Human Streptococcus agalactiae Isolate in Nile Tilapia (Oreochromis niloticus)

Streptococcus agalactiae, the Lancefield group B streptococcus (GBS) long recognized as a mammalian pathogen, is an emerging concern with regard to fish. We show that a GBS serotype Ia multilocus sequence type ST-7 isolate from a clinical case of human neonatal meningitis caused disease and death in Nile tilapia (Oreochromis niloticus).     

Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis

Tuberculosis (TB) is an infectious disease of global public health importance caused by Mycobacterium tuberculosis complex (MTC) in which M. tuberculosis (Mtb) is the major causative agent. Recent advancements in genomic technologies such as next generation sequencing have enabled high throughput cost-effective generation of whole genome sequence information from Mtb clinical isolates, providing new insights into the evolution, genomic diversity and transmission of the Mtb bacteria, including molecular mechanisms of antibiotic resistance. The large volume of sequencing data generated however necessitated effective and efficient management, storage, analysis and visualization of the data and results through development of novel and customized bioinformatics software tools and databases. In this review, we aim to provide a comprehensive survey of the current freely available bioinformatics software tools and publicly accessible databases for genomic analysis of Mtb for identifying disease transmission in molecular epidemiology and in rapid determination of the antibiotic profiles of clinical isolates for prompt and optimal patient treatment.     

Virus-like rods associated with salivary gland hyperplasia in tsetse,Glossina pallidipes

Long, virus-like rods were discovered in hyperplastic salivary glands of Glossina pallidipes Austen from Kibwezi Forest (2 ° 27′ S, 37 ° 55′ E), Kenya. The glands were enlarged up to four times the normal diameter. This increase in size was due to a cellular proliferation of the glandular epithelial cells and hypertrophy of their nuclei and cytoplasm. Nuclear and cytoplasmic inclusions were present in the enlarged cells but were not found in cells of normal-sized glands. Electron microscopy revealed many virus-like rods in the abnormal glands. Males with such glands were often completely sterile. Abnormal growth of the ovarioles was a significant feature of young females with hyperplastic glands. Both sexes of wild and laboratory-bred flies were found with enlarged glands. One way of transmission of the trait seems to be from mother to progeny.     

An outbreak due to echovirus type 30 in a neonatal unit in France in 1997: usefulness of PCR diagnosis.

Between February and August 1997, 53 patients with enterovirus meningitis were hospitalized in Clermont-Ferrand, France. All but one were children. Echovirus type 30 was involved in 70% of cases with identified serotype. The outbreak ceased on August 8. Two months later, a neonate was admitted to the neonatal unit with an echovirus type 30 meningitis thought to be acquired at delivery. Twenty days later a nosocomial outbreak of echovirus type 30 involving five neonates occurred. Two of them presented with meningitis and two with febrile seizure; One was asymptomatic. The retrospective examination of the maternal sera in a neutralization test, using the index case strain as a source of antigen, showed that none of the neonates was passively immunized before hospitalization. The use of genome detection in cerebrospinal fluid allowed rapid diagnosis and infection was contained by re-inforcing hygiene measures. Prospective examination of stools in the neonatal and paediatric units showed no further occurrences of the disease. No sporadic case was observed in the general population. Hence, nosocomial infections can occur a long time after an outbreak in the general population; rapid diagnosis with molecular tools is useful both for a definite diagnosis in patients already hospitalized, and to act as a rapid alert, even in intervals between seasonal outbreaks.     

Extended spectrum ß-lactamase-producing Escherichia coli in neonatal care unit

An outbreak of extended-spectrum β-lactamase–producing Escherichia coli in a neonatal care unit began with transmission from a mother to her newborn twins during vaginal delivery. Subsequently, infection spread by healthcare worker contact with other neonates; a healthcare worker also was infected. Knowledge about transmission may improve infection control measures.     

Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013–2015

Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed.The aim of this study was to investigate the applicability of whole genome sequencing based analysis compared to Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) in epidemiological investigations as well as the development of a user friendly method for daily laboratory use.Out of 14,000 VRE - screening samples, a total of 60 isolates positive for either vanA or vanB gene were isolated of which 38 were from patients with epidemiological links from three suspected outbreaks at Uppsala University Hospital. The isolates were genotypically characterised with PFGE, MLST, and WGS based core genome Average Nucleotide Identity analysis (cgANI). PFGE was compared to WGS and MLST regarding reliability, resolution, and applicability capacity.The PFGE analysis of the 38 isolates confirmed the epidemiological investigation that three outbreaks had occurred but gave an unclear picture for the largest cluster. The WGS analysis could clearly distinguish six ANI clusters for those 38 isolates.As result of the comparison of the investigated methods, we recommend WGS-ANI analysis for epidemiological issues with VRE. The recommended threshold for Enterococcus faecium VRE outbreak strain delineation with core genome based ANI is 98.5%.All referred sequences of this study are available from the NCBI BioProject number PRJNA301929.     

Inter and intra-specific diversity of parasites that cause lymphatic filariasis

Lymphatic filariasis is caused by three closely related nematode parasites: Wuchereria bancrofti, Brugia malayi and Brugia timori. These species have many ecological variants that differ in several aspects of their biology such as mosquito vector species, host range, periodicity, and morphology. Although the genome of B. malayi (the first genome sequenced from a parasitic nematode) has been available for more than five years, very little is known about genetic variability among the lymphatic dwelling filariae. The genetic diversity among these worms is not only interesting from a biological perspective, but it may have important practical implications for the Global Program to Eliminate Lymphatic Filariasis, as the parasites may respond differently to diagnostic tests and/or medical interventions. Therefore, better information on their genetic variability is urgently needed. With improved methods for nucleic acid extraction and recent advances in sequencing chemistry and instrumentation, this gap can be filled relatively inexpensively. Improved information on filarial genetic diversity may increase the chances of success for lymphatic filariasis elimination programs.     

北京市一起新型冠状病毒Omicron变异株聚集性疫情特征分析

目的 分析北京市海淀区一起新型冠状病毒肺炎聚集性疫情流行病学特征及传播链。方法 采用描述性流行病学方法分析疫情流行病学特征,应用现场调查和大数据技术分析传播链。结果 2022年4月27日至5月13日, 海淀区发生一起新型冠状病毒肺炎聚集性疫情,全基因组测序系Omicron变异株（BA.2.2进化分支）;涉及感染者38例,确诊病例34例,无症状感染者4例;临床分型以轻型（88.2%）为主,无重型、危重型和死亡病例;早期临床症状以咽部不适（50.0%）、咳嗽（29.4%）为主;17 d内传播7代,涉及3起社区聚集、2起单位聚集和8个家庭内传播;暴露方式以同住（47.6%）、同时空暴露（31.6%）为主;代间距M（Q₁,Q₃）为3（1,6）d;总续发率为1.5%（37/2 482）,其中家庭续发率为36.7%（18/49）。结论 本起Omicron变异株疫情临床症状轻,家庭、社区聚集性明显,疫情传播速度较快,同时空暴露感染风险较高,需利用信息化技术全面摸排密切接触者,以快制快,有效阻断疫情传播。     

Immunoglobulin G levels in fetal and newborn tammar wallabies (Macropus eugenii)

Immunoglobulin G (IgG) was measured in fetal, neonatal and colostral samples from the tammar wallaby (Macropus eugenii) in order to study the possibility of passively acquired immunity. Samples were obtained from young at a known stage of gestation and at known times (to the minute) after birth. IgG was present (in increasing levels of concentration) in fetal serum, neonatal serum and colostrum. Since the fetus and neonate are probably unable to make immunoglobulin (Ig), it is hypothesized that transplacental and trans-gut transmission takes place from mother to offspring. The vascular yolk sac placenta has a high concentration of IgG, and is the most likely route of transmission from mother to young. Some observations were made of IgA which was found only in colostrum. No Ig of either kind was found in yolk sac fluid.     

81例新生儿化脓性脑膜炎临床分析

 

目的 探讨新生儿化脓性脑膜炎的临床特点,为早期诊疗新生儿化脓性脑膜炎提供依据。方法 回顾性分析2011年1月1日-2018年12月31日某院新生儿病房住院治疗且出院诊断为化脓性脑膜炎新生儿的临床资料,按照起病时出生后日数,以及血培养、脑脊液（CSF）培养结果分成不同组,比较不同组新生儿临床特点的差异。结果 81例新生儿居前4位的临床表现依次为发热（88.89%）、意识改变（37.04%）、吃奶差（24.69%）、前囟张力增高（23.46%）,早发型组（起病日龄≤出生后7 d）吃奶差的发生率高于晚发型组（起病日龄>出生后7 d）（P<0.05）;检出病原菌以大肠埃希菌（E.coli）和B族链球菌（GBS）为主;E.coli组CSF葡萄糖含量比GBS组更低（P<0.05）;CSF培养阳性尤其是CSF和血培养均阳性的新生儿CSF压力和蛋白含量均更高（均P<0.05）;6例新生儿在起病24 h内行第1次腰椎穿刺术的结果为CSF白细胞数在正常范围内,其中4例新生儿在第1次腰椎穿刺术48~72 h后复查CSF白细胞数明显增高;79例新生儿完善了头颅MRI或CT检查,发现7例（8.86%）新生儿出现并发症,其中5例CSF和/或血液中检出病原菌。结论 新生儿化脓性脑膜炎临床表现不典型,新生儿出现发热应引起高度的重视,即使CSF常规、生化正常也不能排除化脓性脑膜炎的诊断,应及时进行CSF复查检测。

     

Bordetella hinzii Meningitis in Patient with History of Kidney Transplant,Virginia, USA

A patient in Virginia, USA, who had previously undergone multiple kidney transplantations showed signs of Bordetella hinzii bacteremia and meningitis. This emerging pathogen has been increasingly identified as a clinically significant pathogen in immunosuppressed and, less frequently, immunocompetent patients. This patient was treated and recovered without further issue.     

Maternal height as an independent risk factor for neonatal size among adolescent bengalees in kolkata, India

Background

Low Birth Weight is a major public health problem in developing countries. The causes of LBW are multifactorial including complication during pregnancy, genetic, environmental, social-cultural, demographic and nutritional variables. Comparison of anthropometric risk factors for neonatal size of adolescent mothers are lacking from West Bengal. Therefore, this study was undertaken to identify maternal anthropometric characteristics, which most strongly influence neonate weight and length among Bengalee mothers.

Methods

A hospital based cross-sectional study was undertaken during 2004 in a Government general hospital in South Kolkata, India. A total of 76 adolescent (age<20years) pregnant women were enrolled from obstetric ward who were admitted for delivery. Due to 4 perinatal deaths; a total of 72 adolescent mother- baby pairs were included in this analysis. Anthropometric measurements were undertaken immediately after delivery following stabilization as well maternal body mass index (BMI) was calculated using standard formula.

Results

The prevalence of low birth weight (LBW) in the present study was 52.8%. The results revealed that 30.6% of mothers were undernourished (BMI<19.8 kg/m²). It was noted that about 64% of undernourished mothers delivered LBW baby. Linear regression analyses of neonatal weight and length as dependent variables revealed that in both cases, maternal height had the most significant impact. It showed 12.9% (birth weight) and 16.1% (birth length) of variation. Moreover, the proportion of LBW was 75%, 52.3% and 25% among short (height ≤145 cm), average (146–155cm) and tall (>155cm) mothers (x²=6.855, p<0.01), respectively. Short mothers had 2.74 and 9.0 fold greater risk of delivering LBW baby than average and tall mothers. In contrast, mean birth weight and length of baby was lower in short mother than their counterparts.

Conclusion

This study revealed that maternal height had the strongest significant impact on neonate size. This strong association could have serious health implications for Bengalee adolescent mothers. However, since this is a preliminary finding, it needs validation using a larger sample of adolescent mothers.     

Phylogenomic analysis of the complete sequence of a gastroenteritis-associated cetacean adenovirus (bottlenose dolphin adenovirus 1) reveals a high degree of genetic divergence

Adenoviruses are common pathogens in vertebrates, infecting a wide range of hosts, but only having rarely been detected and correlated with disease in cetaceans. This article describes the first complete genomic sequence of a cetacean adenovirus, bottlenose dolphin adenovirus 1 (BdAdV-1), detected in captive bottlenose dolphin population (Tursiops truncatus) suffering from self-limiting gastroenteritis. The complete genome sequence of BdAdV-1 was recovered from data generated by high-throughput sequencing and validated by Sanger sequencing. The genome is 34,080 bp long and has 220 nucleotides long inverted terminal repeats. A total of 29 coding sequences were identified, 26 of which were functionally annotated. Among the unusual features of this genome is a remarkably long 4380 bp E3 ORF1, that displays no sequence homology with the corresponding E3 regions of other adenoviruses. In addition, the fiber protein only has 26% identity with fiber proteins described in other adenoviruses. Three hypothetical proteins were predicted. The phylogenetic analysis indicates that the closest known relative to BdAdV-1 is an adenovirus detected in bottlenose dolphin (KR024710), with an amino acid sequence identity between 36 and 79% depending on the protein. Based on the phylogenic analysis, the BdAdV-1 appears to have co-evolved with its host.The results indicate that BdAdV-1 belongs to the Mastadenovirus genus of the Adenoviridae family, however, it is clearly different from other adenoviruses, especially in the 3′-end of the viral genome. The high degree of sequence divergence suggests that BdAdV-1 should be considered as a novel species in the Mastadenovirus genus. The study also demonstrates the usefulness of high-throughput sequencing to obtain full-length genomes of genetically divergent viruses.     

新生儿化脓性脑膜炎的早期临床特征

目的:探讨新生儿化脓性脑膜炎的早期临床特点。方法:选择2008～2010年吉林市儿童医院NICU收治的化脓性脑膜炎患儿,回顾性分析其围生因素、发病时间、临床表现、实验室检查、治疗和预后。结果:新生儿化脓性脑膜炎9例,检出率占同期临床诊断败血症患儿的17.31%,1例早产儿生后6 h发病,表现有反应差、发热、抽搐、硬肿症,1例以屏气发作起病,2例抽搐时出现呼吸停止和频繁呼吸暂停需常频通气治疗,脑脊液常规WBC 42×106/L～脓细胞满视野。2例脑脊液培养阳性,9例血培养均阴性,5例患儿治疗有效,放弃治疗2例,死亡2例。结论:新生儿化脓性脑膜炎起病隐匿,病情重,病死率高,应重视早期临床表现,尽早行病原学检测,选择敏感抗生素治疗,以降低病死率。     

Molecular characteristics of Streptococcus agalactiae in a mother-baby prospective cohort study: Implication for vaccine development and insights into vertical transmission

BackgroundStreptococcus agalactiae (GBS) is a leading cause of neonatal sepsis and meningitis in many countries. This study aimed to determine the molecular characteristics of GBS colonized in mothers and their infants so as to provide implication for vaccine strategies and confirm vertical transmission.MethodsA prospective cohort study was conducted to recruit 1815 mother-neonate pairs. All GBS isolates from pregnant women and her infants were tested for serotypes, multilocus sequence types and virulence genes. The relationship between multiple molecular characteristics of GBS isolates was tested by the correspondence analysis, and the agreement between mother-neonate paired data in molecular characteristics was analyzed using Kappa tests.ResultsThe predominant serotypes were III, Ia and V, and the most prevalent sequence types (STs) were ST19, ST17, ST10, and ST12. All isolates carried at least one pilus island (PI). The most common combination of PIs was PI-2b alone, followed by PI-1+PI-2a and PI-2a alone, and the most prevalent alpha-like protein (alp) genes were rib, epsilon and alphaC. Moreover, a strong relationship was noted between STs, serotypes, alp genes and PIs, including ST17 associated with serotype-III/rib/PI-2b, ST19 with serotype-III/rib/PI-1+PI-2a, and ST485 with serotype-Ia/epsilon/PI-2b. The rate of GBS vertical transmission was 14.1%, and the kappa test revealed good agreement in multiple molecular characteristics among GBS-positive mother-neonate pairs. Notably, the switching of molecular characteristics was found during vertical transmission.ConclusionsOur findings underscore the value of monitoring multiple molecular characteristics so as to provide implication for multivalent strategies and gain insights into GBS vertical transmission and vertical characteristic switching.     

Profil bactériologique des méningites purulentes à l'hôpital d'enfants de Tunis

The therapeutic management of bacterial meningitis is still a matter for concern.Objective – The aim of this study was to analyze the profile of pathogens responsible for meningitis and their resistance to antibiotic drugs.Methods – Between January 1997 and December 1999, 114 strains were collected from CSF.Results – Streptococcus B and Escherichia coli were the most frequently identified pathogen found in neonatal meningitis. In children between three months and three years of age, Haemophilus Influenzae was the most frequently identified pathogen in meningitis (75%), followed by Streptococcus pneumoniae (22%). In children over three years of age, Streptococcus pneumoniae (57%) and Neisseria meningitidis (30%) were predominant. High levels of resistance were found: H. influenzae to ampicillin (33%) and S. pneumoniae to penicillin (56%). H. influenzae was more often isolated in meningitis in our study because of the absence of systematic vaccination in our country.Comments – The increasing prevalence of penicillin resistant S. pneumoniae strains isolated from meningitis make adequate therapeutic management difficult.     

Cytolethal distending toxin producing Escherichia coli O157:H43 strain T22 represents a novel evolutionary lineage within the O157 serogroup

Enterohemorrhagic Escherichia coli (EHEC) O157:H7/NM strains are significant foodborne pathogens intensively studied, while other sero- and pathotypes of the O157 serogroup only began to receive more attention. Here we report the first genome sequence of a cytolethal distending toxin (CDT-V) producing E. coli O157:H43 strain (T22) isolated from cattle. The genome consists of a 4.9 Mb chromosome assembled into three contigs and one plasmid of 82.4 kb. Comparative genomic investigations conducted with the core genomes of representative E. coli strains in GenBank (n = 62) confirmed the separation of T22 from the EHEC and enteropathogenic (EPEC) O157 lineages. Gene content based pangenome analysis revealed as many as 261 T22-specific coding sequences without orthologs in EDL933 EHEC O157 prototypic and two phylogenetically related commensal E. coli strains. The genome sequence revealed 10 prophage-like regions which harbor several virulence-associated genes including cdt and heat-labile enterotoxin (LT-II) encoding operons. Our results indicate that the evolutionary path of T22 is largely independent from that of EHEC and EPEC O157:H7/NM strains. Thus, the CDT-producing T22 E. coli O157:H43 strain represents a unique lineage of E. coli O157.