Zhongya Li

Group A Streptococcal Pharyngitis Serotype Surveillance in North America, 2000–2002

Geographic and interseasonal heterogeneity of pharyngeal group A streptococcal (GAS) genotypes (emm types) is poorly characterized. We evaluated emm type and subtype distribution among pediatric pharyngitis isolates obtained from 9 sites in the United States during 2000-2001 (year 1) and from 10 sites in the United States and 1 site in Canada during 2001-2002 (year 2). The 7 predominant types were the same in both years, although their order changed. emm 12, 1, and 28 accounted for 49.2% of year 1 isolates, and emm 1, 12, and 4 accounted for 47.1% of year 2 isolates; 6 types accounted for 72.1% in year 1 and 69.4% in year 2. From year 1 to year 2, the proportions of emm 12 and 28 decreased and emm 1 and 6 increased. Striking intersite and interseasonal variations in the distribution of predominant emm types were observed. We conclude that the most-predominant GAS genotypes were similar for each year despite fluctuations, that intersite and intrasite variations in the distribution of emm types were apparent, and that emm type surveillance is needed as M protein vaccine development proceeds.

Increased Penicillin Nonsusceptibility of Nonvaccine-Serotype Invasive Pneumococci Other than Serotypes 19A and 6A in Post-7-Valent Conjugate Vaccine Era

According to population-based invasive pneumococcal surveillance in the United States during 2007, 898 (26%) of 3,511 isolates were penicillin nonsusceptible. Non-7-valent pneumococcal conjugate vaccine (PCV7) serotypes other than 19A accounted for 40% of these penicillin-nonsusceptible isolates; of these, serotypes 15A (11%), 23A (8%), 35B (8%), and 6C (5%) were most common (cumulatively 32% of penicillin-nonsusceptible isolates). Each except 6C represented a single serotype and clonal complex combination that predated the introduction of PCV7. We evaluated the genetic characteristics and nonsusceptibility to penicillin of non- PCV7 serotypes, and we found increased proportions of specific penicillin-nonsusceptible clones in serotypes 15A, 23A, 35B, and 6C, which potentially indicates a basic change of population structure within these individual serotypes.

Array of M Protein Gene Subtypes in 1064 Recent Invasive Group A Streptococcus Isolates Recovered from the Active Bacterial Core Surveillance

Using sequence analysis to detect variation within the hypervariable M protein N terminus, we found 41 emm types encompassing 81 subtypes, among 1064 consecutive invasive group A streptococcus isolates from a recent multistate, population-based surveillance. Seventeen of the 30 emm types represented by multiple isolates displayed multiple subtypes. Most subtypes differed from reference strain emm sequences as a result of single base substitutions or other alterations likely to be stably inherited. The Centers for Disease Control and Prevention database (available at: http://www.cdc.gov/ncidod/biotech/strep/strepblast.htm) currently contains 225 distinct emm types encompassing 450 subtypes. Although this subtyping scheme increases specificity, limited variation within individual types favors introduction of M protein type-specific vaccines.

Seven-Year Surveillance of North American Pediatric Group A Streptococcal Pharyngitis Isolates

BACKGROUND Pharyngeal group A streptococcal (GAS) emm type surveillance enhances understanding of the epidemiology of pharyngitis and invasive GAS disease and formulation of multivalent type-specific vaccines. In addition, such surveillance provides pre-GAS vaccine baseline data. We assessed geographic and temporal trends in GAS emm-type distribution among pediatric pharyngeal isolates collected systematically in the United States and Canada from 2000 to 2007. METHODS We collected approximately 100 acute GAS pharyngitis isolates from each of 13 widely scattered sites (10 in the United States and 3 in Canada) annually for 7 seasons (2000-2007) from 3- to 18-year-old children. We assessed emm type and subtype by DNA sequencing and analyzed temporal and geographic trends. RESULTS A total of 7040 US and 1434 Canadian GAS isolates were studied. The 6 most prevalent emm types (in descending order) were 1, 12, 28, 4, 3, and 2 in the United States and 12, 1, 28, 4, 3, 2, and 77 in Canada, constituting 70%-71% of isolates in each country; 10 emm types constituted 87%-89% total. Fifty-six emm types were identified in the United States, including 8 new types, and 33 types in Canada. Although a few types predominated nationally, marked variability among individual sites and at individual sites from year to year was observed. US-Canadian differences in type distribution were apparent. Twenty percent of isolates represented emm subtypes that differed slightly from reference types; 110 new subtypes were identified. An experimental 26-valent M protein vaccine covers 85% of pharyngitis isolates. CONCLUSIONS Although overall US and Canadian emm type distribution was consistent and relatively few types dominated nationally, striking intersite and temporal variations within individual sites in prevalent emm types of GAS occurred. These results have important implications for the development and formulation of type-specific GAS vaccines.

Genetic Relationships Deduced from emm and Multilocus Sequence Typing of Invasive Streptococcus dysgalactiae subsp. equisimilis and S. canis Recovered from Isolates Collected in the United States

ABSTRACT Beta-hemolytic group C and G streptococci cause a considerable invasive disease burden and sometimes cause disease outbreaks. Little is known about the critical epidemiologic parameter of genetic relatedness between isolates. We determined the emm types of 334 Streptococcus dysgalactiae subsp. equisimilis isolates, and attempted emm typing of 5 Streptococcus canis isolates from a recent population-based surveillance for invasive isolates. Thirty-four emm types were observed, including one from S. canis. We formulated multilocus sequence typing (MLST) primers with six of the seven loci corresponding to the Streptococcus pyogenes MLST scheme. We performed MLST with 65 of the 334 surveillance isolates (61 S. dysgalactiae subsp. equisimilis isolates, 4 S. canis isolates) to represent each emm type identified, including 2 to 3 isolates for each of the 25 redundantly represented emm types. Forty-one MLST sequence types (STs) were observed. Isolates within 16 redundantly represented S. dysgalactiae subsp. equisimilis emm types shared identical or nearly identical STs, demonstrating concordance between the emm type and genetic relatedness. However, seven STs were each represented by two to four different emm types, and 7 of the 10 S. dysgalactiae subsp. equisimilis eBURST groups represented up to six different emm types. Thus, S. dysgalactiae subsp. equisimilis isolates were similar to S. pyogenes isolates, in that strains of the same emm type were often highly related, but they differed from S. pyogenes, in that S. dysgalactiae subsp. equisimilis strains with identical or closely similar STs often exhibited multiple unrelated emm types. The phylogenetic relationships between S. dysgalactiae subsp. equisimilis and S. pyogenes alleles revealed a history of interspecies recombination, with either species often serving as genetic donors. The four S. canis isolates shared highly homologous alleles but were unrelated clones without evidence of past recombination with S. dysgalactiae subsp. equisimilis or S. pyogenes.

M Protein Gene Type Distribution among Group A Streptococcal Clinical Isolates Recovered in Mexico City, Mexico, from 1991 to 2000, and Durango, Mexico, from 1998 to 1999: Overlap with Type Distribution within the United States

ABSTRACT To examine the type distribution of pathogenic group A streptococcal (GAS) strains in Mexico, we determined the emm types of 423 GAS isolates collected from ill patients residing in Mexico (Durango or Mexico City). These included 282 throat isolates and 107 isolates from normally sterile sites. Of the other isolates, 38 were recovered from other miscellaneous infections. A total of 31 different emm types were found, revealing a broad overlap between commonly occurring emm types in Mexico and the United States. The information obtained in this study is consistent with the possibility that multivalent, M type-specific vaccines prepared for GAS strain distribution within the United States could theoretically protect against the majority of GAS strains causing disease in the two cities surveyed in Mexico.

Genetically Diverse Group A Streptococci from Children in Far-Western Nepal Share High Genetic Relatedness with Isolates from Other Countries

ABSTRACT The genetic diversity of group A streptococci (GAS) throughout much of the world has not been adequately explored. To assess genetic variation among GAS in western Nepal, 120 noninvasive GAS, collected from eight different villages, were genetically characterized using emm typing, sof sequencing, and multilocus sequence typing (MLST). A high level of genetic diversity was observed among these isolates, with 51 genotypes based upon 51 multilocus sequence types (STs), 45 emm sequence types, and 28 sof sequence types. On the basis of shared ST-emm and sof-emm associations, 40 of the 51 genotypes were identical or highly related to genotypes characterized from locations outside of Nepal, even though most of the emm sequence and clonal types are rare among GAS within the United States. When analyzing all known STs highly related to Nepal STs, only one example of similar STs shared between a sof PCR-positive strain and a sof PCR-negative strain was observed. Since previous data indicate free exchange of MLST loci between sof-positive and sof-negative strains, there is possibly selection against the expansion of subclones resulting from horizontal transfers of sof or emm genes between sof-positive and sof-negative strains. All 45 emm types encountered in Nepal have also been documented from other countries. These data, together with data encompassing the past decade of emm type surveillance, support the possibility that most existing GAS emm types have been discovered. Similarly, since most (40/51) strain types were highly related to strains found elsewhere, it is likely that a major fraction of the existing GAS clonal complexes have been discovered.

Potential nonpneumococcal confounding of PCR-based determination of serotype in carriage.

Monitoring pneumococcal carriage serotype distributions is increasingly used to study pneumococcal biology, disease epidemiology, and vaccine impact. Potentially complicating DNA-based carriage assessment is the well-documented history of genetic recombination between pneumococci and related species

Characterization of highly antimicrobial-resistant clinical pneumococcal isolates recovered in a Chinese hospital during 2009-2010.

Ninety-one consecutive pneumococcal isolates (primarily from sputum), recovered in Chongqing Southwest Hospital during a 12 month period in 2009-2010 from individuals of all ages with suspected cases of pneumococcal disease, were subjected to PCR-serotyping, Quellung reaction serotyping, antimicrobial-susceptibility testing and multilocus sequence typing (MLST). Although 20 different serotypes were observed, most isolates (69, 75.8 %) were of serotypes included in the pneumococcal 13-valent conjugate vaccine (PCV13), including 33 of the 46 (71.7 %) isolates recovered from individuals less than 5 years of age. The prevalent serotypes were 19F (34 %), 19A (9.9 %), 6B (9.9 %), 23F (7.7 %), 14 (6.6 %) and 6A (4.4 %). PCR-determined serotypes were in agreement with Quellung testing, with the exception of two serotype 33C isolates. Most or all isolates within each PCV13 serotype were represented by one genotype, with the globally disseminated MLST sequence types (STs) ST271, ST320, ST90 and ST81 each accounting for the highly resistant isolates within serotypes 19F, 19A, 6B and 23F, respectively. Sixty-six (72.5 %) isolates were resistant to combinations of β-lactam antibiotics (BLAs). A total of 63 of these 66 (95.5 %) BLA-resistant isolates were of serotypes included in PCV13; however, 3 serogroup 15 isolates were also BLA-resistant. Most isolates (88/91 = 96.7 %) were resistant to erythromycin and clindamycin. The majority of isolates were also resistant to tetracycline (76, 84 %) and to cotrimoxazole (67, 74 %). This work revealed that the majority of antimicrobial-resistant isolates (50/91 = 54.9 %) recovered in this Chinese hospital were represented by four global clones. Serotypes for these as well as more obscure strains were readily determined by using PCR.

Invasive Serotype 35B Pneumococci Including an Expanding Serotype Switch Lineage, United States, 2015–2016

We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015–2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post–pneumococcal 7-valent conjugate vaccine years (2001–2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage. 35B/ST558 and vaccine serotype 9V/ST156 lineages were implicated as cps35B donor and recipient, respectively, for a single capsular switch event that generated emergent 35B/ST156 progeny in 6 states during 2015–2016. Three additional capsular switch 35B variants were identified, 2 of which also involved 35B/ST558 as cps35B donor. Spread of 35B/ST156 is of concern in view of past global predominance of pathogenic ST156 vaccine serotype strains. Protection against serotype 35B should be considered in next-generation pneumococcal vaccines.