key: cord-320548-oigyut2k
authors: Zumla, Alimuddin; Memish, Ziad A; Maeurer, Markus; Bates, Matthew; Mwaba, Peter; Al-Tawfiq, Jaffar A; Denning, David W; Hayden, Frederick G; Hui, David S
title: Emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options
date: 2014-09-01
journal: Lancet Infect Dis
DOI: 10.1016/s1473-3099(14)70828-x
sha: 
doc_id: 320548
cord_uid: oigyut2k

The emergence and spread of antimicrobial-resistant bacterial, viral, and fungal pathogens for which diminishing treatment options are available is of major global concern. New viral respiratory tract infections with epidemic potential, such as severe acute respiratory syndrome, swine-origin influenza A H1N1, and Middle East respiratory syndrome coronavirus infection, require development of new antiviral agents. The substantial rise in the global numbers of patients with respiratory tract infections caused by pan-antibiotic-resistant Gram-positive and Gram-negative bacteria, multidrug-resistant Mycobacterium tuberculosis, and multiazole-resistant fungi has focused attention on investments into development of new drugs and treatment regimens. Successful treatment outcomes for patients with respiratory tract infections across all health-care settings will necessitate rapid, precise diagnosis and more effective and pathogen-specific therapies. This Series paper describes the development and use of new antimicrobial agents and immune-based and host-directed therapies for a range of conventional and emerging viral, bacterial, and fungal causes of respiratory tract infections.

The emergence of diffi cult-to-treat known and novel bacterial, viral, and fungal respiratory tract pathogens with epidemic potential is of major global concern. Treatment options are limited by increasing antimicrobialdrug resistance. However, new viral infections causing severe respiratory tract disease with pandemic potential have focused global attention. 1 A substantial rise in the number of patients with multidrug-resistant pulmonary tuberculosis 2 and pan-drug-resistant bacteria 3 has been noted. Increasing use of immunosuppressive agents, broad-spectrum antibiotics, and anticancer agents, coupled with resistance to azoles, has led to an increase in the number of invasive pulmonary fungal infections 4 with resultant high morbidity and mortality. Successful treatment outcomes for patients with respiratory tract infections across all health-care settings require appropriate, eff ective, and pathogen-specifi c drug or alternative treatments. We describe a range of conventional and emerging viral, bacterial, and fungal causes of respiratory tract infections for which new antimicrobial drugs and immune-based and host-directed therapies are being developed and studied.

The outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV), 5 re-emergence of avian infl uenza A H5N1, 6 global circulation of oseltamivirresistant seasonal infl uenza A H1N1, 7 and subsequent emergence of the pandemic infl uenza A H1N1 strain pdm09 virus (which continues to circulate), 8 have shown the potential limitations of current antiviral treatments for severe respiratory viral infections. Epidemic waves of avian infl uenza A H7N9, 9 sporadic cases of avian infl uenza A H10N8, 10 the ongoing outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection, and the burden of common respiratory viruses 11 -such as seasonal infl uenza, respiratory syncytial virus, rhinoviruses, and adenoviruses-show that the development of more eff ective therapies to reduce morbidity and mortality is urgently needed. Research is focused on the repurposing of available antiviral drugs for generic or specifi c use and for 

Two classes of antiviral drugs are approved for the prevention and treatment of infl uenza in most countries: M2 inhibitors (amantadine and rimantadine) and neuraminidase inhibitors (oseltamivir, peramivir, zanamivir, and laninamivir; table 1). In general, antiviral treatment is indicated as early as possible for any patient with confi rmed or suspected infl uenza who has severe, complicated, or progressive illness or is admitted to hospital, and in outpatients at higher risk of infl uenza complications. 12, 13 Time to treatment after onset of symptoms, illness severity, and extent of viral replication are key variables with respect to response. Starting of treatment should not be delayed for diagnostic testing. M2 inhibitors-also known as adamantanes-are ineff ective against infl uenza B viruses and recently circulating infl uenza A H3N2 and 2009 pandemic infl uenza A H1N1 viruses, which are resistant because of an S31N mutation in the M2 ion channel. 12 However, a proportion of avian infl uenza A H5N1 strains will be susceptible, 14 and the combined use of an adamantane and a neuraminidase inhibitor improves antiviral activity for susceptible isolates. 15 Two neuraminidase inhibitors are approved for use in most countries: oseltamivir and zanamivir. Laninamivir is approved for use in Japan only, and peramivir in China, Japan, and South Korea. Several observational studies have shown that when adults admitted to hospital with severe infl uenza are given oseltamivir, mortality falls and clinical outcomes improve, especially when treatment is initiated within 2 days of the onset of symptoms (but positive eff ects are noted when it is begun as late as 4-5 days after onset). 12, 13, 16, 17 Oseltamivir reduces mortality in infl uenza A H5N1 infection when given before the onset of respiratory failure, 18 and might be benefi cial when started as late as 6-8 days after symptom onset. 19 In patients admitted to hospital with severe infl uenza A H7N9 infection, reduction of viral load after treatment with oseltamivir correlated with improved outcome, whereas the emergence of virus resistant to neuraminidase inhibitors that harbours an Arg292Lys substitution is associated with poor outcomes and poor response to oseltamivir and peramivir. 20 The standard duration of oseltamivir treatment is 5 days; longer treatment is recommended for critically ill patients with respiratory failure, who often have prolonged viral replication in the lower respiratory tract despite treatment. 13 Whether increased doses provide greater antiviral eff ects in such patients is under investigation. A randomised controlled trial 21 of patients in hospital (76% of whom were children) showed no virological or clinical advantages when a double dose of oseltamivir was given rather than a standard dose. No additional benefi t was noted with high-dose oseltamivir in adults admitted with infl uenza A, although a faster virological response was noted in those with infl uenza B. 22 However, in a randomised controlled trial 23 of 18 critically ill patients with 2009 pandemic infl uenza A H1N1, a triple-dose oseltamivir regimen was associated with signifi cantly higher proportions of viral clearance at 5 days than was standard therapy (78% vs 11%; p=0·015). 23 Studies of intravenous neuraminidase inhibitors that are underway should provide further data on the value of high-dose therapy.

Zanamivir and laninamivir have generally similar profi les of susceptibility. For example, the His275Tyr mutation confers high-level resistance to oseltamivir carboxylate and reduced susceptibility to peramivir in N1containing viruses but does not substantially diminish susceptibility to zanamivir and laninamivir. 30 Inhaled zanamivir has not been studied in detail in severely ill patients or those admitted to hospital, in whom eff ective delivery to sites of viral replication and tolerability could be an issue. By contrast, intravenous zanamivir has been used widely on a compassionate basis since the 2009 H1N1 pandemic, particularly for late treatment of critically ill adults with 2009 pandemic infl uenza A H1N1 virus infection and those with suspected or proven oseltamivir resistance. 31 One trial 32 has shown no drug-related trends in safety measures, and a subset of 93 patients positive at baseline for infl uenza showed a median decrease in nasopharyngeal viral RNA load of 1·42 log 10 copies per mL after 2 days of treatment. A phase 3 trial in patients who have been admitted to hospital is underway (NCT01014988). A phase 2 randomised controlled trial of inhaled laninamivir in uncomplicated infl uenza failed to show superiority in illness alleviation (primary endpoint) compared with placebo. The trial, involving 639 patients, tested 40 mg and 80 mg doses of the inhaled drug. The median time to alleviate fl u symptoms was 102·3 h for the 40 mg dose and 103·2 h for the 80 mg dose, compared with 104·1 h for the placebo (NCT01793883). DAS181 has host-directed receptor-destroying action, which is inhibitory for parainfl uenza and infl uenza viruses, including those resistant to amino adamantanes and neuraminidase inhibitors. 15 When delivered topically, it is eff ective in animal models of lethal infl uenza caused by the H5N1 and H7N9 viruses, including the neuraminidase-inhibitor-resistant Arg292Lys -containing variant. 35 In a phase 2 randomised controlled trial, 36 inhaled DAS181 reduced pharyngeal viral replication in uncomplicated infl uenza but did not reduce nasal viral loads or improve clinical outcomes. Case reports 37 suggest that inhaled or nebulised DAS181 might be eff ective in immunocompromised hosts with severe parainfl uenza lung disease.

Favipiravir (T-705; 6-fl uoro-3-hydroxy-2-pyrazinecarboxamide) is active against infl uenza A, B, and C viruses, including strains resistant to approved antivirals, and a broad range of other RNA viruses when given at Series somewhat higher concentrations. 38 Combinations of favipiravir and neuraminidase inhibitors have additive and synergistic eff ects in preclinical models, 39 but clinical trials have been restricted to uncomplicated infl uenza so far. These clinical trials (combination amantadine, ribavirin, and oseltamivir vs oseltamivir mono therapy [NCT01227969], nitazoxanide vs oseltamivir vs combination vs placebo [NCT01610245], favipiravir vs placebo randomised controlled trial in outpatients [NCT02008344, NCT2026349]), which have not been published, suggest that favipiravir has antiviral eff ects similar to those of oseltamivir. 40 A randomised controlled trial 41 showed that favipiravir shortened the time to alleviation of infl uenza symptoms by about 15 hours compared with placebo, and further studies are underway.

Nitazoxanide is an oral antiparasitic drug with immunomodulatory eff ects, including upregulation of interferon and various interferon-inducible genes and a specifi c infl uenza-inhibitory eff ect related to blockade of haemagglutinin maturation. 42 Nitazoxanide inhibits infl uenza replication in vitro 43 and in a phase 2 randomised controlled trial 44 had signifi cant antiviral eff ects (1·0 log 10 reduction in nasal viral loads) and resulted in a signifi cantly faster time to alleviation of illness (roughly 20 h diff erence in medians from placebo) in uncomplicated infl uenza. 44 A placebocontrolled randomised trial of nitazoxanide versus oseltamivir-and the com bination thereof-in uncomplicated infl uenza and a hospital-based study of its use in severe respiratory illness are in progress (NCT01610245).

Non-randomly assigned studies and case reports suggest that convalescent plasma with neutralising antibodies is a useful add-on therapy for patients with SARS and severe infl uenza pneumonia, including that caused by infl uenza A H5N1. 45 A recently published systematic review of available SARS and infl uenza treatment studies employing convalescent plasma or serum found a signifi cant overall mortality benefi t. 46 A prospective observational study 47 showed lower crude mortality and faster nasopharyngeal viral clearance in plasma-treated patients who were admitted with severe 2009 pandemic infl uenza A H1N1 infection, whereas in a randomised controlled trial 48 a reduction in mortality was reported in severe illness when hyperimmune globulin was given within 5 days of the onset of symptoms (table 2) . Heterosubtypic haemagglutinin stem-neutralising antibodies, which are highly eff ective in animals, 49 are entering clinical evaluation in human beings.

The combination of antivirals with diff erent mechanisms of actions (eg, a neuraminidase inhibitor with a polymerase inhibitor such as favipiravir, 38 a broad-spectrum antihaemagglutinin-neutralising antibody, 49 (20) Oral rimantadine and nebulised saline (21) Post-hoc analysis showed faster cough resolution but no signifi cant diff erences in the proportion of patients shedding virus by treatment day 3 (57% zanamivir plus rimantadine, 67% placebo plus rimantadine), or in the durations of hospitalisation and supplemental oxygen use Underpowered because of low enrolment Oseltamivir and corticosteroids (19) More rapid improvement in partial pressure of oxygen, fraction of inspired oxygen, and sequential organ failure assessment scores; shorter ventilator use (median 7 days vs 15 days, p=0·03); and faster viral clearance in the sirolimus than in the control group RCT=randomised controlled trial. 51 In a retrospective study 53 of critically ill adults, mortality rates did not diff er between those who received a triple combination of antiviral drugs and those receiving oseltamivir only, and a randomised controlled trial sponsored by the National Institute of Allergy and Infectious Diseases in higher-risk outpatients is underway (NCT01227969).

Host-directed therapies aim to reduce the damaging consequences of the host immune response to the pathogen. Combinations of antivirals with host-directed therapies such as the immunomodulator sirolimus, an mTOR inhibitor that blocks host pathways needed for viral replication (table 2) , 54 might also enhance antiviral activity.

Other host-directed therapies inhibiting cellular targets needed for effi cient viral replication (eg, the Raf-MEK-ERK mitogenic kinase cascade and the IKK-NF-κB module) might provide future options for clinical testing. 15 The role of adjunctive immunomodulatory therapies in severe infl uenza and other respiratory viral infections remains uncertain. Several observational studies show that systemic corticosteroids given for 2009 pandemic infl uenza A H1N1-associated viral pneumonia increased the risk of mortality and morbidity (eg, secondary infections), especially when there was a delay in initiation, or absence of, eff ective antiviral therapy. 45 Their use might delay viral clearance and increase the risk of the emergence of resistance 20 and fungal infections. 45 Other potential adjunctive therapies for infl uenza include intravenous immunoglobulin, N-acetylcysteine, statins, macrolides, peroxisome proliferator-activated receptor agonists, celecoxib, mesalazine, plasmapheresis, and haemo perfusion. 45 Chloroquine was eff ective against infl uenza A H5N1 infection in one animal model 55 but was ineff ective in other animal models and one human randomised controlled trial. 56, 57 

Interferons MERS-CoV infection can cause severe respiratory disease, and has higher mortality in those with medical comorbidities. Although empirical treatment with a range of antivirals has been tried for severe respiratory tract infections caused by MERS-CoV and SARS-CoV, no regimens have been rigorously assessed in clinical trials (panel). 58,59 MERS-CoV elicits attenuated innate immune responses with delayed proinfl ammatory cytokine induction in cell culture and in vivo. 60, 61 It is also readily inhibited by type 1 interferons (interferon alfa and especially interferon beta), suggesting a potential therapeutic use for interferons. Early pegylated interferon alfa therapy was eff ective in a SARS primate model, and treatment with interferon-alfa-consensus-1 plus systemic corticosteroids was associated with improved oxygen saturation and more rapid resolution of radiographic lung opacities than were systemic corticosteroids alone in an uncontrolled study of patients with SARS patients. 62 Further studies of interferons in MERS-CoV seem warranted.

Ribavirin was used extensively in patients with SARS without any benefi cial eff ects and was complicated by haemolytic anaemia and metabolic disturbances in many cases. 58, 59 A combination of interferon alfa 2b and ribavirin reduced lung injury and moderately decreased viral replication (<1·0 log 10 reduction in lung titres) when given to rhesus macaques within 8 h of inoculation with MERS-CoV. 63 The treatment combination was given to several severely ill patients with MERS, but the infections proved fatal, probably because of late administration in the advanced stage of the disease. 64, 65 Ribavirin has in-vitro inhibitory eff ects against MERS-CoV. 66 

The use of protease inhibitors with lopinavir and ritonavir as initial therapy in SARS was associated with signifi cantly less death (2·3% vs 15·6%, p<0·05) and intubation (0% vs 11·0%, p<0·05) than was use of ribavirin alone in a matched historical cohort (n=44 for lopinavir and ritonavir as intial treatment vs n=634 for the matched historical cohort). 68 However, one study reported that nelfi navir and lopinavir have high 50% eff ective inhibitory concentrations (EC 50 ) against MERS-CoV in vitro, 66 whereas another found inhibition with lopinavir at clinically achievable concentrations. 69

Several drugs have shown inhibitory eff ects against MERS-CoV in cell cultures, including interferons, ciclosporin, and mycophenolic acid. 66, 67, 69 Mycophenolic acid was inhibitory at clinically achievable concentrations, and the combination of mycophenolic acid and interferon β1b lowered the EC 50 of each drug by one-to-three times. 66 Dipeptidyl peptidase 4 (DPP4), also known as CD26, is a functional receptor for MERS-CoV, and an anti-CD26 polyclonal antibody showed in-vitro inhibitory eff ects on MERS-CoV. 70 By contrast, inhibitors of the enzymatic action of DPP4 (eg, gliptins) did not inhibit viral replication.

Timely administration of neutralising antibodies could have a high likelihood of therapeutic success. 46 Treatment with convalescent plasma (from patients who have recovered from SARS-CoV infection) containing high levels of neutralising antibody within 2 weeks of illness onset resulted in a higher proportion of discharges at day 22 than did treatment more than 14 days after onset (58% vs 16%, p<0.001). 71 75 showed worse outcomes when systemic corticosteroids were given in SARS. Consequently, their use should be avoided unless a carefully controlled prospective study is done to test their eff ectiveness when combined with an antiviral. Several observational studies have shown that systemic corticosteroids given for 2009 pandemic infl uenza A H1N1-asssociated viral pneumonia or acute respiratory distress syndrome increased the risk of mortality and morbidity (eg, secondary bacterial or fungal infections), especially if there is delay or lack of eff ective antiviral therapy. 45 Use of systemic corticosteroids has probably contributed to delayed viral clearance and emergence of antiviral resistance in patients with severe infl uenza A H7N9 infection requiring extracorporeal membrane oxy genation. 20 Infl uenza increases the risk of invasive aspergillosis, especially among immunocompromised patients, and this is often a silent infection in the early stages, 76 so direct surveillance with aspergillus antigen and PCR testing on respiratory secretions is advisable. Patients treated for fungal infections will have to undergo antifungal therapeutic drug monitoring. 77 Data are insuffi cient to support routine use of any of the immune therapies. Better animal data and careful systematic clinical studies, including serial virological measurements of priority treatments such as convalescent plasma and interferons (and randomised controlled trials if case numbers are suffi cient), are needed. Currently, clinical management of patients with severe respiratory tract infections due to MERS-CoV largely relies on meticulous intensive care supportive treatment and prevention of complications.

Research done in patients with haemopoietic stem-cell transplants shows that adoptive transfer of antigenspecifi c T cells can restore protective immunity and prevent or reverse disease due to opportunist viral infections such as cytomegalovirus. 78 In transplant recipients, transfer of donor-derived T cells can result in resolution of infection through expansion of virusspecifi c T cells, with associated clinical improvement. 79 Transfer of donor T cells is associated with the risk of severe acute graft-versus-host disease, and thus most T-cell therapies have been done in patients who have low lymphocyte counts. Lymphopenia enables only a very low number of T cells to be transferred, which then proliferate in lymphopenic hosts, most likely as a result of the interleukins 7 and 15 if the patient does not receive immunosuppressive treatment during T-cell therapy. 80 T-cell therapy targeting cytomegalovirus strains resistant to drug treatment is clinically relevant in lung transplant recipients. 81 T-cell expansion requires time to induce clinical regression of viral infection. Several other approaches might be applicable in situations that necessitate fast clinical action-eg, use of synthetic MHC antigens loaded with the relevant peptide from the pathogen of interest (so-called tetramer or multimer MHC-peptide complexes), which engage pathogenspecifi c lymphocytes expressing the pathogen-specifi c T-cell receptors. Pathogen-specifi c T cells can be isolated through use of soluble MHC-peptide complexes, and can immediately be transferred into patients for salvage treatments for viral infections. 82 T-cell expansion can also be achieved with several stimuli targeting several infectious pathogens. 83 Expansion of T cells targeting several antigens of cytomegalovirus, Epstein-Barr virus, and adenovirus provides broad antiviral specifi city after stem-cell transplantation. 84 An alternative approach to Series become independent of ex-vivo expansion of T cells is the identifi cation of T-cell receptors that would recognise viral infected cells that could be transferred into recipient eff ector cells. 85 T cells can also be engineered to produce an antiviral RNA that would block viral infection. 86

Synthetic antisense molecules, such as phosphorodiamidate morpholino oligomers, are structurally similar to RNA but the phosphorodiester linkage is replaced with a neutral phosphorodiamidate linkage and the ribose ring with a six-membered morpho lino ring. 87 They change gene expression by inhibiting translation, disrupting RNA secondary structure, and interfering with pre-mRNA splicing. 88 The usefulness of phosphorodiamidate morpho lino oligomers coupled to argininerich cell-penetrating peptides has been repeatedly demonstrated against bacterial pathogens 89 and could be a viable option for any microbial gene of interest.

Specifi c biological therapy for infectious pathogens targets not only drug-resistant pathogens but also their immune evasion mechanisms. 90 An antibody directed against CD19 (a B-cell marker) fused to a T-cell signalling molecule can be expressed in T cells and could kill target cells once they encounter their nominal target antigen. Such CD19 chimeric-antigen-receptor cells are used to remove Epstein-Barr-virus-positive lymphoma cells in the case of post-transplantation proliferative diseases. 91 Similar approaches can be used for the eff ective removal of pathogen-infected cells when very specifi c antibodies exist and if target molecules are expressed on infected cells only. 92

The frequency and spectrum of resistance to antibiotics in specifi c bacterial pathogens that cause respiratory tract infections continues to increase worryingly. Multidrugresistant Streptococcus pneumoniae-with resistance to three or more antibiotics-was initially noted in 1977 in South Africa 93 and subsequently in many other countries, with alarming rates of 30-50% of S pneumoniae that are multidrug resistant in the USA and Spain. [94] [95] [96] The European Antimicrobial Resistance Surveillance System showed that 22·2% of S pneumoniae were intermediate penicillin susceptible, 10·9% were penicillin resistant, and 21·1% were resistant to erythromycin. 97 Concerns about multidrug-resistant and pan-antibioticresistant Gram-negative bacteria 98, 99 are focused on Klebsiella pneumoniae, Enterobacter spp (production of extended spectrum β lactamase, Klebsiella pneumoniae carba penemase, NDM1, and AmpC), Acinetobacter baumannii, and Pseudomonas aeruginosa. In one survey of US health centres, 78% of Gram-negative bacteria were resistant to all antibiotics except colistin (to which 62% of Acinetobacter spp, 59% of Pseudomonas spp, and 52% of Enterobacter spp were resistant). 98 Therapeutic options to treat these infections are limited. 100, 101 Carbapenems are recommended for organisms that produce extended-spectrum β lactamases. 101 In a metaanalysis, [102] [103] [104] [105] [106] doripenem was more eff ective for P aeruginosa infections than were comparators in a modifi ed intention-to-treat analyses. Polymyxin B and colistin are concentration-dependent bactericidal agents that bind to bacterial cell membranes and have reliable activity against Acinetobacter spp. Novel β-lactamase inhibitors 107 and antibiotic com bination therapies 108 might provide stopgap measures for fulfi lling clinical need. Antibiotic development pipelines remain thin, 109, 110 and global attention is focused on increasing awareness for investments into the development of new antibacterial agents 111 and other antibacterial innovations, coupled to raising global awareness for more prudent use of available drugs. 112

In 2012, an estimated 1·3 million people died worldwide from tuberculosis, 170 000 of whom had multidrugresistant disease. 113 Multidrug-resistant tuberculosis, which is caused by Mycobacterium tuberculosis bacilli resistant to at least isoniazid and rifampicin, is now widespread globally, with an estimated half a million cases in 2012. 2 Extensively drug-resistant tuberculosisresistance to rifampicin, isoniazid, any fl uoroquinolone, and at least one of the three injectable second-line drugs, amikacin, kanamycin, and capreomycin-has been reported in 92 countries. 113 WHO recommends use of second-line drugs for 18-24 months or longer for extensively drug-resistant or multidrug-resistant disease. 114, 115 Treatment success rates are low in both individualised and standard regimens and new drugs and regimens are needed.

In the past 5 years, a promising pipeline of new drugs for the treatment of multidrug-resistant and extensively drug-resistant tuberculosis has emerged. 115 Progress has been made by repurposing drugs that are already available, including re-engineering existing antibacterial compounds and redesigning scaff olds, leading to discovery of new compounds. 116, 117 Two new drugs, delamanid (OPC-67683) and bedaquiline (TMC207 or R207910), have been approved by regulatory authorities. These new drugs are combined with older drugs to treat multidrug-resistant disease. 118, 119 Host-directed adjunct therapies Several approaches to rational development of adjunct immune-based therapies for multidrug-resistant tuberculosis have been developed. 120, 121 Non-steroidal antiinfl ammatory drugs can reduce M tuberculosis load and Series alleviate lung disease 122 in mice. 123 Effl ux pump inhibitors such as verapamil and reserpine reduce macrophageinduced drug tolerance, and thus could be used as adjunct host-directed therapies. 124, 125 Phosphodiesterase inhibitors such as cilostazol and sildenafi l improve mycobacterial clearance and decrease time to sterilisation by reducing tissue infl ammation. 126 A range of adjunct immunotherapy approaches implicating cytokines or their inhibitors and other biological immunomodulatory compounds are being assessed as means to limit damage from infl ammatory responses against M tuberculosis. Various cytokine regimens, including interferon c or interleukin 2, have been assessed, with variable eff ect. 127, 128 The antiinfl ammatory eff ects of macrolide antibiotics need to be further studied. 129 Whole genome sequencing might allow for rapid determination of resistance patterns of M tuberculosis strains, enabling tailored treatment regimens. Other immunomodulatory strategies include restoration of eff ective antipathogen-directed immunoresponses-and consequent decreasing of damaging host responses in lung tissues-in multidrug-resistant tuberculosis with infusions of the patient's own bonemarrow-derived stromal cells. A phase 1 trial showed that the procedure is safe, 130 and phase 2 trials are planned to assess the eff ects of mesenchymal stromal cell adjunct therapy on clinical and microbiological outcomes.

Invasive fungal respiratory tract infections are increasingly reported worldwide (table 3) . 131, 132 The two most common pulmonary fungal pathogens are Aspergillus fumigatus and Pneumocystis jirovecii. They increasingly represent primary causes of morbidity and mortality in critically ill patients across Europe, Africa, and Asia as a result of more people living with HIV, increased use of immunomodulatory drugs in patients with cancer, transplantations, and use of broad-spectrum antibiotics. Some patients with relapsed or micro biologically unconfi rmed multidrug-resistant tuber culosis have alternative diagnoses, including chronic pulmonary aspergillosis, and more com prehensive searches for alternative fungal diagnoses in smear and culture negative cases should be done in patients with multidrug-resistant disease. 133

Aspergillus is the most important fungal cause of invasive pulmonary disease, and A fumigatus is the cause in more than 75% of cases. Voriconazole is the most eff ective treatment for invasive aspergillosis but resistance has been noted on all continents except South America. 134, 135 Widespread use of the azoles as fungicides in agriculture has led to the environmental development of pan-azole resistance. 136 Resistance can also emerge during treatment, typically to itraconazole, and is possibly linked to a combination of low blood concentrations of the drug and high fungal loads. [137] [138] [139] Modelling suggests that more than 6·5 million people have severe asthma with fungal sensitisations, as much as 50% of adults with asthma who attend secondary care have fungal sensitisation, and an estimated 4·8 million adults have allergic bronchopulmonary aspergillosis. 140, 141 People with asthma who are sensitised to A fumigatus have a much higher rate of bronchiectasis than do those who are unsensitised. Reclassifi cation of aspergillosis in adults with cystic fi brosis by aspergillus serology (IgE and IgG) and both PCR and antigen on sputum showed three distinct classes of aspergillosis. 18% had allergic bronchopulmonary disease, 15% had aspergillus sensitisation, and 30% had aspergillus bronchitis; the remaining patients had no disease. Long-term oral antifungal therapy is benefi cial for 60-80% of patients with asthma, but is of unproven benefi t in cystic fi brosis. 142 Resistance in A fumigatus has been reported throughout Europe in roughly 4% of samples from patients with cystic fi brosis. 143, 144 

A new fungus causing disseminated infections in patients with AIDS was identifi ed in 2009. 145 Molecular identifi cation on the basis of ITS1 and ITS2 sequencing showed that all isolates of this new species were tightly clustered and were most similar to Emmonsia pasteuriana and Emmonsia parva, and slightly more distantly related to Histoplasma capsulatum. Clinical features of infection included fever, loss of weight, anaemia, skin lesions akin to those in disseminated histoplasmosis, and a chest radiograph similar to that noted in pulmonary tuberculosis. The fungus was cultured from skin and blood, but not sputum or CSF. Signifi cant clinical responses were noted when patients were given intravenous amphotericin B followed by itraconazole. 145 

A large combination study 146 Series did not reach its primary endpoint of reduced mortality, although patients with positive galactomannan seemed to benefi t most. Guidelines for management of invasive aspergillosis still favour voriconazole over all other treatments and combination therapy is not usually recommended. A tablet formulation of posaconazole, which is more bioavailable than the oral suspension, is available and can be given once a day, 147 and the US Food and Drug Administration has approved an intravenous suspension of the drug. The only new drug to be approved is isavuconazole, a broad-spectrum azole, which will be available in intravenous and oral forms (application for approval was submitted in July, 2014). Itraconazole seems safe in the fi rst trimester of pregnancy, whereas fl uconazole increases the risk of Fallot's tetralogy by a factor of three to one in 1000. 148 Drivers for the development of new antifungal drugs include inadequate response rates, the absence of oral preparations of echinocandins, drug interactions, important drug toxic eff ects (especially amphotericin B and voriconazole), and triazole and echinocandin resistance. Several drugs are being repurposed for use as antifungals, and new drugs are under development (table 4) . [149] [150] [151] [152] [153] [154] [155] Sertraline, which is used for depression, has synergistic activity with fl uconazole in a murine model of cryptococcal infection. 156 Calcineurin and targets of rapamycin inhibitors have antifungal activity, which is synergsitic with that of azoles. 157 Hsp90 inhibitors initially developed for cancer treatment can improve fl uconazole activity in vitro and in animals. 158 Enoxacin, a fl uoroquinolone antibiotic, shows activity in a murine candidiasis model. 159

Although azoles are important for the treatment of invasive pulmonary aspergillosis, the degree of immunosuppression and other immunological factors have a role in treatment outcomes. Antifungal immune responses could be improved by adaptive transfer of pathogen-specifi c T cells directed against invasive and pulmonary fungal infections, particularly infections with candida, aspergillus, and mucormycetes, especially after allogeneic stem-cell transplantation. T-cell responses are MHC class I restricted (for CD8positive T cells) or MHC class II restricted (for CD4positive T cells), and thus an eff ective T-cell response needs to match the genetic background of the patient. T-cell transfer was developed on the basis of the promising fi nding that transfer of pathogen-specifi c T-cell clones induces clinically signifi cant responses. 160, 161 Several approaches have been used to obtain these pathogen-specifi c T cells. Anti-pathogenspecifi c T cells can be expanded ex vivo under appropriate conditions (usually with the help of recombinant cytokines, synthetic peptides, or cellular components representing the pathogen). Responder T cells are identifi ed by interferon-γ production, removed via an interferon-capture assay, and transferred into the patient. This approach requires time for expansion of T cells (either the patient's own or those of an MHC-matched donor). This protocol enabled the expansion of Aspergillus spp, Candida spp, with the terms "respiratory tract", "pneumonia", "infections", "bacteria", "virus", "fungus", and "mycobacteria". We also combined these terms with the words "antibiotic", "antibiotic resistance", "treatment", "drugs", "drug development", "drug pipeline", "antibiotic development", "host-directed", "therapy", "adjunct therapy", "steroids", and "immunotherapy". We complemented the search with publications from WHO, the US Centers for Disease Control and Prevention, http://clinicaltrials. gov, and Google Scholar. We also reviewed studies cited by articles identifi ed by this search.

and Mucor spp-reactive T cells defi ned by interferon-γ production. Upon re-encounter with the nominal target antigen, the T cells proliferated and increased the antifungal reactivity of phagocytes. 162

New and antimicrobial-resistant species of bacteria, viruses, and fungi continue to emerge because of the remarkable genetic and adaptable plasticity of the microbiota. 163 Respiratory tract infections are among the top two causes of death globally. 164, 165 Microorganisms do not respect international boundaries, and ease of travel and airborne spread make them a threat to global health security. The increasing frequency of antibiotic resistance and limited therapeutic options emphasise the urgent need for more international cooperation to tackle new emerging microbial threats and multidrug-resistant microbes. Development of new therapeutic options needs to be coupled to international regulations on the use and prescription of antimicrobial drugs.

DSH and AZ coordinated the writing of this Series paper and wrote the draft outline, and subsequent and fi nal drafts. All authors contributed relevant text and tables on their expert sections or sections and contributed to fi nalising the paper.

FGH has served as non-paid consultant for multiple companies engaged in marketing and/or clinical development of antivirals for respiratory viral infections including several whose therapeutics are discussed in this review (Adamas, Biocryst, GSK, Genentech, Janssen, Roche, Romark, Toyama/Medivector, Visterra). DWD holds founder shares in F2G, a University of Manchester spin-out company. He acts as a consultant to Trinity Group, T2 Biosystems, GlaxoSmithKline, Sigma Tau, Oxon Epidemiology, and has consulted for Merck and Astellas and he has been paid to give talks on behalf of Astellas, Gilead, and Pfi zer. All other authors declare no confl icts of interest.

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WHO. Avian infl uenza A(H7N9) virus

Clinical and epidemiological characteristics of a fatal case of avian infl uenza A H10N8 virus infection: a descriptive study

Addressing the public health burden of respiratory viruses: the battle against respiratory viruses (BRaVe) Initiative

for the NIAID Collaborative Antiviral Study Group. Safety and effi cacy of nebulized zanamivir in hospitalized patients with serious infl uenza

Antiviral agents for the treatment and chemoprophylaxis of infl uenza. Recommendations of the Advisory Committee on Immunization Practices (ACIP)

Antiviral resistance among highly pathogenic infl uenza A (H5N1) viruses isolated worldwide in 2002-2012 shows need for continued monitoring

Newer infl uenza antivirals, biotherapeutics and combinations

Complications and outcomes of pandemic 2009 infl uenza A (H1N1) virus infection in hospitalized adults: how do they diff er from those in seasonal infl uenza?

Eff ectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with infl uenza A H1N1pdm09 virus infection: a metaanalysis of individual participant data

Determinants of antiviral eff ectiveness in infl uenza virus A subtype H5N1

Eff ectiveness of antiviral treatment in human infl uenza A(H5N1) infections: analysis of a global patient registry

Association between adverse clinical outcome in human disease caused by novel infl uenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance

Eff ect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe infl uenza: double blind randomised controlled trial

A prospective intervention study on higher-dose oseltamivir treatment in adults hospitalized with infl uenza A and B infections

Viral clearance with standard or triple dose oseltamivir therapy in critically ill patients with pandemic (H1N1) 2009 infl uenza

Intravenous peramivir for treatment of infl uenza A and B virus infection in high-risk patients

A clinical trial of intravenous peramivir compared with oral oseltamivir for the treatment of seasonal infl uenza in hospitalized adults

Intravenous peramivir for treatment of infl uenza in hospitalized patients

Business Wire. BioCryst announces outcome from the peramivir phase 3 interim analysis

Early emergence of an H275Y mutation in a hematopoietic cell transplant recipient treated with intravenous peramivir

Rapid selection of oseltamivir-and peramivirresistant pandemic H1N1 virus during therapy in 2 immunocompromised hosts

CS-8958, a prodrug of the new neuraminidase inhibitor R-125489, shows long-acting anti-infl uenza virus activity

Clinical experience with intravenous zanamivir under an emergency investigational new drug program in the United States

Safety and pharmacokinetics of intravenous zanamivir treatment in hospitalized adults with infl uenza: an open-label, multicenter, single-arm, phase II study

Long-acting neuraminidase inhibitor laninamivir octanoate versus oseltamivir for treatment of infl uenza: a doubleblind, randomized, noninferiority clinical trial

A randomized double-blind controlled study of laninamivir compared with oseltamivir for the treatment of infl uenza in patients with chronic respiratory diseases

An investigational antiviral drug, DAS181, eff ectively inhibits replication of zoonotic infl uenza A virus subtype H7N9 and protects mice from lethality

A phase II study of DAS181, a novel host directed antiviral for the treatment of infl uenza infection

DAS181 treatment of hematopoietic stem cell transplant patients with parainfl uenza virus lung disease requiring mechanical ventilation

Favipiravir (T-705), a novel viral RNA polymerase inhibitor

Combinations of favipiravir and peramivir for the treatment of pandemic infl uenza A/California/04/2009 (H1N1) virus infections in mice

Clinical eff ectiveness and safety of favipiravir, a novel anti-infl uenza drug with a selective inhibition activity against viral RNA polymerase. 51st Interscience Conference on

A Phase 2, randomized, double blind, placebocontrolled, multicenter study evaluating the safety and pharmacokinetics of diff erent dosing regimens of favipiravir (T-705) in adult subjects with uncomplicated infl uenza, VIII Options for Control of Infl uenza

A new class of anti-infl uenza molecules targeting viral hemagglutinin at the post-translational level

Romark announces clinical trial results for new infl uenza drug presented at IDSA meeting

Eff ect of nitazoxanide in adults and adolescents with acute uncomplicated infl uenza: a double-blind, randomised, placebo-controlled, phase 2b/3 trial

Adjunctive therapies and immunomodulatory agents in the management of severe infl uenza

The eff ectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral aetiology: a systematic review and exploratory meta-analysis

Convalescent plasma treatment reduced mortality in patients with severe pandemic infl uenza A (H1N1) 2009 virus infection

Hyperimmune IV immunoglobulin treatment: a multicenter double-blind randomized controlled trial for patients with severe 2009 infl uenza A(H1N1) infection

An in vivo human-plasmablast enrichment technique allows rapid identifi cation of therapeutic infl uenza A antibodies

Antiviral combinations for severe infl uenza infections: a review

Triple combination of amantadine, ribavirin, and oseltamivir is highly active and synergistic against drug resistant infl uenza virus strains in vitro

Effi cacy of oseltamivirzanamivir combination compared to each monotherapy for seasonal infl uenza: a randomized placebo-controlled trial

Triple-combination antiviral drug for pandemic H1N1 infl uenza virus infection in critically ill patients on mechanical ventilation

Adjuvant treatment with a mammalian target of rapamycin inhibitor, sirolimus, and steroids improves outcomes in patients with severe H1N1 pneumonia and acute respiratory failure

Anti-malaria drug chloroquine is highly eff ective in treating avian infl uenza A H5N1 virus infection in an animal model

Eff ectiveness of chloroquine against infl uenza

Chloroquine for infl uenza prevention: a randomised, double-blind, placebo controlled trial

International Severe Acute Respiratory and Emerging Infections Consortium Treatment of MERS-CoV: information for clinicians. Clinical decision-making support for treatment of MERS-CoV patients

Severe acute respiratory syndrome and coronavirus

Tropism of and innate immune responses to the novel human betacoronavirus lineage C virus in human ex vivo respiratory organ cultures

Distinct immune response in two MERS-CoV-infected patients: can we go from bench to bedside?

Interferon alfacon-1 plus corticosteroids in severe acute respiratory syndrome: a preliminary study

Treatment with interferon-α2b and ribavirin improves outcome in MERS-CoVinfected rhesus macaques

Ribavirin and interferon therapy in patients infected with the Middle East respiratory syndrome coronavirus: an observational study

Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection

Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus

Inhibition of novel β coronavirus replication by a combination of interferon-α2b and ribavirin

Treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicenter retrospective matched cohort study

MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-α treatment

Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC

Use of convalescent plasma therapy in SARS patients in Hong Kong

Contact investigation of a case of human novel coronavirus infection treated in a German hospital

Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection

Eff ects of early corticosteroid treatment on plasma SARS-associated Coronavirus RNA concentrations in adult patients

The use of corticosteroid as treatment in SARS was associated with adverse outcomes: a retrospective cohort study

Invasive aspergillosis after pandemic (H1N1)

Pharmacokinetics and pharmacodynamics of a novel triazole, isavuconazole: mathematical modeling, importance of tissue concentrations, and impact of immune status on antifungal eff ect

Immune reconstitution after allogeneic transplantation and expanding options for immunomodulation: an update

Monoculture-derived T lymphocytes specifi c for multiple viruses expand and produce clinically relevant eff ects in immunocompromised individuals

Infusion of cytomegalovirus (CMV)-specifi c T cells for the treatment of CMV infection not responding to antiviral chemotherapy

Transferring functional immune responses to pathogens after haploidentical hematopoietic transplantation

Clinical grade generation of hexon-specifi c T cells for adoptive T-cell transfer as a treatment of adenovirus infection after allogeneic stem cell transplantation

Rapid salvage treatment with virus-specifi c T cells for therapy-resistant disease

Expansion of T cells targeting multiple antigens of cytomegalovirus, Epstein-Barr virus and adenovirus to provide broad antiviral specifi city after stem cell transplantation

Morpholino antisense oligomers: design, preparation, and properties

Antisense-mediated modulation of splicing: therapeutic implications for Duchenne muscular dystrophy

Viral strategies of immune evasion

Viral interference with antigen presentation to CD8+ T cells: lessons from cytomegalovirus

Stimulation of human EBV-and CMV-specifi c cytolytic eff ector function using allogeneic HLA molecules

T cell allorecognition via molecular mimicry

Treating B-cell cancer with T cells expressing anti-CD19 chimeric antigen receptors

Cytotoxic therapy for severe swine fl u A/H1N1

Emergence of multiply resistant pneumococci

Molecular characterization of Streptococcus pneumoniae invasive serotype 19A isolates from adults in two Spanish regions

Trends in antibacterial resistance among Streptococcus pneumoniae isolated in the USA: update from PROTEKT US Years 1-4

Streptococcus pneumoniae: does antimicrobial resistance matter?

Antimicrobial activity of ceftaroline tested against drug-resistant subsets of Streptococcus pneumoniae from US medical centers

Variation in defi nitions and isolation procedures for multidrug-resistant gram-negative bacteria: a survey of the Society for Healthcare Epidemiology of America research network

WHO. Antimicrobial resistance-global report and surveillance

Variation in potency and spectrum of tigecycline activity against bacterial strains from U.S. medical centers since its approval for clinical use

New developments in carbapenems

Meta-analysis of doripenem vs comparators in patients with pseudomonas infections enrolled in four phase III effi cacy and safety clinical trials

Current control and treatment of multidrug-resistant Acinetobacter baumannii infections

Polymyxins revisited

Global assessment of the antimicrobial activity of polymyxin B against 54 731 clinical isolates of Gram-negative bacilli: report from the SENTRY antimicrobial surveillance programme

In vitro activity of colistin (polymyxin E) against 3,480 isolates of gram-negative bacilli obtained from patients in Canadian hospitals in the CANWARD study

Determination of in vitro activities of polymyxin B and rifampin in combination with ampicillin/sulbactam or cefoperazone/ sulbactam against multidrug-resistant Acinetobacter baumannii by the E-test and checkerboard methods

Antibiotics in phase II and III clinical trials

Antibiotics currently in clinical development

WHO. WHO global strategy for containment of antimicrobial resistance

Discovery and preclinical development of new antibiotics

WHO guidelines for the programmatic management of drug-resistant tuberculosis: 2011 update

New antituberculosis drugs, regimens, and adjunct therapies: needs, advances, and future prospects

Advances in the development of new tuberculosis drugs and treatment regimens

Tuberculosis drug discovery in the post-post-genomic era

Provisional CDC guidelines for the use and safety monitoring of bedaquiline fumarate (Sirturo) for the treatment of multidrugresistant tuberculosis

Rational development of adjunct immunebased therapies for drug-resistant tuberculosis: hypotheses and experimental designs

Host genotype-specifi c therapies can optimize the infl ammatory response to mycobacterial infections

Ibuprofen therapy resulted in signifi cantly decreased tissue bacillary loads and increased survival in a new murine experimental model of active tuberculosis

Antitubercular specifi c activity of ibuprofen and the other 2-arylpropanoic acids using the HT-SPOTi whole-cell phenotypic assay

Effl ux inhibition with verapamil potentiates bedaquiline in Mycobacterium tuberculosis

Acceleration of tuberculosis treatment by adjunctive therapy with verapamil as an effl ux inhibitor

Adjuvant host-directed therapy with types 3 and 5 but not type 4 phosphodiesterase inhibitors shortens the duration of tuberculosis treatment

Diff erential gene expression in response to adjunctive recombinant human interleukin-2 immunotherapy in multidrug-resistant tuberculosis patients

Totally drugresistant tuberculosis and adjunct therapies

Anti-infl ammatory activity of macrolide antibiotics

Autologous mesenchymal stromal cell infusion as adjunct treatment in patients with multidrug and extensively drug-resistant tuberculosis: an openlabel phase 1 safety trial

Human fungal infections: the hidden killers

The frequency of Pneumocystis jirovecii in sputum samples of HIV and TB patients received at the Central Reference Laboratory in Windhoek, Namibia

Global burden of chronic pulmonary aspergillosis as a sequel to pulmonary tuberculosis

Voriconazole resistance in Aspergillus fumigatus-should we be concerned?

Risk assessment on the impact of environmental usage of triazoles on the development and spread of resistance to medical triazoles in Aspergillus species

Clinical implications of azole resistance in Aspergillus fumigatus, the Netherlands

Frequency and evolution of azole resistance in Aspergillus fumigatus associated with treatment failure

Azole antifungal resistance in Aspergillus fumigatus

High frequency triazole resistance found in non-culturable Aspergillus fumigatus from lungs of patients with chronic fungal disease

Global burden of ABPA in adults with asthma and its complication chronic pulmonary aspergillosis

Allergic bronchopulmonary aspergillosis: review of literature and proposal of new diagnostic and classifi cation criteria

Allergic bronchopulmonary aspergillosis in cystic fi brosis. A European epidemiological study

Novel immunologic classifi cation of aspergillosis in adult cystic fi brosis

High prevalence of azole-resistant Aspergillus fumigatus in adults with cystic fi brosis exposed to itraconazole

A dimorphic fungus causing disseminated infection in South Africa

A randomised, double-blind study of combination antifungal therapy with voriconazole and anidulafungin versus voriconazole monotherapy for primary treatment of invasive aspergillosis. 22nd European Congress of Clinical Microbiology and Infectious Diseases

A new solid oral tablet formulation of posaconazole: a randomized clinical trial to investigate rising single-and multiple-dose pharmacokinetics and safety in healthy volunteers

Oral fl uconazole during pregnancy and risk of birth defects

Therapy for fungal diseases: opportunities and priorities

A Phase 1, randomized, open-label crossover study to evaluate the safety and pharmacokinetics of 400 mg albaconazole administered to healthy participants as a tablet formulation versus a capsule formulation

Enfumafungin derivative MK-3118 shows increased in vitro potency against clinical echinocandin-resistant Candida species and Aspergillus species isolates

Activity of MGCD290, a Hos2 histone deacetylase inhibitor, in combination with azole antifungals against opportunistic fungal pathogens

Modeling nikkomycin Z dosing and pharmacology in murine pulmonary coccidioidomycosis preparatory to phase 2 clinical trials

In vitro and in vivo antifungal activities of T-2307, a novel arylamidine

Advancing antifungal R&D. www.f2g.com/f2g-ltd-completes-30-million-fi nancing-round-to-fund-pre-clinical-and-clinical-developmentof-novel-anti-fungal-compounds/ (accessed May

The antidepressant sertraline provides a promising therapeutic option for neurotropic cryptococcal infections

Signaling cascades as drug targets in model and pathogenic fungi

Progress and prospects for targeting Hsp90 to treat fungal infections

Inhibition of Candida albicans virulence factors by novel levofl oxacin derivatives

Restoration of viral immunity in immunodefi cient humans by the adoptive transfer of T cell clones

Adoptive cellular therapy for early cytomegalovirus infection after allogeneic stem-cell transplantation with virus-specifi c T-cell lines

Clinical-scale generation of multi-specifi c anti-fungal T cells targeting Candida, Aspergillus and mucormycetes

Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis

Deaths due to respiratory tract infections in Africa: a review of autopsy studies

Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study