Serotype and Genotype Distribution among Invasive Streptococcus pneumoniae Isolates in Colombia, 2005–2010

In Colombia, a laboratory-based surveillance of invasive Streptococcus pneumoniae isolates as part of SIREVA II PAHO has been conducted since 1994. This study describes the serotype distribution, antimicrobial resistance, and genetic relationships of pneumococcal isolates recovered in Colombia from 2005 to 2010. In this study, demographic data of invasive S. pneumoniae isolates were analyzed, and antimicrobial susceptibility patterns were determined. Pulse field gel electrophoresis (n = 629) and multilocus sequence typing (n = 10) were used to determine genetic relationship of isolates with minimal inhibitory concentration to penicillin ≥0.125 µg/mL. A total of 1775 isolates of S. pneumoniae were obtained. Fifteen serotypes accounted for 80.7% of isolates. Serotype 14 (23.1%) was the most frequent in the general population. Penicillin resistance was 30.7% in meningitis and 9.0% in non-meningitis. Clones Spain^6BST90, Spain^9VST156, Spain^23FST81, and Colombia^23FST338 were associated to isolates. Additionally, serotype 6A isolates were associated with ST460 and ST473, and 19A isolates with ST276, ST320, and ST1118. In conclusion, the surveillance program provided updated information of trends in serotype distribution, antimicrobial resistance and the circulation of clones in invasive pneumococcal diseases. These results could be helpful to understand the epidemiology of S. pneumoniae in Colombia, and provide a baseline to measure the impact of vaccine introduction.     

Serotypes and Genotypes of Invasive Streptococcus pneumoniae Before and After PCV10 Implementation in Southern Brazil

To reduce the burden of pneumococcal diseases, different formulations of pneumococcal conjugate vaccines (PCV) have been introduced in many countries. In Brazil, PCV10 has been available since 2010. We aimed to analyze the serotype and genetic composition of invasive pneumococci from Brazil in pre- and post- vaccination periods (2007–2012). Antibiotic susceptibility was determined and genotypes of macrolide and fluoroquinolone resistance were characterized. The genotypes of isolates of the most frequent serotypes were determined by multilocus sequence typing. The study included 325 isolates, which were primarily recovered from blood. The most common serotypes recovered were 14, 3, 4, 23F, 7F, 9V, 12F, 20, 19F, 8, 19A, and 5. Thirty-eight pneumococci (11.7%) were from children ≤5 years old. Considering the overall population, PCV10 and PCV13 serotype coverage was 50.1% and 64.9%, respectively. During the pre-vaccine period, isolates with serotypes belonging to the PVC10 represented 51.5% (100/194), whereas in the post vaccine they represented 48.0% (63/131). PCV13 serotypes represented 67.5% (131/194) and 59.2% (77/131) of total for pre- and post-vaccination periods, respectively. Seventy different sequence types [STs] were found, accounting for 9 clonal complexes [CCs] and 45 singletons. Eight STs (156, 180, 218, 8889, 53, 191, 770, and 4967) represented the majority (51.5%) of isolates. Fifty STs were associated with the pre-vaccination period (27 exclusive) and 43 (20 exclusive) with the post-vaccination period; 23 STs were identified in both periods. Some serotypes were particularly clonal (7F, 8, 12F, 20). Non-susceptibility to penicillin was associated with serotype 19A, CC320. Erythromycin resistance was heterogeneous when considering serotype and ST. A single serotype 23F (ST4967) isolate was resistant to levofloxacin. Continued surveillance is required to determine vaccine impact and to monitor changes in pneumococcal population biology post-PCV10 introduction in Brazil.     

Molecular Characterization and Antimicrobial Susceptibility of Streptococcus pneumoniae Isolated from Children Hospitalized with Respiratory Infections in Suzhou,China

Background

Dissemination of antibiotic resistant clones is recognized as an important factor in the emergence and prevalence of resistance in pneumococcus. This study was undertaken to survey the antimicrobial susceptibility and serotypes distribution of pneumococci and to explore the circulating clones in hospitalized children in Suzhou, China.

Methods

The pneumococci were isolated from the nasopharyngeal aspirates of children less than 5 years of age admitted to Soochow-University-Affiliated-Children''s-Hospital with respiratory infections. The capsular serotypes were identified by multiplex polymerase chain reaction (PCR). Antimicrobial susceptibility was tested by E-test. The presence of ermB, mefA/E genes were detected by PCR and the genotypes were explored by Multilocus sequence typing (MLST).

Results

From July 2012 to July 2013, a total of 175 pneumococcal isolates were collected and all strains were resistant to erythromycin and clindamycin, about 39.4% strains were non-susceptible to penicillin G. Overall, 174 (99.4%) isolates were resistant to ≥3 types of antibiotics. Serotypes 19F (28.1%), 6B (19.7%), 19A (18.0%), and 23F (17.4%) were the most common serotypes in all identified strains. The serotypes coverage of PCV7 and PCV13 were 71.9% and 89.9%, respectively. Four international antibiotic-resistant clones, including Taiwan^19F-14 (n = 79), Spain^23F-1(n = 25), Taiwan^23F-15(n = 7) and Spain^6B-2(n = 7), were identified. The Taiwan^19F-14 clones have a higher non-susceptibility rate in β-lactams than other clones and non-clone isolates (p<0.001). In addition, 98.7% Taiwan^19F-14 clones were positive of both ermB and mefA/E genes, compare to 33.3% in other clones and non-clone strains.

Conclusions

The spread of international antibiotic-resistant clones, especially Taiwan^19F-14 clones, played a predominant role in the dissemination of antimicrobial resistant isolates in Suzhou, China. Considering the high prevalence of PCV7 serotypes and serotype 19A, the introduction of PCV13 may be a promising preventive strategy to control the increasing trend of clonal spread in China.     

Human-associated fluoroquinolone-resistant Escherichia coli clonal lineages,including ST354, isolated from canine feces and extraintestinal infections in Australia

Phylogenetic group D extraintestinal pathogenic Escherichia coli (ExPEC), including O15:K52:H1 and clonal group A, have spread globally and become fluoroquinolone-resistant. Here we investigated the role of canine feces as a reservoir of these (and other) human-associated ExPEC and their potential as canine pathogens. We characterized and compared fluoroquinolone-resistant E. coli isolates originally identified as phylogenetic group D from either the feces of hospitalized dogs (n = 67; 14 dogs) or extraintestinal infections (n = 53; 33 dogs). Isolates underwent phylogenetic grouping, random amplified polymorphic DNA (RAPD) analysis, virulence genotyping, resistance genotyping, human-associated ExPEC O-typing, and multi-locus sequence typing. Five of seven human-associated sequence types (STs) exhibited ExPEC-associated O-types, and appeared in separate RAPD clusters. The largest subgroup (16 fecal, 26 clinical isolates) were ST354 (phylogroup F) isolates. ST420 (phylogroup B2); O1-ST38, O15:K52:H1-ST393, and O15:K1-ST130 (phylogroup D); and O7-ST457, and O1-ST648 (phylogroup F) were also identified. Three ST-specific RAPD sub-clusters (ST354, ST393, and ST457) contained closely related isolates from both fecal or clinical sources. Genes encoding CTX-M and AmpC β-lactamases were identified in isolates from five STs. Major human-associated fluoroquinolone-resistant ± extended-spectrum cephalosporin-resistant ExPEC of public health importance may be carried in dog feces and cause extraintestinal infections in some dogs.     

Serotypes and Clonal Diversity of Streptococcus pneumoniae Causing Invasive Disease in the Era of PCV13 in Catalonia,Spain

The aim of this study was to study the serotypes and clonal diversity of pneumococci causing invasive pneumococcal disease in Catalonia, Spain, in the era of 13-valent pneumococcal conjugate vaccine (PCV13). In our region, this vaccine is only available in the private market and it is estimated a PCV13 vaccine coverage around 55% in children. A total of 1551 pneumococcal invasive isolates received between 2010 and 2013 in the Molecular Microbiology Department at Hospital Sant Joan de Déu, Barcelona, were included. Fifty-two serotypes and 249 clonal types—defined by MLST—were identified. The most common serotypes were serotype 1 (n = 182; 11.7%), 3 (n = 145; 9.3%), 19A (n = 137; 8.8%) and 7F (n = 122; 7.9%). Serotype 14 was the third most frequent serotype in children < 2 years (15 of 159 isolates). PCV7 serotypes maintained their proportion along the period of study, 16.6% in 2010 to 13.4% in 2013, whereas there was a significant proportional decrease in PCV13 serotypes, 65.3% in 2010 to 48.9% in 2013 (p<0.01). This decrease was mainly attributable to serotypes 19A and 7F. Serotype 12F achieved the third position in 2013 (n = 22, 6.4%). The most frequent clonal types found were ST306 (n = 154, 9.9%), ST191 (n = 111, 7.2%), ST989 (n = 85, 5.5%) and ST180 (n = 80, 5.2%). Despite their decrease, PCV13 serotypes continue to be a major cause of disease in Spain. These results emphasize the need for complete PCV13 vaccination.     

Characterization of uropathogenic E. coli O25b-B2-ST131, O15:K52:H1, and CGA: Neutrophils apoptosis,serum bactericidal assay,biofilm formation,and virulence typing

Pathogenic and drug-resistant strains of Escherichia coli (E. coli) O25b-B2-ST131, O15:H1-D-ST393, and CGA (clonal group A) clonal groups have spread worldwide. This study aimed at determining E. coli epidemic clonal groups, their virulence factors, biofilm formation, neutrophils apoptosis, and antimicrobial resistance pattern of uropathogenic E. coli. A total of 95 CTX-M-1-producing E. coli clinical isolates were enrolled. E. coli O25b-B2-ST131, CGA, and O15:K52:H1 were identified by serotyping and phylogrouping and allele-specific polymerase chain reaction-based assay. Antibiotic susceptibility, biofilm formation, hemolysis, and human serum bactericidal assay were performed. Neutrophil apoptosis was assayed by flow cytometry. Nine E. coli clonal groups including six O25b-B2-ST131 strains, two CGA, and one O15:K52:H1-D-ST393 strains were detected. One O25b-B2-ST131 isolate was a strong biofilm-producer. Three ST131 isolates had type I fimbriae. Furthermore, all the CGA and O15:K52:H1 and three of ST131 isolates harbored the P fimbriae. The virulence genes ompT, fimH, and traT were detected among all the clonal groups. The apoptosis was induced by O25b-B2-ST131, CGA, and O15:K52:H1 E. coli. There was no significant difference regarding apoptosis induction among clonal groups. Furthermore, the presence of the cdt, usp, and vat genes was significantly associated with the apoptosis of neutrophils by O25b-B2-ST131, CGA, and O15:K52:H1-D-ST393 clonal groups.     

Characterization of Methicillin-Resistant and -Susceptible Staphylococcal Isolates from Bovine Milk in Northwestern China

Emergence of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) in bovine milk is a major public health concern. The primary purpose of this research was to determine molecular genetic characteristics and antibiotic resistance of staphylococcal isolates recovered from milk of mastitic cows in the Shaanxi Province in Northwestern China. One hundred and thirteen methicillin-susceptible Staphylococcus aureus (MSSA), one mecA-positive and phenotype-positive MRSA, seven mecA- and mecC- negative but phenotype-positive MRSA and two MR-CoNS including one oxacillin-susceptible mecA-positive Staphylococcus haemolyticus (OS-MRSH) and one mecA-positive and methicillin-resistant Staphylococcus epidermidis (MRSE) isolates were recovered from 214 quarter milk samples on 4 dairy farms. All above 123 isolates were subjected to antibiotic resistance profiling. S. aureus isolates were also genotyped using the spa typing and the multilocus sequence typing (MLST). Eight MRSA and 2 MR-CoNS isolates were additionally tested for SCCmec types. Resistance was common among isolates against ampicillin or penicillin (80.5%), kanamycin (68.3%), gentamicin (67.5%), tetracycline (43.9%) and chloramphenicol (30.1%). However, no isolate was resistant to vancomycin or teicoplanin. Twenty, 29 and 58 isolates showed resistance to 1, 2 or more than 2 antibiotics, respectively. The predominant multidrug resistance profile was penicillin/ampicillin/kanamycin/gentamicin/tetracycline (46 isolates). Most S. aureus isolates belonged to spa types t524 (n = 63), t11772 (a new type, n = 31) and t4207 (n = 15). At the same time, MLST types ST71 (n = 67) and ST2738 (a new type, n = 45) were identified as dominant sequence types. The mecA-positive and phenotype-positive MRSA isolate had a composite genotype t524-ST71-SCCmecIVa, while 7 mecA-negative but phenotype-positive MRSA isolates were all t524-ST71. The OS-MRSH isolate contained a type V SCCmec cassette, while the MRSE isolate possessed a non-typeable SCCmec. The spa-MLST types t11772-ST2738 (n = 27), t11807-ST2683 (n = 4) and t11771-ST2738 (n = 3) were newly identified genotypes of S. aureus. These new genotypes and multidrug-resistant staphylococci could pose additional threat to animal and human health.     

Population pattern of pneumococci with lower susceptibility to penicillin and prospects of antipneumococcal vaccination to control antibiotic resistance distribution

Large-scale antipneumococcal vaccination is followed by changes in the serotype composition and level of antibiotic resistance in pneumococci. The aim of the study was to evaluate the serotype composition and population pattern of pneumococci with lower susceptibility to penicillin before large-scale antipneumococcal vaccination. Among 260 Streptococcus pneumoniae strains isolated in the Russian Federation within 2003-2007, serotypes 23F (37.2%) and 19F (13.9%) were the most frequent ones. 19.3% of the isolates belonged to serogroup 6, 3.6% of the isolates each belonged to serotype 3 and serogroup 18, 4.9% of the isolates belonged to serotype 14 and 2.2% of the isolates belonged to serotype 19A. 66.8% of the isolates belonged to serotypes of the 7-valent conjugated pneumococcal vaccine, 67.3 and 82.1% of the isolates belonged to the 10- and 13-valent conjugated pneumococcal vaccines respectively. The isolates with lower susceptibility to penicillin were characterized by significant clonality and 56.9% of them belonged to 4 global clonal complexes (CC81, CC156, CC320 and CC315). Inclusion of the conjugated antipneumococcal vaccine to the National Vaccination Time-Table of the Russian Federation could promote lower levels of antibiotic resistance in pneumococci.     

Identification of Two Multidrug-Resistant <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> Clonal Lineages with a Countrywide Distribution in Hungary

The aim of this study was to identify class 1 integrons from extended-spectrum and metallo-β-lactamase-negative, multidrug-resistant Pseudomonas aeruginosa clinical isolates from Hungary and to characterize the isolates by phenotypic and molecular methods. Fourteen selected P. aeruginosa isolates resistant to ceftazidime, gentamicin, and ciprofloxacin were subjected to serotyping, random amplification of polymorphic DNA (RAPD), integron content analysis, and a phenotypic test to detect high-level production of AmpC. Four representative isolates were further analyzed by multilocus sequence typing. Two P. aeruginosa multidrug-resistant clonal lineages were identified with a countrywide distribution. The first lineage is characterized by serotype O4, RAPD genotype A, sequence type ST175, and the presence of a class 1 integron harbouring aadB and aadA13 gene cassettes in its variable region. The second lineage is characterized by serotype O6, RAPD genotype B, sequence type ST395, and a class 1 integron carrying a single aadB cassette. The corresponding isolates were recovered from altogether 11 towns in Hungary. ST175 and ST395 are the presently calculated founders of two distinct P. aeruginosa clonal complexes that appear to have a wide geographical distribution also outside Hungary. The multidrug-resistant phenotype associated with these two clonal lineages might have contributed to an increase in their frequency and to their subsequent diversification. Both P. aeruginosa lineages displayed ≥8-fold synergy with boronic acid/ceftazidime combinations, suggesting an AmpC-mediated resistance to ceftazidime. Our observations underscore the role of class 1 integrons in the spread of aminoglycoside resistance by clonal dissemination among P. aeruginosa clinical isolates in Hungary.     

Molecular Characterization of Streptococcus agalactiae Isolated from Bovine Mastitis in Eastern China

One hundred and two Streptococcus agalactiae (group B streptococcus [GBS]) isolates were collected from dairy cattle with subclinical mastitis in Eastern China during 2011. Clonal groups were established by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE), respectively. Capsular polysaccharides (CPS), pilus and alpha-like-protein (Alp) family genes were also characterized by molecular techniques. MLST analysis revealed that these isolates were limited to three clonal groups and were clustered in six different lineages, i.e. ST (sequence type) 103, ST568, ST67, ST301, ST313 and ST570, of which ST568 and ST570 were new genotypes. PFGE analysis revealed this isolates were clustered in 27 PFGE types, of which, types 7, 8, 14, 15, 16, 18, 23 and 25 were the eight major types, comprising close to 70% (71/102) of all the isolates. The most prevalent sequence types were ST103 (58% isolates) and ST568 (31% isolates), comprising capsular genotype Ia isolates without any of the detected Alp genes, suggesting the appearance of novel genomic backgrounds of prevalent strains of bovine S. agalactiae. All the strains possessed the pilus island 2b (PI-2b) gene and the prevalent capsular genotypes were types Ia (89% isolates) and II (11% isolates), the conserved pilus type providing suitable data for the development of vaccines against mastitis caused by S. agalactiae.     

199株猪链球菌临床分离株血清型、毒力基因及多位点序列分型分析

【背景】猪链球菌（Streptococcus suis,SS）血清型、基因型众多,毒力因子复杂。【目的】了解SS临床分离株血清型、毒力基因分布、分子分型特征及其之间的相关性。【方法】针对199株SS临床分离株,应用PCR技术进行血清分型和毒力基因检测,采用多位点序列分型方法（multilocus sequence typing,MLST）进行基因分型,并分析SS血清型、毒力基因型和序列型（sequence type,ST型）的流行特点及其关联性。【结果】199株SS临床分离株分属于16种血清型（1、2、3、4、6、7、8、9、10、12、15、16、21、24、29和30型）,主要以2、4、3型为主,分别占26.13%（52/199）、14.57%（29/199）和12.06%（24/199）,未定型（NT）菌株占21.61%（43/199）。共鉴定出72种ST型,其中ST1、ST94、ST117、ST7、ST28和ST87为主要ST型,分别占12.56%（25/199）、11.56%（23/199）、9.56%（19/199）、9.04%（18/199）、6.03%（12/199）和3.01%（6/199）,另有24种新发现的ST型（ST1224—ST1227,ST1229—ST1235,ST1241—ST1242,ST1300—ST1310）;分为12个克隆群（cloning complexes,CC）和32个单个ST型。199株SS分离株中毒力基因fbps的检出率最高,为96.98%（193/199）;共有19种毒力基因型,其中66株（33.17%）epf-/mrp-/sly-/gapdh+/fbps+/orf2+型SS为优势毒力基因型。【结论】近年来SS的优势血清型为2、4和3型;ST型具有明显的遗传异质性,种内分化程度较高且与ST型存在一定交叉性;毒力基因分布情况存在差异,毒力基因型呈现多样化。本研究对SS临床分离株的流行特征进行探究,为猪SS病诊断、治疗和制定防控措施提供科学依据。     

Population Genetic Structure of Streptococcus pneumoniae in Kilifi,Kenya, Prior to the Introduction of Pneumococcal Conjugate Vaccine

Background

The 10-valent pneumococcal conjugate vaccine (PCV10) was introduced in Kenya in 2011. Introduction of any PCV will perturb the existing pneumococcal population structure, thus the aim was to genotype pneumococci collected in Kilifi before PCV10.

Methods and Findings

Using multilocus sequence typing (MLST), we genotyped >1100 invasive and carriage pneumococci from children, the largest collection genotyped from a single resource-poor country and reported to date. Serotype 1 was the most common serotype causing invasive disease and was rarely detected in carriage; all serotype 1 isolates were members of clonal complex (CC) 217. There were temporal fluctuations in the major circulating sequence types (STs); and although 1-3 major serotype 1, 14 or 23F STs co-circulated annually, the two major serotype 5 STs mainly circulated independently. Major STs/CCs also included isolates of serotypes 3, 12F, 18C and 19A and each shared ≤2 MLST alleles with STs that circulate widely elsewhere. Major CCs associated with non-PCV10 serotypes were predominantly represented by carriage isolates, although serotype 19A and 12F CCs were largely invasive and a serotype 10A CC was equally represented by invasive and carriage isolates.

Conclusions

Understanding the pre-PCV10 population genetic structure in Kilifi will allow for the detection of changes in prevalence of the circulating genotypes and evidence for capsular switching post-vaccine implementation.     

Population structure of Pseudomonas aeruginosa from five Mediterranean countries: evidence for frequent recombination and epidemic occurrence of CC235

Several studies in recent years have provided evidence that Pseudomonas aeruginosa has a non-clonal population structure punctuated by highly successful epidemic clones or clonal complexes. The role of recombination in the diversification of P. aeruginosa clones has been suggested, but not yet demonstrated using multi-locus sequence typing (MLST). Isolates of P. aeruginosa from five Mediterranean countries (n = 141) were subjected to pulsed-field gel electrophoresis (PFGE), serotyping and PCR targeting the virulence genes exoS and exoU. The occurrence of multi-resistance (≥3 antipseudomonal drugs) was analyzed with disk diffusion according to EUCAST. MLST was performed on a subset of strains (n = 110) most of them had a distinct PFGE variant. MLST data were analyzed with Bionumerics 6.0, using minimal spanning tree (MST) as well as eBURST. Measurement of clonality was assessed by the standardized index of association (I_A ^S). Evidence of recombination was estimated by ClonalFrame as well as SplitsTree4.0. The MST analysis connected 70 sequence types, among which ST235 was by far the most common. ST235 was very frequently associated with the O11 serotype, and frequently displayed multi-resistance and the virulence genotype exoS ⁻/exoU ⁺. ClonalFrame linked several groups previously identified by eBURST and MST, and provided insight to the evolutionary events occurring in the population; the recombination/mutation ratio was found to be 8.4. A Neighbor-Net analysis based on the concatenated sequences revealed a complex network, providing evidence of frequent recombination. The index of association when all the strains were considered indicated a freely recombining population. P. aeruginosa isolates from the Mediterranean countries display an epidemic population structure, particularly dominated by ST235-O11, which has earlier also been coupled to the spread of ß-lactamases in many countries.     

Molecular Characterization of Pneumococcal Isolates from Pets and Laboratory Animals

Background

Between 1986 and 2008 Streptococcus pneumoniae was isolated from 41 pets/zoo animals (guinea pigs (n = 17), cats (n = 12), horses (n = 4), dogs (n = 3), dolphins (n = 2), rat (n = 2), gorilla (n = 1)) treated in medical veterinary laboratories and zoos, and 44 laboratory animals (mastomys (multimammate mice; n = 32), mice (n = 6), rats (n = 4), guinea pigs (n = 2)) during routine health monitoring in an animal facility. S. pneumoniae was isolated from nose, lung and respiratory tract, eye, ear and other sites.

Methodology/Principal Findings

Carriage of the same isolate of S. pneumoniae over a period of up to 22 weeks was shown for four mastomys. Forty-one animals showed disease symptoms. Pneumococcal isolates were characterized by optochin sensitivity, bile solubility, DNA hybridization, pneumolysin PCR, serotyping and multilocus sequence typing. Eighteen of the 32 mastomys isolates (56%) were optochin resistant, all other isolates were optochin susceptible. All mastomys isolates were serotype 14, all guinea pig isolates serotype 19F, all horse isolates serotype 3. Rats had serotypes 14 or 19A, mice 33A or 33F. Dolphins had serotype 23F, the gorilla serotype 14. Cats and dogs had many different serotypes. Four isolates were resistant to macrolides, three isolates also to clindamycin and tetracyclin. Mastomys isolates were sequence type (ST) 15 (serotype 14), an ST/serotype combination commonly found in human isolates. Cats, dogs, pet rats, gorilla and dolphins showed various human ST/serotype combinations. Lab rats and lab mice showed single locus variants (SLV) of human STs, in human ST/serotype combinations. All guinea pig isolates showed the same completely new combination of known alleles. The horse isolates showed an unknown allele combination and three new alleles.

Conclusions/Significance

The isolates found in mastomys, mice, rats, cats, dogs, gorilla and dolphins are most likely identical to human pneumococcal isolates. Isolates from guinea pigs and horses appear to be specialized clones for these animals. Our data redraw attention to the fact that pneumococci are not strictly human pathogens. Pet animals that live in close contact to humans, especially children, can be infected by human isolates and also carriage of even resistant isolates is a realistic possibility.     

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex''s entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that up-regulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype.     

Genetic Diversity and Quinolone Resistance in Campylobacter jejuni Isolates from Poultry in Senegal

We used the multilocus sequence typing (MLST) method to evaluate the genetic diversity of 46 Campylobacter jejuni isolates from chickens and to determine the link between quinolone resistance and sequence type (ST). There were a total of 16 ST genotypes, and the majority of them belonged to seven clonal complexes previously identified by using isolates from human disease. The ST-353 complex was the most common complex, whereas the ST-21, ST-42, ST-52, and ST-257 complexes were less well represented. The resistance phenotype varied for each ST, and the Thr-86-Ile substitution in the GyrA protein was the predominant mechanism of resistance to quinolone. Nine of the 14 isolates having the Thr-86-Ile substitution belonged to the ST-353 complex. MLST showed that the emergence of quinolone resistance is not related to the diffusion of a unique clone and that there is no link between ST genotype and quinolone resistance. Based on silent mutations, different variants of the gyrA gene were shown to exist for the same ST. These data provide useful information for understanding the epidemiology of C. jejuni in Senegal.     

The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

Outbreaks of hospital infections caused by multidrug resistant Acinetobacter baumannii strains are of increasing concern worldwide. Although it has been reported that particular outbreak strains are geographically widespread, little is known about the diversity and phylogenetic relatedness of A. baumannii clonal groups. Sequencing of internal portions of seven housekeeping genes (total 2,976 nt) was performed in 154 A. baumannii strains covering the breadth of known diversity and including representatives of previously recognized international clones, and in 19 representatives of other Acinetobacter species. Restricted amounts of diversity and a star-like phylogeny reveal that A. baumannii is a genetically compact species that suffered a severe bottleneck in the recent past, possibly linked to a restricted ecological niche. A. baumannii is neatly demarcated from its closest relative (genomic species 13TU) and other Acinetobacter species. Multilocus sequence typing analysis demonstrated that the previously recognized international clones I to III correspond to three clonal complexes, each made of a central, predominant genotype and few single locus variants, a hallmark of recent clonal expansion. Whereas antimicrobial resistance was almost universal among isolates of these and a novel international clone (ST15), isolates of the other genotypes were mostly susceptible. This dichotomy indicates that antimicrobial resistance is a major selective advantage that drives the ongoing rapid clonal expansion of these highly problematic agents of nosocomial infections.     

Streptococcus pneumoniae serotype 3 genotypes in invasive isolates from Colombia

Introduction: Streptococcus pneumoniae serotype 3 is an important cause of pneumonia, bacteremia, and meningitis.Objective: To establish the circulating genotypes of S. pneumoniae serotype 3 isolates recovered from the invasive disease between 1994 to 2015 in Colombia.Materials and methods: Of the 365 S. pneumoniae serotype 3 isolates recovered through the laboratory national surveillance program, 117 isolates were analyzed. Pulsed-field gel electrophoresis was used for genotyping, and multilocus sequence typing was determined in representative isolates.Results: The frequency of this serotype increased from 2.7% between 1994 and 1998 to 9.1% between 2011 and 2015 (p=0.000); 91.7% of the isolates showed a genetic similarity greater than 77% and were related to the Netherlands³-31(PMEN31) clone CC180. Several subtypes were identified, two of which showed antimicrobial resistance.Conclusion: In Colombia, the pneumococcal population of the capsular type 3 shows a continuous and homogeneous circulation relating to the clonal group ST-180.     

Molecular characterization of Streptococcus pneumoniae,particularly serotype19A/ST320, which emerged in Krasnoyarsk,Russia

Streptococcus pneumoniae , a common human pathogen, colonizes the nasopharynx and causes diseases including acute otitis media (AOM). Herein, pneumococcal serotype distributions in children before and after PCV7 vaccination and in patients with pneumococcal disease in Siberian Russia (Krasnoyarsk) are reported. Analyses included antimicrobial susceptibility testing, sequence typing (ST), pulsed field gel electrophoresis, virulence‐related surface protein gene (VSG) typing with novel primers and structural analysis by scanning electron microscopy. In healthy children (HC) prior to administration of PCV7, drug‐susceptible serotype23F/ST1500 was a major pneumococcal genotype. In the PCV7 trial, multidrug‐resistant serotype19A/ST320 emerged in vaccinees after PCV7, exhibiting a PCV7‐induced serotype replacement. Multidrug‐resistant serotype19A/ST320 was evident in patients with AOM. Community‐acquired pneumonia (CAP) isolates showed genetic similarities to the AOM (ST320) genotype, constituting a common non‐invasive AOM–CAP group. In contrast, meningitis isolates were more divergent. Overall, 25 ST types were identified; five (20%) of which were Krasnoyarsk‐native. Regarding VSGs, PI‐1 (rlrA /rrgB ), PI‐2 (pitA /B ), psrP and cbpA were present at 54.3%, 38.6%, 48.6%, and 95.7%, respectively, with two major VSG content types, PI‐1^?/PI‐2^?/psrP ⁺/cbpA ⁺ and PI‐1⁺/PI‐2⁺/psrP ^‐/cbpA ⁺, being found for HC and non‐invasive diseases, respectively. A major clone of serotype19A/ST320 (PI‐1⁺/PI‐2⁺) produced the longest pneumococcal wire (pilus) structures in colonies. ST1016 (PI‐1^?/PI‐2^?) in HC had HEp‐2 cell‐adherent pili. These results suggest that serotype19A/ST320 and related genotypes, with the VSG content type PI‐1⁺/PI‐2⁺/psrP ^?/cbpA ⁺, emerged in vaccinees after PCV7 in Siberia, accompanying diseases in non‐vaccinated children, and that some genotypes (serotypes19A/ST320 and 18/ST1016) produced novel pneumococcal structures, predicting their roles in colony formation and adherence.

     

The establishment of Neisseria meningitidis serogroup W135 of the clonal complex ET-37/ST-11 as an epidemic clone and the persistence of serogroup A isolates in Burkina Faso

We analyzed 48 invasive isolates of Neisseria meningitidis that were isolated from meningitis cases in Burkina Faso (April 2002 to April 2003). Thirty-nine of these isolates had the phenotype (serogroup:serotype:serosubtype) W135:2a:P1.5,2, eight isolates were A:4:P1.9 and one isolate was nongroupable:nonserotypable:nonserosubtypable. Genotyping of meningococcal isolates showed that W135 isolates belonged to the sequence type (ST)-11. The nongroupable isolate was of genogroup W135 and belonged to ST-192. Isolates of serogroup A belonged to ST-2859 (a member of the subgroup III/ST-5 clonal complex). W135 (ST-11) isolates involved in meningitis outbreaks in Burkina Faso differed from those involved in the Hajj-2000 associated outbreak by their pulsed-field gel electrophoresis profile. These data confirm the changing epidemiology of meningococcal infection in Burkina Faso with the establishment and expansion of serogroup W135 N. meningitidis strains of the ET-37/ST-11 clonal complex, as well as the emergence of a new clone within the subgroup III/ST-5 clonal complex.