Background Fluoroquinolones have been used broadly since the end of the 1980s and have been recommended for Neisseria meningitidis prophylaxis since 2005 in China. The aim of this study was to determine whether and how N. meningitidis antimicrobial susceptibility, serogroup prevalence, and clonal complex (CC) prevalence shifted in association with the introduction and expanding use of quinolones in Shanghai, a region with a traditionally high incidence of invasive disease due to N. meningitidis. Methods and Findings A total of 374 N. meningitidis isolates collected by the Shanghai Municipal Center for Disease Control and Prevention between 1965 and 2013 were studied. Shifts in the serogroups and CCs were observed, from predominantly serogroup A CC5 (84%) in 1965–1973 to serogroup A CC1 (58%) in 1974–1985, then to serogroup C or B CC4821 (62%) in 2005–2013. The rates of ciprofloxacin nonsusceptibility in N. meningitidis disease isolates increased from 0% in 1965–1985 to 84% (31/37) in 2005–2013 (p < 0.001). Among the ciprofloxacin-nonsusceptible isolates, 87% (27/31) were assigned to either CC4821 (n = 20) or CC5 (n = 7). The two predominant ciprofloxacin-resistant clones were designated ChinaCC4821-R1-C/B and ChinaCC5-R14-A. The ChinaCC4821-R1-C/B clone acquired ciprofloxacin resistance by a point mutation, and was present in 52% (16/31) of the ciprofloxacin-nonsusceptible disease isolates. The ChinaCC5-R14-A clone acquired ciprofloxacin resistance by horizontal gene transfer, and was found in 23% (7/31) of the ciprofloxacin-nonsusceptible disease isolates. The ciprofloxacin nonsusceptibility rate was 47% (7/15) among isolates from asymptomatic carriers, and nonsusceptibility was associated with diverse multi-locus sequence typing profiles and pulsed-field gel electrophoresis patterns. As detected after 2005, ciprofloxacin-nonsusceptible strains were shared between some of the patients and their close contacts. A limitation of this study is that isolates from 1986–2004 were not available and that only a small sample of convenience isolates from 1965–1985 were available. Conclusions The increasing prevalence of ciprofloxacin resistance since 2005 in Shanghai was associated with the spread of hypervirulent lineages CC4821 and CC5. Two resistant meningococcal clones ChinaCC4821-R1-C/B and ChinaCC5-R14-A have emerged in Shanghai during the quinolone era. Ciprofloxacin should be utilized with caution for the chemoprophylaxis of N. meningitidis in China., Minggui Wang and colleagues assess the genetic origin and changing prevalence of N. meningitidis resistance to ciprofloxacin., Editors' Summary Background Meningitis is a viral, bacterial, or fungal infection of the meninges, the thin membrane that covers the brain and the spinal cord. Neisseria meningitidis is the most common cause of bacterial meningitis in children and is a leading cause of meningitis in adults. N. meningitidis lives harmlessly in the mucous membranes of the nose and throat of 10%–20% of human beings. These symptom-free (asymptomatic) carriers are crucial to the transmission of N. meningitidis, which spreads from person to person through droplets of respiratory or throat secretions produced by infected individuals. Although N. meningitidis usually causes no harm, it occasionally overwhelms its host’s immune system and spreads through the bloodstream and into the brain. The characteristic symptoms of meningococcal meningitis—a rash, fever, stiff neck, sensitivity to light, confusion, headaches, and vomiting—then develop rapidly. Even with early treatment with intravenous antibiotics, about 10% of the 1.2 million people affected by meningococcal meningitis every year die, usually within 24–48 hours of symptom development. Why Was This Study Done? Meningococcal meningitis can be prevented by vaccination against N. meningitidis. In addition, experts recommend that the family and close contacts of anyone with meningococcal meningitis be treated immediately with antibiotics to stop the disease spreading (N. meningitidis prophylaxis). The quinolone antibiotic ciprofloxacin is sometimes recommended for N. meningitidis prophylaxis, but quinolones have been used to treat many bacterial infections since the late 1980s and ciprofloxacin-resistant strains of N. meningitidis have recently emerged in some countries. Thus, policymakers in countries where ciprofloxacin may be used for meningococcal prophylaxis (for example, China, which has recommended several antibiotics, including ciprofloxacin, for meningococcal prophylaxis since 2005) need to know whether and how the susceptibility of N. meningitidis to ciprofloxacin is changing in their country. In this time trend analysis, the researchers investigate how the ciprofloxacin susceptibility, serogroup prevalence, and clonal complex prevalence of N. meningitidis have shifted in association with increasing use of quinolones in Shanghai (China), a region where many cases of meningococcal disease occur. A serogroup is a group of bacteria that carries a common antigen (a molecule recognized by the immune system); the prevalence of a serogroup is the proportion of the infected population that carries that serogroup. Only some N. meningitidis serogroups cause meningococcal disease. A clonal complex is a group of genetically related bacteria that may share genes that confer resistance to antibiotics. A strain of N. meningitidis is classified by both its serogoup and its clonal complex; the changing composition of prevalent strains can inform projections for disease spread and plans for disease management, including recommendations for prophylaxis. What Did the Researchers Do and Find? The researchers analyzed the characteristics of 374 N. meningitidis isolates collected in Shanghai between 1965 and 2013 from patients with meningococcal disease, their close contacts, and asymptomatic N. meningitidis carriers identified in throat swab surveys. N. meningitidis serogroups and clonal complexes (CCs) shifted from predominantly serogroup A CC5 among isolates collected in 1965–1973, to serogroup A CC1 in 1974–1985, and to serogroup C or B CC4821 in 2005–2013. Notably, the rate of nonsusceptibility to ciprofloxacin in isolates from people with meningococcal meningitis increased from 0% in 1965–1985 to 84% in 2005–2013, and 87% (27/31) of the ciprofloxacin-nonsusceptible disease isolates belonged to either CC4821 or CC5. The researchers identified the two predominant ciprofloxacin-resistant strains (designated ChinaCC4821-R1-C/B and ChinaCC5-R14-A) and showed that a different genetic alteration was responsible for the acquisition of antibiotic resistance in the two strains. Finally, the researchers report that, after 2005, the rate of ciprofloxacin nonsusceptibility among N. meningitidis isolates from asymptomatic carriers was 47%, and that some of the individuals with meningococcal meningitis shared nonsusceptible strains with their close contacts. What Do These Findings Mean? These findings suggest that the increased prevalence of ciprofloxacin resistance seen in Shanghai since 2005 is associated with the spread of two hypervirulent clonal complexes of N. meningitidis (CC4821 and CC5) among individuals with meningococcal disease and within the healthy population. The findings also identify two resistant meningococcal strains (ChinaCC4821-R1-C/B and ChinaCC5-R14-A) that have emerged in Shanghai since the use of quinolones to treat bacterial infections became widespread. Because this time trend analysis is based on a limited number of meningococcal isolates and because the researchers analyzed very few isolates collected between 1965 and 1985 and none collected between 1986 and 2004, this study cannot pinpoint exactly when, where, or how ciprofloxacin-resistant N. meningitidis emerged in Shanghai. Nevertheless, these findings suggest that the use of fluoroquinolones for N. meningitidis prophylaxis should be discouraged in China. Instead, the researchers suggest, physicians should turn to one of the other antibiotics recommended in China’s 2005 national scheme (for example, rifampicin) for the prevention and control of meningococcal meningitis. Additional Information These websites can be accessed when viewing the PDF on a device, or via the online version of this article at http://dx.doi.org/10.1371/journal.pmed.1001838. The US Centers for Disease Control and Prevention provide information about meningococcal disease The World Health Organization has a fact sheet about meningococcal meningitis The UK National Health Service Choices website provides information about meningitis, including some personal storiesThe non-profit Meningitis Foundation of America also provides information about meningitis and stories from survivors of meningitis MedlinePlus has links to further resources about meningitis and about meningococcal infections; the MedlinePlus Encyclopedia also provides information about meningococcal meningitis (in English and Spanish)