Meningococcal bacteria, same as pneumococcus, are able to change their serogroups.Invasive meningococcal disease in Quebec, Canada, due to an emerging clone of ST-269 serogroup B meningococci with serotype antigen 17 and serosubtype antigen P1.19 (B: 17: P1.19). 2006, Law, J Clin Microbiol
Serogroup B meningococcal disease outbreak in Québec in 2004. The authors believe that it probably happened due to serogroup replacement due to vaccination with the polysaccharide vaccine against serogroup C.Effectiveness of monovalent rotavirus vaccine (Rotarix) against severe diarrhea caused by serotypically unrelated G2P  strains in Brazil. 2010, Correia, J Infect Dis
In 15 months after the introduction of the vaccination in Brazil, G2P(4) rotavirus strain has replaced all other strains, even though it was only seen in 19%-30% of cases prior to the introduction of vaccination. Effectiveness of the vaccine (Rotarix) against this strain was 77% among children of 6-11 months of age, and -24% (negative) among children over 12 months of age. More: , .
It is reported here, that after the introduction of vaccination in Brazil, regular rotavirus strains got replaced with the new GP12(8) strain. Strain replacement also took place in Paraguay https://www.ncbi.nlm.nih.gov/pubmed/20213281] and in Argentina.
Since the rotavirus genome consists of separate segments, when two different strains of the virus infect the same cell, they can exchange segments and create a new strain. This is the same reassortment, which happens on its own.
A case of gastroenteritis in a 7-year-old girl is reported here. A rotavirus strain was isolated from her stool sample. The strain was reassortant of two other human-bovine strains from the RotaTeq vaccine. However, the girl has not been vaccinated against rotavirus. Moreover, she has not been in contact with anyone who has been vaccinated. Her two brothers also had similar gastroenteritis symptoms, and they also have not been vaccinated or in contact with anyone who has been.
The isolated reassortant strain of the virus turned out to be stable and very contagious. The authors believe that this new virus is most likely circulating in the population. Reassortant viruses have previously been isolated, but only in those recently vaccinated with RotaTeq: , , .
Cases of detecting new virus strains from reassortment of wild virus with Rotarix vaccine strain are reported here.
It is reported here, that 17% of children secreted the virus after vaccination, and 37% of them secreted a double reassortant virus. Some children secreted the virus for a long time after the vaccination, form 9 to 84 weeks after the last dose.
The authors analyzed the rotavirus genome of the vaccinated children suffering from gastroenteritis in Nicaragua, and found new strains of the virus, which formed due to reassortment between the wild strain and the RotaTeq vaccine strains.Identification of strains of RotaTeq rotavirus vaccine in infants with gastroenteritis following routine vaccination. 2012, Donato, J Infect Dis
Among children who had diarrhea within two weeks of vaccination, 21% had been infected with the vaccine strain. 37% of the isolated vaccine strains were reassortant from two RotaTeq strains.Rapid pneumococcal evolution in response to clinical interventions. 2011, Croucher, Science
In response to antibiotics and for vaccination, pneumococcus quickly mutates.Pneumococcus bacteria can change their serotype.Emergence of Multidrug-Resistant Pneumococcal Serotype 35B among Children in the United States. 2017, Olarte, J Clin Microbiol
After the vaccination began, a new serotype 35B appeared, which was rarely seen before, but now year after year is responsible for an increasing number of pneumococcal infections, this serotype is 5 times more deadly than other serotypes, and often insensitive to antibiotics.
The incidence of pneumococcus decreased 2-fold within 2 years after the start of vaccination, and remained approximately at the same level. More: .
After the start of vaccination, the incidence of pneumococcal infection in Barcelona increased by 58%, and among children by 135%.
The incidence of vaccine serotypes decreased by 40%, and the non-vaccine serotypes increased by 531%.
Incidence of pneumonia and empyema among children under 5 years old rose by 320%.
After vaccination began, between 1997 and 2003, the number of cases of pneumococcal infection in Salt Lake City (Utah) decreased by 27%. The incidence of vaccine serotypes decreased from 73% to 50%. The number of cases of non-vaccine serotypes increased The number of cases with complicated pleural empyema increased from 16% to 30%, and the proportion of severe cases increased from 57% to 71%. More: .Invasive pneumococcal disease caused by nonvaccine serotypes among Alaska native children with high levels of 7-valent pneumococcal conjugate vaccine coverage. 2007, Singleton, JAMA
Aboriginal children in Alaska are infected with invasive pneumococcal infection 3 times more often than Americans on average. For the first 3 years after the start of vaccination (2001-2003), the incidence of pneumococcal infection among indigenous children under 2 years of age in Alaska decreased by 67%, but then in 2004-2006, the incidence increased by 82%.
The incidence of vaccine serotypes decreased by 96%, and the non-vaccine serotypes increased by 140%.
The share of cases complicated by pleural empyema increased from 2% to 13%.The share of cases with pneumonia and bacteremia increased from 40% to 57%.
41% of the population were carriers of pneumococcus in 2004. The share of seven vaccine serotypes decreased from 41% to 5%, and of non-vaccine serotypes increased from 47% to 88%.
The incidence of invasive pneumococcal infection among children under 5 years decreased by 78% between 2002 and 2010, but it increased among children older than 5 years, adults and the elderly. Vaccine strains were replaced by non-vaccine strains. In 2006-2007, a pneumococcal outbreak was registered among beggars and drug addicts (British Columbia, Canada)The changing role of exposure to children as a risk factor for bacterial pneumococcal disease in the post conjugate vaccine era. 2010, Metlay, Arch Intern Med
In Philadelphia, the incidence of vaccine serotypes among adults decreased by 29% per year in 2002-2008, and by non-vaccine serotypes increased by 13% per year. In general, the incidence of pneumococcal infection increased by 7% per year.
Blacks were twice as likely to be white, the more children in the home, the lower the risk of the disease Diabetes increases the risk of the disease 2.5 times, smoking 2.2 times.
Several more articles on the replacement of pneumococcal strains from vaccine to vaccine to non-vaccine: , , , , , , , , , , , , , , , , 
....and about the replacement of pneumococcus with hemophilic and other bacteria: , , , , , , .
Because the invasion requires bacterial colonization in the nasopharynx to begin with, the goal of vaccination is also to reduce the colonization of pneumococcus. For the first time, conjugated pneumococcal vaccine was tested in infants in the Gambia in 1993, where it was found that while colonization with vaccine serotypes decreased by 78% -89%, colonization by non-vaccine serotypes increased 4.5-fold.Carriage of Haemophilus influenzae is associated with pneumococcal vaccination in Italian children. 2015, Camilli, Vaccine
Colonization with pneumococcus among vaccinated and unvaccinated in Italy did not differ: the haemophilus influenza was much more common among the vaccinated.Effect of 10-valent pneumococcal conjugate vaccine on nasopharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae among children in São Paulo, Brazil. 2016, Brandileone, Vaccine
After vaccination began, colonization with vaccine serotypes was significantly reduced and increased by a non-vaccine one.2-5 times more often than in unvaccinated people (Sao Paulo, Brazil)Post-PCV7 changes in the colonization of pneumococcal serotypes in 16 Massachusetts communities, 2001 and 2004. 2005, Huang, Pediatrics
Between 2001 and 2004, in children under 7 years old in Massachusetts, the colonization of seven vaccine serotypes of pneumococcus in the nasopharynx decreased, and colonization by other serotypes increased. In general, colonization with pneumococcus did not change much, the immunity to penicillin increased from 8 % to 25% among non-vaccine serotypes, and from 45% to 56% among vaccine serotypes.Continued impact of pneumococcal conjugate vaccine on carriage in young children. 2009, Huang, Pediatrics
Continuation of the previous study. By 2007, vaccine serotypes had practically disappeared, and were replaced by non-vaccine and penicillin-insensitive serotypes.In general, the level of colonization by pneumococcus was 30% as before, but among children under 6 months of age has grown significantly.Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts. 2014, Lee, J Pediatric Infect Dis Soc
13-valent vaccine (PCV13) also did not change colonization with pneumococcus. Colonization with vaccine serotypes decreased, and non-vaccine serotypes increased by 12% per year.
Colonization level among vaccinated PCV13 children and unvaccinated did not differ. Colonization with PCV13 strains was 70% lower among healthy vaccinated children, but not among children with ARVI.
In Japan, after the start of vaccination against Hib and pneumococcus, colonization with pneumococcal vaccine serotypes decreased, and non-vaccine serotypes increased. In general, colonization with pneumococcus did not change, colonization with the haemophilic rod increased.Effect of Pneumococcal Conjugate Vaccination on Serotype-Specific Carriage and Invasive Disease in England: A Cross-Sectional Study. 2011, Flasche, PLoS Med
In England colonization with vaccine serotypes has decreased, and non-vaccine serotypes has increased.In general, colonization increased by 6% (no statistical significance).Changing epidemiology of invasive Haemophilus influenzae in Ontario, Canada: evidence for herd effects and strain replacement due to Hib vaccination. 2010, Adam, Vaccine
Vaccination reduced the incidence of Hib in Ontario (Canada) by 57%, but the incidence of serotype f increased 2.4-fold and the incidence of noncapsular strains tripled. Hib incidence declined by 7% per year among children under 5 years of age, and the incidence of noncapsular strains increased among children aged 5-19 years by 7% per year.In general, the incidence of hemophilic infection was almost unchanged, the incidence of meningitis decreased, and the incidence of sepsis increased.
Capsule-free strains colonize upper respiration in 65% of children.
A year after the start of vaccination in Brazil, the number of cases of meningitis from Hib decreased by 69% (from 2.62 to 0.81 per 100,000).The number of cases of meningitis from Hia (hemophilic rod of serotype A) increased 8-fold (from 0.02 to 0.16 per 100,000.) Clinically, the virulence of Hib and Hia does not differ, the mortality from Hia was 23%.Haemophilus influenzae Serotype a Invasive Disease, Alaska, USA, 1983-2011. 2013, Bruce, Emerg Infect Dis
Before the vaccination, the incidence of Hib in Alaska was the highest in the world. Thanks to the vaccine, the number of Hib cases dropped sharply, but cases from other serotypes, mostly serotype A and noncapsular strainsInvasive Haemophilus influenzae disease in adults. 2000, Sarangi, Epidemiol Infect
After the start of the vaccination, the number of Hib cases among adults in England (15 and older) decreased, but the total number of cases of hemophilic infection increased due to a sharp increase in infections with non-capsular strains, especially among the elderly, with a mortality rate of 59%.Trends in Haemophilus influenzae type of infection in England and Wales: surveillance study. 2004, McVernon, BMJ
The incidence of Hib among adults in England has declined after the introduction of vaccination (due probably to collective immunity), reached a minimum in 1998, and in 2003 already returned to the pre-vaccination level.
The number of antibodies to Hib in adults decreased after the start of vaccination.
Among children, the same thing happened: first, the incidence of Hib declined sharply, and then, despite the high vaccination coverage, began to increase dramatically.
Since 1998, the number of cases among children has doubled every year, and most of the patients were sex awn vaccinated.
Vaccination reduced the number of Hib cases among children by 99%, but the incidence of hemophilic infection among adults increased 11.5-fold between 1998 and 2008. Most of the cases were in the serotype F and in the capsule-free strains.The mortality was 22%.Invasive Haemophilus influenzae in British Columbia: non-Hib and non-typeable strains causing disease in children and adults. 2011, Shuel, Int J Infect Dis
In 1989, 24 cases of Hib were reported in British Columbia before vaccination in Canada, 45-53 cases per year were recorded in 2008-2009, the incidence of serotype B decreased, and the incidence of serotype A.If children used to be ill earlier, now adults are sick too.The changing epidemiology of invasive Haemophilus influenzae disease, especially in persons> or = 65 years old. 2007, Dworkin, Clin Infect Dis
Between 1996 and 2004, the number of Hib cases in Illinois increased by 2.5 times, and among the elderly by 3.5 times.
The number of cases of infection with HQ-free increased by 657%.If in 1996, Hib's bespaksulnaya was responsible for 17.5% of the cases, in 2004 it was responsible already in 70.7% of cases, the lethality was 12.7%, and among the elderly - 20.6%. The mortality of serotype F among the elderly was 11.1%, and the serotype E - 38.5%.
The incidence of serotype F increased 3.8-fold between 1989 and 1994, and constitutes 17% of all cases of hemophilia, and the mortality of this serotype is 30% among adults and 21% among children.Increase in the number of invasive Haemophilus influenzae type b infections. 2005, Spanjaard, Ned Tijdschr Geneeskd
The Netherlands, the incidence of Hib declined after vaccination began, reached a minimum in 1993, and then began to grow again, probably because the bacteria "natural booster" are much less likely to disappear, which leads to a weakening of immunity, and to increased susceptibility to infection. And maybe because that vaccination has destroyed strains with a thin capsule, and left strains with more thick capsule. More: , , .Epidemiology of invasive pneumococcal and Haemophilus influenzae diseases in Northwestern Ontario, Canada, 2010-2015. 2017, Eton, Int J Infect Dis
The incidence of serotype A (Hia) in Ontario is 76% higher than the incidence of Hib in the pre-vaccination era.Prevalence of HPV After the Introduction of the Vaccination Program in the United States. 2016, Markowitz, Pediatrics
Nature abhors a vacuum. By preventing girls from getting the infection from two or four strains of HPV, the vaccine only causes them to be replaced with other strains.
There is a decrease in prevalence of the four strains of HPV in young girls, but there is no change in the prevalence of HPV, taking into account all strains of the virus.
Oncogenic strains of HPV, 16 and 18, have been replaced with other oncogenic strains: 31, 51, 53, 56 and 66.
Three more studies with the same conclusions in Italy, Netherlands and the USA.