (phenotypic and genotypic) that emerge during infection; e.g., Staphylococcus aureus small colony variants that promote persistent infections (Proctor et al., 2006); antibiotic resistance of Pseudomonas aeruginosa biofilms (Høiby et al., 2010); the evolution and spread of multidrug-resistant pneumococcal variants (Croucher et al., 2011), and heteroresistant subpopulations of vancomycin-susceptible S. aureus (El-Halfawy and Valvano, 2015). Despite this knowledge, the role of host–pathogen interactions in antibiotic resistance is poorly understood, and the use of host models as a primary approach to understanding resistance is not often considered or explored. For the past several decades, drug development has followed a standard sequential procedure wherein: (i) efficacy is determined in vitro; (ii) pharmacokinetic/pharmacodynamic (PK/PD) parameters are measured in vivo; and (iii) dosing efficacy/toxicity in vivo is established for a limited number of model pathogens (Ambrose et al., 2007; Clinical and Laboratory Standards Institute, 2012; Food and Drug Administration, 2009). However, along with a limited amount of patient-dosing data, physicians rely on in vitro antimicrobial susceptibility testing (AST) of clinical isolates grown on the universal media standard Mueller–Hinton Broth (MHB) for therapeutic intervention (Clinical and Laboratory Standards Institute, 2012; European Committee on Antibiotic Suscepibility Testing, 2014). This standard procedure does not replicate mammalian biochemistry and may not correlate with patient outcome. To overcome these limitations, we investigated antibiotic resistance in the context of animal models of disease, and have identified a mechanism that stimulates bacterial resistance to multiple antibiotics during infection, while promoting the emergence of drug-resistant bacteria.