Complete genome sequences of Cytobacillus sp., Domibacillus sp., Enterobacter sp., Neisseria sp., Pseudomonas sp., and Streptococcus sp. strains from human clinical infections collected at diagnostic units in 2020.

Members of Bacillota and Pseudomonadota phyla are frequently considered bacterial infectious agents in humans. As part of a large sequencing project of clinically relevant pathogens, we hybrid-assembled complete genomes of Cytobacillus, Domibacillus, Enterobacter, Neisseria, Pseudomonas, and Streptococcus species isolated from clinical specimens.

Prevalence of extended spectrum Beta-Lactamase producing Klebsiella species from patients' specimens in a tertiary teaching hospital in Ile-Ife, Southwest Nigeria.

Objective: This study determined the prevalence of ESBL genes amongst Klebsiella species isolated from patients' specimens attending a Tertiary Teaching Hospital, in Ile-Ife, Southwest Nigeria. Methods: A cross sectional study of presumptive isolates of Klebsiella (n=180) were collected, after ethical approval in the microbiology laboratory. Isolates were identified to species level by conventional biochemical tests and MicrobactTM 24E Identification Kits. Antibiotic susceptibility testing was performed by the Kirby Bauer's disk diffusion method. ESBL production was detected by the double disc synergy and ESBL genes by the multiplex PCR protocol. Results: The Klebsiella species identified were Klebsiella pneumoniae 95.6%, Klebsiella oxytoca 3.3%, Klebsiella ornithinolytica 0.6% and Klebsiella terrigena 0.6%. The prevalence of ESBL genes among the Klebsiella isolates was 47.2%, and the most common ESBL gene was blaSHV (38.9%), also 75% of the study isolates had MAR index greater than 0.2. Conclusions: The study establishes the prevalence of Extended Spectrum Beta-Lactamase producing Klebsiella sp in the hospital and identified the most prevalent ESBL genes circulating as blaSHV followed by blaTEM and blaCTX-M in this environment. This underscores the need for regular and continuous surveillance of antimicrobial resistance trend as a strong component of the antibiotics stewardship and infection prevention and control programs in the hospital.

Antibiotic resistance pattern of Pseudomonas spp. from patients in a tertiary hospital in South-West Nigeria.

INTRODUCTION: Pseudomonads constitute critical agents of opportunistic infections in hospital settings particularly in immunocompromised patients and Pseudomonas aeruginosa is a major flagship member of these infectious agents. This study assessed the distribution of Pseudomonas spp. associated with infections in patients and their antibiotic resistance patterns as part of an antibiotic stewardship intervention program and resistance surveillance. METHODS: One hundred and fifty Pseudomonas spp. from different clinical specimens were obtained from the Obafemi Awolowo University Teaching Hospitals Complex Ile-Ife. Culture was carried out on MacConkey and blood agar while phenotypic characterization was done by Gram staining, oxidase, and catalase test. Species identification was done using MICROBACTTM 24E bacterial identification kit and confirmed by 16S rDNA polymerase chain reaction (PCR) assay. Antibiotic susceptibility testing to eight antibiotics in four classes was done. RESULTS: Pseudomonas aeruginosa was the most frequently occurring species (96.0%); P. putida (2.67%) and P. fluorescens (0.67%) were also identified as well as an isolate of Burkholderia pseudomallei (0.67%). The highest resistance rate among isolates was observed towards gentamicin (35.4%); piperacillin/tazobactam was the most active antibiotic. Multidrug-resistant (MDR) strains constituted 12.8% of the isolates and most MDR strains also displayed a high multiple antibiotic resistance index (MAR). CONCLUSIONS: Pseudomonas aeruginosa is emerging as a highly MDR pathogen in our hospital setting. This calls for the establishment of a surveillance system and antimicrobial stewardship programme in place. Furthermore, we propose a review of the current antibiotics prescription policy, and infection control programmes (ICPs) if we must control the spread of MDR-P. aeruginosa in this environment.

Group B streptococcus colonization and HIV in pregnancy: A cohort study in Nigeria.

BACKGROUND: Group B streptococcus (GBS) is a leading cause of maternal and neonatal infectious morbidity. HIV is prevalent among pregnant women in Nigeria. AIM: To determine the rates of anogenital GBS colonization in our institution and compare GBS colonization rates between HIV positive and negative pregnant women. METHODS: A cross-sectional comparative study was conducted over 6 months. Patients were separated according to their HIV status: positive and negative. GBS colonization was assessed by vaginal and anal swabs collected at 35-37 weeks of gestation and cultured in Todd-Hewitt broth, followed by a confirmatory test. Socio-demographic characteristics and CD4 count were extracted from patient medical records. Secondary outcomes were identification of risk factors for GBS colonization, antibiotic sensitivity, and any association between CD4 count and GBS colonization. Appropriate statistical analysis was done. RESULTS: A total of 200 patients attended the clinic; 67 HIV positive and 133 negative. Analyzed samples were 198; the overall prevalence of GBS was 18.2%. No significant difference in GBS colonization was noted between HIV positive (19.4% [13]) and negative patients (17.6% [23/131]). Most GBS isolates were susceptible to ampicillin (87%) and penicillin (81%). A high body mass index (BMI) was independently associated with GBS colonization (OR = 1.25, 95% CI: 1.04-1.51). No association was observed between CD4 counts and GBS colonization. CONCLUSION: A high prevalence of GBS colonization was observed in our institution. Colonization rates were independent of the HIV status but associated with a high BMI in HIV positive women.

Extended-spectrum Beta-lactamase Orthopedic Wound Infections in Nigeria.

BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria are emerging and impacting significantly on the management of patients and hospital costs. Besides, they are not being routinely sought after in diagnostic laboratories thus contributing to treatment failure. MATERIALS AND METHODS: Bacterial isolates from wounds of 45 patients were identified using commercial identification kits and antibiotic susceptibility was evaluated by the Bauer-Kirby method. Screening and phenotypic confirmation of ESBL production were done as prescribed by the Clinical and Laboratory Standards Institute. The conjugation experiment was performed by the mating assay in broth between the ESBL producers and E. coli ATCC 25922 as the recipient. RESULTS: Out of 102 Gram-negative bacteria isolated, 36 were positive for ESBL mainly of the Enterobacteriaceae family (33) and the rest were oxidase-positive bacilli (3). The predominant bacteria were Klebsiella spp. and E. coli. Others were Serratia rubidae, Citrobacter freundii, Morganella morgannii, Proteus spp., Providencia stuartii, and Enterobacter spp. There was a significant association between treatment with third-generation cephalosporins (3GCs) and isolation of ESBLs (P=0.0020). The ESBL producers were multiply resistant and moderately sensitive to colistin. The conjugation experiment showed that the ESBL gene was transferred horizontally and tetracycline, cotrimoxazole, nitrofurantoin, gentamicin, and aztreonam resistance genes were co-transferred. No mortality was recorded but the mean length of stay in the hospital was 82 days. CONCLUSION: The development and spread of ESBL among Gram-negative bacteria and possible horizontal transfer calls for concern, especially in view of treatment failure, high treatment cost, and consequent discomfort to patients.

Hospital acquired infection in Obafemi Awolowo University Teaching Hospital, Ile-Ife, Southwest, Nigeria: a ten year review (2000-2009)

Surveillance and proper hygiene have been identified as key components in the fight against HAIs and antimicrobial resistance in hospital setting. This study assesses the pattern of hospital acquired infections (HAIs) and state of hygiene in a tertiary hospital in southwest; Nigeria. Data collected routinely between January 2000 and December 2009 by the infection control committee on HAI and primary data generated on hygiene in the wards were analysed using appropriate statistical techniques. A total of 37;957 patients were admitted during the period under review and 1129 cases (3.0) of HAI were reported. The highest prevalence of 9.0 was reported in 2006. The Intensive Care Unit (ICU) had the highest period prevalence of 14.7 followed by Orthopaedics ward (7.7). Surgical ward contributed the highest number of cases with 433. Gram negative organisms were the most implicated (78) of which Klebsiella species was 38 while Staphylococcus aureus was the only Gram positive organism identified (28). Hand washing was practised universally by health workers but facilities for proper hand washing were inadequate. The pattern of HAI has not changed significantly in the past 10 years and Klebsiella was the most implicated organism in HAIs and ICU. Facilities for proper hand washing are suboptimal. We recommend the introduction of hand washing policy for the hospital and the provision of an environment conducive for its implementation by the hospital management as well as adequate support for the infection control committee in the discharge of her duties

Invasive bacteria isolates from children with severe infections in a Nigerian hospital.

BACKGROUND: Little information is available about the aetiology and epidemiology of serious bacterial infections in Nigeria. This study determined bacterial isolates from blood and cerebrospinal fluid (CSF) of children presenting in the emergency room of a teaching hospital in Nigeria. METHOD: From October 2005 to December 2006, children aged two to 60 months presenting with signs of acute systemic infections were recruited. Blood culture and CSF specimens were collected and processed using standard microbiological protocols. Data were analysed using SPSS version 11 software. RESULTS: Two hundred and two blood and 69 CSF samples were cultured. Fifty-five (27%) of the blood cultures yielded Gram-negative bacilli and Gram-positive cocci in almost equal proportions. The most common isolates from the blood cultures were Staphylococcus aureus, 26 (12.9%) and atypical coliforms, 13 (6.5%). Others are Klebsiella spp, 3 (1.5%); Klebsiella pneumonia, 2 (1.0%); Escherichia coli, 3 (1.5%); Enterobacter agglomerans, 2 (1.1%); Proteus mirabilis, 2(1%); Pseudomonas spp, 2 (1.0%); Haemophilus influenza, 1 (1.0%); and Coagulase-negative Staphylococcus, 1 (1.0%). Fourteen out of 67 (20.9%) of the CSF samples yielded bacterial isolates: Streptococcus pneumonia, 3 (4.5%); Haemophilus influenza, 8 (11.9%); Hemophilus spp, 1 (1.5%); E. Coli, 1 (1.5%); and atypical coliform, 1 (1.5%). Gram-negative coliform isolates were predominantly resistant to penicillin based antibiotics and co-trimoxazole but sensitive to third-generation cephalosporins and quinolones. A high percentage of S. aureus isolates were multi-drug resistant. CONCLUSIONS: Bacterial infections contribute to the significant morbidity among children in our environment. S. aureus was more frequently isolated in sepsis while H. influenzae appears to play a major role in meningitis. Appropriate use of antibiotics is needed to manage affected children effectively. We also recommend improved vaccine coverage of children under the age of five years.

Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis?

Mycobacterium bovis is best identified by screening those isolates of the Mycobacterium tuberculosis complex that have any pyrazinamide (PZA) resistance, using a confirmatory test such as spoligotyping, biochemical testing, or genomic deletion analysis. The sensitivity for detection of M. bovis is lowered to 82% when only PZA-monoresistant isolates are screened.

Genomic analysis distinguishes Mycobacterium africanum.

Mycobacterium africanum is thought to comprise a unique species within the Mycobacterium tuberculosis complex. M. africanum has traditionally been identified by phenotypic criteria, occupying an intermediate position between M. tuberculosis and M. bovis according to biochemical characteristics. Although M. africanum isolates present near-identical sequence homology to other species of the M. tuberculosis complex, several studies have uncovered large genomic regions variably deleted from certain M. africanum isolates. To further investigate the genomic characteristics of organisms characterized as M. africanum, the DNA content of 12 isolates was interrogated by using Affymetrix GeneChip. Analysis revealed genomic regions of M. tuberculosis deleted from all isolates of putative diagnostic and biological consequence. The distribution of deleted sequences suggests that M. africanum subtype II isolates are situated among strains of "modern" M. tuberculosis. In contrast, other M. africanum isolates (subtype I) constitute two distinct evolutionary branches within the M. tuberculosis complex. To test for an association between deleted sequences and biochemical attributes used for speciation, a phenotypically diverse panel of "M. africanum-like" isolates from Guinea-Bissau was tested for these deletions. These isolates clustered together within one of the M. africanum subtype I branches, irrespective of phenotype. These results indicate that convergent biochemical profiles can be independently obtained for M. tuberculosis complex members, challenging the traditional approach to M. tuberculosis complex speciation. Furthermore, the genomic results suggest a rational framework for defining M. africanum and provide tools to accurately assess its prevalence in clinical specimens.