Cryptosporidium species from human immunodeficiency–infected patients with chronic diarrhea in Jakarta,Indonesia

PurposeCryptosporidium is an opportunistic parasite that manifests as chronic and severe diarrhea in the immune-compromised subject. We investigated the species of Cryptosporidium to understand the epidemiology, mode of transmission, response to treatment, and prevention.MethodsPolymerase chain reaction/restriction fragment length polymorphism of the 18 S rRNA gene and sequencing were performed on 41 Cryptosporidium-positive stools from 36 patients with HIV AIDS, which comprised 36 pretreatment stools and 5 stools after treatment with Paromomycin.ResultsC. hominis, C. meleagridis, C. felis, and C. parvum were detected; 28 of 36 (77.7%) patients were infected with C. hominis and two (5.5%) patients with multiple species of Cryptosporidium. Treatment with Paromomycin resulted in different outcomes, perhaps because patients harbored other intestinal parasitic infections.ConclusionsMultiple infection with various Cryptosporidium species in the presence of other intestinal parasites occurs in patients with HIV AIDS suffering from chronic diarrhea who are severely immune-compromised. Common transmission of Cryptosporidium is anthroponotic.     

Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species

Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39 Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9–17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7–30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.     

A study of drug resistance among Salmonella typhi and Salmonella paratyphi A in an endemic area, 1977–1979

Tests for antibiotic resistance were carried out on 198 strains of Salmonella typhi and S. paratyphi A isolated from cases of enteric fevers. Their minimal inhibitory concentrations for streptomycin, chloramphenicol, ampicillin, furazolidine and co-trimoxazole were estimated by plate dilution technique. Four strains of S. typhi and one strain of S. paratyphi A were found to show multiple resistance with a set pattern of resistance to chloramphenicol, streptomycin, sulphonamide, tetracycline and spectinomycin. All the five strains carried R-factors. Three of the resistant S. typhi belonged to Phage type ‘O’ and one was in Phage type ‘A’. The single resistant S. paratyphi A belonged to Phage type ‘2’.     

A study of Campylobacter fetus subsp. jejuni strains isolated from the stools of diarrhoeic children in Sri Lanka

Nine strains of Cambylobacter fetus subsp. jejuni were isolated from the stools of diarrhoeic children in Colombo (Sri Lanka). The morphology of most of the strains was typical but three strains produced a spreading film of growth. No discrete domed colonies were seen. All were able to grow in a candle jar, and in a medium containing 1% glycine. All produced hydrogen sulphide. All were susceptible to ampicillin, carbenicillin, tetracycline, chloramphenicol, neomycin, erythromycin, gentamicin and furoxone.     

Rickettsioses in Australia: isolation of Rickettsia tsutsugamushi and R. australis from naturally infected arthropods

The vectors of scrub typhus and Queensland tick typhus have not previously been positively identified in Australia. Small mammals were trapped at Mossman (north Queensland) and 4 strains of Rickettsia tsutsugamushi were isolated in mice inoculated with suspensions of Leptotrombidium deliense removed from bandicoots. No strains were isolated from unfed, larval L. deliense collected from the forest floor, but 21 further strains were obtained from tissues of 141 animals of 5 species.A focus of infected ticks was defined when cases of Queensland tick typhus were identified in soldiers at Canungra (S.E. Queensland). Rickettsia australis was subsequently isolated in suckling mice from 2 pools of scrub ticks (Ixodes holocyclus) and 1 pool of I. tasmani.     

Enquête épidémiologique sur la résistance aux antibiotiques de Streptococcuspneumoniae observatoire régional de Brie: résultats 1999–évolution 1997/1999

Antimicrobial resistance in Streptococcus pneumoniae, in Brie (France), during 1999.ObjectivesThe authors had for aim to study antimicrobial resistance of Streptococcus pneumoniae strains isolated in the French Brie region during 1999.MethodFrom February 1999 to February 2000, nine microbiology hospital laboratories in “Seine et Marne” studied the antimicrobial resistance of Streptococcus pneumoniae strains isolated from various clinical samples (blood cultures, respiratory samples, cerebrospinalfluid, otitis).ResultsThree hundred seventy eight strains of Streptococcus pneumoniae were collected:169 (45%) in adults and 209 (55%) in children. The global prevalence of penicillin resistant S. pneumoniae was 61%. This prevalence was higher in children (70%) than in adults (48%), higher in pediatric otitis (68%) than in adults blood cultures (44%). The prevalence of high-level resistance strains to penicillin G, amoxicillin and cefotaxime was not elevated (22%, 2% and 0,2% respectively). Resistance to other antibiotics was high:erythromycin:66%, tetracycline : 38%, chloramphenicol : 29%, cotrimoxazole : 49%. The most prevalent serotypes were found in adults : 14, 23, 9 and in children : 19, 23, 6. Comparison with results of the same study made in 1997 shows an increase of resistance.     

Genetic diversity of Francisella tularensis in Poland with comments on MLVA genotyping and a proposition of a novel rapid v4-genotyping

We investigated the genotypes of Francisella tularensis (F. tularensis) strains isolated in Poland during the period 1953–2013 and studied their genetic relationship to F. tularensis strains isolated in other countries using MLVA. We examined the mosquito and tick samples collected in Poland for the presence of F. tularensis DNA using PCR. Our results revealed a high genetic diversity among the strains of F. tularensis collected from Poland, suggesting that the bacterium is commonly found in the environment. However, we did not detect F. tularensis DNA in ticks and mosquitoes, showing that the arthropod bites might not be the main source of infection.We also propose the application of a practical assay called v4-genotyping that can be directly performed on the clinical and environmental samples.In addition, we discovered genetic variations among Schu S4 reference strains used in various laboratories and showed that MLVA analysis should not be based on amplicon sizes only because point mutations occurring within the MLVA loci might not always be manifested by a change in the amplicon size.     

Antimicrobial resistance in Streptococcus pneumoniae in Brie (France), during 1999

ObjectivesThe authors had for aim to study antimicrobial resistance of Streptococcus pneumoniae strains isolated in the French Brie region during 1999.MethodFrom February 1999 to February 2000, nine microbiology hospital laboratories in “Seine et Marne” studied the antimicrobial resistance of Streptococcus pneumoniae strains isolated from various clinical samples (blood cultures, respiratory samples, cerebrospinal fluid, otitis).Results378 strains of Streptococcus pneumoniae were collected: 169 (45%) in adults and 209 (55%) in children. The global prevalence of penicillin resistant S. pneumoniae was 61%. This prevalence was higher in children (70%) than in adults (48%), higher in pediatric otitis (68%) than in adults blood cultures (44%). The prevalence of high-level resistance strains to penicillin G, amoxicillin and cefotaxime was not elevated (22%, 2% and 0,2% respectively). Resistance to other antibiotics was high: erythromycin: 66%, tetracycline: 38%, chloramphenicol: 29%, cotrimoxazole: 49%. The most prevalent serotypes were found in adults: 14, 23, 9 and in children: 19, 23, 6. Comparison with results of the same study made in 1997 shows an increase of resistance.     

Salmonella and Shigella in adult diarrhoea in Addis Ababa--prevalence and antibiograms

Ninety Shigella and 45 Salmonella strains were isolated from 1000 adult diarrhoeal out-patients from various hospitals and clinics in Addis Ababa. The Shigella species were isolated in the order of frequency of S. flexneri, S. dysenteriae, S. boydii and S. sonnei and the Salmonella in the order of Group C, Group B, S. typhi, other Group D and Groups A and E. Almost all Shigella isolates were sensitive to cephalothin, gentamicin, kanamycin, polymyxin B and trimethoprim-sulphamethoxazole. About 17% were sensitive to the 11 drugs tested. Multiple resistance was detected in 62%, the most common to six drugs (27%). All Salmonella isolates were sensitive to gentamicin, polymyxin B and trimethoprim-sulphamethoxazole. About 69% were sensitive to all drugs tested. 22% were multiply resistant and the most common was to eight drugs (18%).     

182株儿童患者肺炎链球菌的分子生物学鉴定及分型

目的对来自患儿的肺炎链球菌进行分型,为肺炎链球菌疫苗的正确选择提供科学依据。方法收集2014年来自河北省儿童医院的182株肺炎链球菌,普通PCR对肺炎链球菌进行种属鉴定,应用多重PCR方法对菌株进行菌型分析。结果经PCR检测182株菌的cpsA基因扩增均为阳性;经多重PCR检测,除8株未分型菌株外,其余174株肺炎链球菌中,以19F、19A和6A/6B型数量最多,分别为68株(37.36%)、33株(18.13%)和26株(14.28%),其余型别有35B型、14型、6C/6D型、23F型、15B/15C型等。结论 182株肺炎链球菌的菌型主要为19F、19A和6A/6B,为该省肺炎链球菌疫苗的正确选择和制订使用策略提供了科学依据。     

Human salmonella carriers in a tropical urban environment

Salmonella sp. were isolated from rectal swab specimens from 39 of 464 (8·4%) of apparently healthy adults and children in central Jakarta, Indonesia. A wide variety of species of Salmonella were found with S. oranienburg predominating. Most of the S. oranienburg isolated were resistant to a wide range of antibiotics, probably because of their previous widespread and inappropriate administration. The yield of carriers identified increased significantly with the use of double enrichment procedures. This study emphasizes the importance of high rates of carriage of Salmonella sp. as potential causes of diarrhoeal disease in overcrowded, unhygienic cities in the tropics.     

Current trend of pneumococcal serotypes distribution and antibiotic susceptibility pattern in Malaysian hospitals

From January 2008 to December 2009, 433 Streptococcus pneumoniae strains were examined to determine the serotype distribution and susceptibility to selected antibiotics. About 50% of them were invasive isolates. The strains were isolated from patients of all age groups and 33.55% were isolated from children below 5 years. The majority was isolated from blood (48.53%) and other sterile specimens (6.30%). Community acquired pneumonia (41.70%) is the most common diagnosis followed by sepsis (9.54%). Serotyping was done using Pneumotest Plus-Kit and antibiotic susceptibility pattern was determined by modified Kirby-Bauer disk diffusion method and measurement of minimum inhibitory concentration (MIC) using E-test strip. Ten most common serotypes were 19F (15.02%), 6B (10.62%), 19A (6.93%), 14 (6.70%), 1 (5.08%), 6A (5.08%), 23F (4.85%), 18C (3.93%), 3 (2.08%) and 5 (1.85%). Penicillin MIC ranged between ≤0.012-4 μg/ml with MIC₉₀ of 1 μg/ml. Penicillin resistant rate is 31.78%. The majority of penicillin less-susceptible strains belonged to serotype 19F followed by 19A and 6B. Based on the serotypes distribution 22 (44.00%), 28 (56.00%) and 39 (78.00%) of the invasive isolates from children ≤2 years were belonged to serotypes included in the PCV7, PCV10 and PCV13, respectively.     

Prevalence, haemolytic and haemagglutination activities and antibiotic susceptibility profiles of Campylobacter spp. isolated from human diarrhoeal stools in Vhembe District, South Africa

Campylobacter species are increasingly being recognized as agents of gastroenteritis worldwide. However, data on the pathogenic characteristics of the organism isolated in rural communities in South Africa are lacking. In this study, the prevalence of Campylobacter spp. from diarrhoeal stools, haemolytic and haemagglutinating activities of the isolates, and antibiotic susceptibility profiles, including minimum inhibitory concentration (MIC) patterns to different antibiotics, were determined using the standard microbiological techniques. Campylobacter spp. were isolated from individuals of all age-groups; however, the infection rate was higher among individuals aged less than two years (30.4%). Of 115 Campylobacter strains isolated, polymerase chain reaction (PCR) analysis indicated that 98 (85%) were C. jejuni, while 17 (15%) were C. coli. Seventy-one (62%) of the strains showed haemolysis on human blood, and 80% agglutinated human blood, whereas 22.6% were beta-lactamase-positive. Resistance to antimicrobials, such as erythromycin, ciprofloxacin, vancomycin, and fusidic acid, was high. Increased resistance to macrolide and quinolone antibiotics poses major risks for treatment failure. Haemolytic and haemagglutinating activities may be useful in preliminary characterization of pathogenic strains in settings where Campylobacter-associated infections are common.     

The spectrum of infection and sensitivity of organisms isolated from African and Indian children in a Durban hospital

A prospective study was undertaken over a period of six months to determine the spectrum of infection, sensitivity of organisms isolated, and suitability of antibiotics chosen in 520 consecutive patients admitted to a paediatric unit. Culture and sensitivity of stool, urine and blood yielded 752 isolates; in 147 cases, more than one pathogen was isolated from the same or different sites. High rates of resistance to chloramphenicol, ampicillin, and kanamycin were seen in salmonellae other than Salmonella typhi, which differed in retaining its original sensitive susceptibility profile. Most Enterobacteria were sensitive to gentamicin. Penicillin-resistance was seen in 9% of meningococci, and several Haemophilus influenzae strains (20%) were resistant to ampicillin. Methicillin-resistance was encountered in 13% of Staphylococcus aureus strains and 17% of pneumococci were resistant to penicillin G. The sensitivity pattern of organisms isolated was probably directly related to widespread use of antibiotics.     

The changing phenotypes and genotypes of invasive pneumococcal isolates from children in Shenzhen during 2013–2017

BackgroundThe phenotypes and genotypes of Streptococcus pneumoniae isolated from invasive pneumococcal diseases (IPDs) were changing all the time. To monitor these changes of phenotypes and genotypes of S. pneumoniae isolates from children, we examined antibiotic susceptibility, serotype distribution and sequence types (STs) of S. pneumoniae, which were isolated before the 13-valent pneumococcal conjugate vaccine (PCV13) introduced into China.MethodsStrains were isolated from children less than 14 years old between January 2013 and May 2017 from Shenzhen Children’s Hospital. Serotypes, antibiotic resistance, and genotypes of these isolates were determined using capsular swelling, E-test, and multi-locus sequence typing, respectively.ResultsA total of 94 S. pneumoniae strains were isolated, which belonged to 15 serotypes. The five most prevalent serotypes were 19F (25.5%), 19A (19%), 14 (17%), 23F (7.5%), and 6B (9.6%). We found 42 STs for these isolates. The most abundant STs were ST271 (24.4%), ST876 (17%), and ST320 (10.6%), mainly related to 19F, 14, and 19A, respectively. The potential coverage of PCV13 was 87.2%. Among non-meningitis isolates, the resistance rates to penicillin and ceftriaxone were 0% and 2%. However, the meningitis isolates showed high resistance to penicillin (80%) and ceftriaxone (20%). Most of these isolates (95.7%) were resistant to erythromycin, and 66 (70.2%) strains carried the ermB gene and 24 (25.5%) strains carried both the ermB and mefA/E genes. Serotype 19A showed the highest mean minimum inhibitory concentration (MIC) for penicillin (MIC = 1.486) than the other serotypes, but no significant difference in penicillin MIC among the three main STs (ST271, ST320, and ST876).ConclusionsThe phenotypes and genotypes of invasive pneumococcal isolates from Shenzhen Children’s Hospital have changed with the passage of time. Compared with PCV7, PCV13 can more effectively protect Chinese children from IPDs. To some extent, these changes are possibly related to the usage of antibiotics and vaccines.     

Genomics of Streptococcus salivarius,a major human commensal

The salivarius group of streptococci is of particular importance for humans. This group consists of three genetically similar species, Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus. S. salivarius and S. vestibularis are commensal organisms that may occasionally cause opportunistic infections in humans, whereas S. thermophilus is a food bacterium widely used in dairy production. We developed Multilocus sequence typing (MLST) and comparative genomic analysis to confirm the clear separation of these three species. These analyses also identified a subgroup of four strains, with a core genome diverging by about 10%, in terms of its nucleotide sequence, from that of S. salivarius sensu stricto. S. thermophilus species displays a low level of nucleotide variability, due to its recent emergence with the development of agriculture. By contrast, nucleotide variability is high in the other two species of the salivarius group, reflecting their long-standing association with humans. The species of the salivarius group have genome sizes ranging from the smallest (∼1.7 Mb for S. thermophilus) to the largest (∼2.3 Mb for S. salivarius) among streptococci, reflecting genome reduction linked to a narrow, nutritionally rich environment for S. thermophilus, and natural, more competitive niches for the other two species. Analyses of genomic content have indicated that the core genes of S. salivarius account for about two thirds of the genome, indicating considerable variability of gene content and differences in potential adaptive features. Furthermore, we showed that the genome of this species is exceptionally rich in genes encoding surface factors, glycosyltransferases and response regulators. Evidence of widespread genetic exchanges was obtained, probably involving a natural competence system and the presence of diverse mobile elements. However, although the S. salivarius strains studied were isolated from several human body-related sites (all levels of the digestive tract, skin, breast milk, and body fluids) and included clinical strains, no genetic or genomic niche-specific features could be identified to discriminate specific group.     

Immunochemical and antigenic characterization ofCoxiella burnetii strains isolated in Europe and Mongolia

SDS-PAGE, immunoblotting and serological methods such as microimmunofluorescence (MIF) test and ELISA were used to compare protein and lipopolysaccharide (LPS) profiles and antigenicity of 12Coxiella burnetii strains isolated mostly from ticks in Europe and Mongolia with three referenceC. burnetii strains originating from USA, namelyNine Mile from tick,Priscilla from goat placenta and S from human heart valve. Among strains from Europe and Mongolia, no significant differences in protein and LPS profiles were observed, irrespective of their origin, i.e. the country and source of isolation. The LPS profiles of these strains appeared to be more related to those ofNine Mile strain associated with acute Q fever, than to those of strainsS andPriscilla associated with chronic Q fever. In immunoblots all strains isolated from Slovakia and Poland reacted more expressively with rabbit serum againstNine Mile than with serum againstPriscilla strain. In the MIF test and ELISA there were no substantial differences in antibody-binding capacity between the reference and newly isolatedC. burnetii strains, except for strainPriscilla reacting with homologous serum in lower antigenic concentration than other strains under study. However, in the MIF test much higher antigenic concentrations of eachC.burnetii strain was required to detect antibodies in thePriscilla serum than in theNine Mile, Luga andS sera.     

Prevalence of Salmonella serotypes in India: a 16-year study

During the period 1958-73, 8 027 strains of Salmonella were tested at the National Salmonella and Escherichia Centre: 3 834 strains from man, 3 018 from animals, 839 from sewage and water sources, and 336 of unknown origin. A total of 99 serotypes were identified: 47 from man, 83 from animals, and 35 from sewage and water sources. S. typhi was the commonest serotype in man, followed by S. weltevreden and S. paratyphi A. S. typhimurium was the commonest serotype isolated from animals, followed by S. weltevreden and S. anatum. In sewage and other water sources S. weltevreden was the commonest serotype identified followed by S. typhimurium and S. bareilly. Infection due to S. weltevreden in both man and animals increased considerably after 1970. Out of a total of 99 serotypes isolated from different sources, 13 were isolated from man only, 49 from animals only, 34 from both man and animals, 30 from both animals and water sources, and 22 from man, animals, and water sources.     

HEp-2-adherent Escherichia coli strains associated with acute infantile diarrhea,São Paulo,Brazil

In this paired case-control study of infants with diarrhea in São Paulo, we examined the association between HEp-2–adherent Escherichia coli strains and diarrhea. We tested isolates from stool specimens of infants with diarrhea and matched controls in an HEp-2 cell adherence assay; we then hybridized isolates with DNA probes and identified enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and diffusely adherent E. coli (DAEC). From 100 patient-control pairs, we isolated 78 HEp-2–adherent strains; of these, 61 strains were single pathogens identified in stools of infants with diarrhea. While typical EPEC was significantly associated with diarrhea (p<0.001), EAEC was more frequently associated with diarrhea in clinical cases (20%) compared with healthy controls (3%) (p<0.001). Atypical EPEC, showing a localized adherence-like pattern, was also more common in patients than controls (p>0.1). DAEC was isolated with equal frequency from patients and controls (p>0.1).