Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14

Fabeni, L.; Alteri, C.; Di Carlo, D.; Orchi, N.; Carioti, L.; Bertoli, A.; Gori, C.; Forbici, F.; Continenza, F.; Maffongelli, G.; Pinnetti, C.; Vergori, A.; Mondi, A.; Ammassari, A.; Borghi, V.; Giuliani, M.; De Carli, G.; Pittalis, S.; Grisetti, S.; Pennica, Alfredo; Mastroianni, Claudio Maria; Montella, F.; Cristaudo, A.; Mussini, C.; Girardi, E.; Andreoni, M.; Antinori, A.; Ceccherini silberstein, F.; Perno, C. F.; Santoro, M. M.; Girardi, E.; Capobianchi, M. R.; Perno, C. F.; Orchi, N.; Navarra, A.; Palummieri, A.; Abbate, I.; Ammassari, A.; D'Arrigo, R.; De Carli, G.; Fabeni, L.; Forbici, F.; Fusco, F. M.; Gori, C.; Grisetti, S.; Mariano, A.; Nicastri, E.; Nurra, G.; Pinnetti, C.; Pittalis, S.; Puro, V.; Sampaolesi, A.; Sciarrone, M. R.; Scognamiglio, P.; Selleri, M.; Sias, C.; Zaccarelli, M.; Di Carlo, A.; Giuliani, M.; Vullo, Vincenzo; Falciano, Mario; Pennica, A.; Errigo, F.; Gattari, P.; Spizzichino, L.; Schito, S.; Andreoni, M.; Sarmati, L.; Buonomini, A. R.; Cerva, C.; Mastroianni, C.; Lichtner, Miriam; Mercurio, V. S.; Anzalone, E.; Pitorri, A.; Caterini, A.; Aviani Barbacci, S.

doi:10.1093/jac/dkx231

BACKGROUND: Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. METHODS: In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. RESULTS: Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. CONCLUSIONS: The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.

Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14 / Fabeni, L.; Alteri, C.; Di Carlo, D.; Orchi, N.; Carioti, L.; Bertoli, A.; Gori, C.; Forbici, F.; Continenza, F.; Maffongelli, G.; Pinnetti, C.; Vergori, A.; Mondi, A.; Ammassari, A.; Borghi, V.; Giuliani, M.; De Carli, G.; Pittalis, S.; Grisetti, S.; Pennica, Alfredo; Mastroianni, Claudio Maria; Montella, F.; Cristaudo, A.; Mussini, C.; Girardi, E.; Andreoni, M.; Antinori, A.; Ceccherini silberstein, F.; Perno, C. F.; Santoro, M. M.; Girardi, E.; Capobianchi, M. R.; Perno, C. F.; Orchi, N.; Navarra, A.; Palummieri, A.; Abbate, I.; Ammassari, A.; D'Arrigo, R.; De Carli, G.; Fabeni, L.; Forbici, F.; Fusco, F. M.; Gori, C.; Grisetti, S.; Mariano, A.; Nicastri, E.; Nurra, G.; Pinnetti, C.; Pittalis, S.; Puro, V.; Sampaolesi, A.; Sciarrone, M. R.; Scognamiglio, P.; Selleri, M.; Sias, C.; Zaccarelli, M.; Di Carlo, A.; Giuliani, M.; Vullo, Vincenzo; Falciano, Mario; Pennica, A.; Errigo, F.; Gattari, P.; Spizzichino, L.; Schito, S.; Andreoni, M.; Sarmati, L.; Buonomini, A. R.; Cerva, C.; Mastroianni, C.; Lichtner, Miriam; Mercurio, V. S.; Anzalone, E.; Pitorri, A.; Caterini, A.; Aviani Barbacci, S.. - In: JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. - ISSN 0305-7453. - STAMPA. - 72:10(2017), pp. 2837-2845. [10.1093/jac/dkx231]